Contacts of the helix formed by residues 114 - 138 (chain C) in PDB entry 2GD4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 114 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PRO* 5.7 2.7 - - - -
13C ARG* 5.6 3.4 - - - -
47C ARG* 3.1 33.2 - - - +
113C GLU* 1.3 75.1 - - - +
115C THR* 1.3 67.1 + - - +
117C ASP* 2.6 28.0 + - - +
118C GLN* 3.0 17.9 + - + +
122C PHE* 4.8 4.7 - - + -
1G ZDO 3.0 47.4 + - - +
2G IDS 2.6 54.5 + - - +
3G SUS 3.3 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ARG* 3.0 47.3 + - + +
50C GLU* 3.3 12.2 + - - +
51C LEU* 5.2 5.8 - - + -
111C ILE* 4.1 11.4 - - + -
112C SER* 2.6 32.0 + - - -
113C GLU 2.9 0.6 + - - -
114C LYS* 1.3 72.7 - - - +
116C SER* 1.3 52.0 + - - -
117C ASP 2.3 15.4 + - - -
119C ILE* 2.5 27.8 + - - +
122C PHE* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 5.7 0.3 - - - -
23C TYR* 4.8 9.1 + - - +
24C ARG* 4.5 7.9 - - - -
91C LYS* 4.7 5.7 - - - +
103C MET* 4.4 17.3 - - - +
108C PHE 4.3 4.9 - - - -
111C ILE* 3.4 30.0 - - - +
112C SER 3.0 16.0 + - - -
113C GLU 2.6 10.4 + - - -
115C THR* 1.3 71.7 - - - +
117C ASP* 1.3 63.5 + - - +
119C ILE* 3.5 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASN* 4.9 10.5 - - - +
19C PRO* 5.4 11.9 - - + +
22C ILE* 3.3 31.1 - - + +
23C TYR 4.6 0.2 - - - +
24C ARG* 3.0 35.0 + - - -
91C LYS* 5.2 2.2 - - - +
113C GLU 3.1 11.4 - - - +
114C LYS* 2.6 10.7 + - - +
115C THR 2.3 16.2 + - - -
116C SER* 1.3 76.2 - - - +
118C GLN* 1.3 65.4 + - + +
119C ILE* 2.8 18.7 + - - +
120C HIS* 3.7 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PRO* 4.1 21.4 - - + +
13C ARG* 3.6 8.6 - - - +
15C ILE* 5.1 3.0 - - - +
17C MET* 3.0 37.1 - - - +
18C ASN* 3.0 24.2 + - - +
19C PRO* 5.5 1.3 - - - +
114C LYS* 3.0 24.2 + - + +
117C ASP* 1.3 78.8 - - + +
119C ILE* 1.3 52.0 + - - +
120C HIS* 3.1 18.9 + - - -
121C PHE* 2.5 44.2 + - + +
122C PHE* 3.4 22.1 + - + -
1G ZDO 4.0 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.5 21.6 - - + +
88C ALA* 4.4 5.6 - - + -
91C LYS* 4.1 19.3 - - + -
103C MET* 5.8 0.4 - - + -
108C PHE* 3.9 32.3 - - + -
111C ILE* 4.6 0.9 - - + -
115C THR 2.5 28.7 + - - +
116C SER* 3.5 8.7 - - - +
117C ASP* 2.9 22.4 - - - +
118C GLN* 1.3 70.3 - - - +
120C HIS* 1.3 68.1 + - + +
121C PHE 2.9 0.5 + - - -
122C PHE* 3.0 9.9 + - - -
123C PHE* 2.8 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 6.2 3.8 - - + -
16C PRO 5.9 2.0 - - - -
17C MET* 6.2 1.0 - - - -
19C PRO* 5.0 7.4 - - + +
88C ALA* 3.9 15.0 - - - +
89C MET* 3.4 29.9 - - + +
91C LYS* 6.4 0.4 - - + -
92C LEU* 3.5 35.5 - - + +
117C ASP 3.7 16.3 + - - -
118C GLN* 2.8 17.8 + - - -
119C ILE* 1.3 84.5 - - + +
121C PHE* 1.3 90.0 + + + +
123C PHE* 3.8 4.6 - - - +
124C ALA 3.6 7.3 + - - -
161C ILE* 4.0 21.5 - - + +
165C VAL* 3.1 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.5 19.7 - - + -
10C ALA 2.9 29.2 - - - -
11C LYS* 3.9 2.2 - - - -
12C PRO* 3.2 49.4 - - + -
15C ILE* 4.6 13.7 - - + -
118C GLN* 2.5 20.7 + - + +
120C HIS* 1.3 86.8 + + + +
122C PHE* 1.3 67.5 + + - +
124C ALA* 2.6 37.0 + - + +
125C LYS* 3.0 30.5 + - + -
164C LEU 5.9 0.7 - - - -
165C VAL* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PRO* 4.2 7.9 - - + -
45C ASN* 4.2 4.5 - - - -
47C ARG* 3.1 46.9 - - + -
48C VAL* 4.6 15.8 - - + +
51C LEU* 3.5 20.0 - - + -
114C LYS* 4.8 3.4 - - + -
115C THR* 4.1 17.7 - - + -
118C GLN* 3.4 34.7 + - + -
119C ILE 3.0 1.9 + - - +
121C PHE* 1.3 91.4 - + - +
123C PHE* 1.3 57.8 + - - +
125C LYS* 2.5 29.8 + - + +
126C LEU* 2.6 12.8 + - - +
3G SUS 3.7 33.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.0 35.9 - - + +
55C ASN* 5.1 4.0 - - + -
81C LEU* 5.0 3.6 - - + -
84C SER* 3.7 16.2 - - - -
85C THR* 3.1 32.1 - - + +
88C ALA* 3.4 24.2 - - + -
108C PHE* 3.3 43.1 - + - -
119C ILE* 2.8 33.0 + - + +
120C HIS* 3.8 7.2 - - - +
122C PHE* 1.3 69.1 - - - +
124C ALA* 1.3 52.1 + - - +
126C LEU* 3.3 21.5 - - + +
127C ASN* 2.5 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.7 16.6 - - + -
85C THR* 5.3 0.4 - - - +
120C HIS 3.6 4.6 + - - +
121C PHE* 2.6 20.0 + - + +
122C PHE 2.6 3.6 + - - -
123C PHE* 1.3 69.8 - - - +
125C LYS* 1.3 53.0 + - - +
126C LEU 2.6 15.9 + - - -
127C ASN* 2.8 20.4 + - - +
128C CYS* 3.0 13.5 + - - +
165C VAL* 3.3 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.2 24.4 - - - +
8C CYS* 4.6 13.7 + - - +
9C THR* 5.3 1.6 - - - +
10C ALA 4.7 3.4 - - - +
11C LYS* 4.5 18.0 - - - +
45C ASN* 4.9 0.2 - - - +
48C VAL* 4.2 9.6 - - + -
121C PHE* 3.0 29.3 + - + -
122C PHE* 2.5 18.6 + - + +
124C ALA* 1.3 74.7 - - - +
126C LEU* 1.3 58.8 + - - +
128C CYS* 4.2 8.0 - - - +
129C ARG* 3.8 11.6 + - - +
3G SUS 4.0 8.8 + - - +
4G BDP 3.2 35.6 + - - +
5G SGN 3.4 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL* 3.3 33.8 - - + +
51C LEU* 5.1 3.6 - - + -
52C SER* 4.5 17.5 - - - +
81C LEU* 3.3 31.9 - - + -
122C PHE 2.6 11.8 + - - +
123C PHE* 3.3 31.6 - - + +
124C ALA 2.6 4.8 + - - -
125C LYS* 1.3 69.0 - - - +
127C ASN* 1.3 68.8 + - - +
128C CYS 3.1 1.1 - - - -
129C ARG* 2.9 18.1 + - - +
130C LEU* 3.0 21.7 + - + -
417C LEU* 3.6 19.3 - - + -
419C THR* 4.4 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 2.8 32.4 - - - +
85C THR* 3.6 23.8 + - - +
123C PHE 2.5 25.5 + - - -
124C ALA* 2.8 13.9 + - - +
126C LEU* 1.3 78.2 - - - +
128C CYS* 1.3 50.2 + - - +
130C LEU* 3.1 8.1 + - - +
131C TYR* 2.5 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 5.1 1.3 - - + -
8C CYS* 2.0 55.9 - - + -
124C ALA 3.0 14.2 + - - +
125C LYS* 4.2 5.8 - - - +
127C ASN* 1.3 74.7 - - - +
129C ARG* 1.3 57.5 + - - +
131C TYR* 2.5 33.6 + - - +
132C ARG* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA* 3.3 20.7 + - - +
44C THR* 3.5 17.3 + - - -
48C VAL* 4.8 2.9 - - - -
125C LYS 3.8 7.6 + - - +
126C LEU 2.9 11.4 + - - +
128C CYS* 1.3 77.2 - - - +
130C LEU* 1.3 65.7 + - + +
131C TYR 3.0 0.5 + - - -
132C ARG* 3.4 28.7 + - - +
133C LYS* 3.0 48.6 + - + +
414C GLU* 2.7 30.9 + - - +
416C PRO* 3.7 14.1 - - - +
417C LEU* 3.6 23.6 - - - +
5G SGN 3.5 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 3.8 20.2 - - + -
126C LEU* 3.0 23.5 + - + +
127C ASN* 3.2 9.2 - - - +
129C ARG* 1.3 77.7 - - + +
131C TYR* 1.3 60.3 + - - +
133C LYS* 5.2 3.1 - - + +
134C ALA* 3.2 21.7 + - - +
140C LEU* 4.1 6.9 - - + +
279C ILE* 5.2 1.4 - - + +
414C GLU* 3.3 44.9 - - + +
417C LEU* 4.8 2.9 - - + -
419C THR* 3.6 31.9 - - + +
421C ILE* 4.0 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ASN* 2.5 16.9 + - + +
128C CYS* 2.5 26.7 + - - +
130C LEU* 1.3 71.0 - - - +
132C ARG* 1.3 72.5 + - + +
134C ALA* 3.4 4.0 - - - +
135C ASN* 2.9 54.3 + - + -
140C LEU* 3.5 25.9 + - + -
141C VAL* 5.5 1.5 - - - +
142C SER* 5.1 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C CYS* 4.6 13.1 + - - +
9C THR* 6.0 1.0 - - - +
128C CYS* 2.9 30.5 + - - +
129C ARG* 3.4 27.2 + - - +
131C TYR* 1.3 76.8 - - + +
133C LYS* 1.3 68.4 + - + +
134C ALA 2.7 3.8 + - - -
135C ASN* 2.8 4.8 + - - -
136C LYS* 2.6 37.4 + - + -
5G SGN 5.1 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ARG* 3.0 65.1 + - + +
130C LEU* 5.2 0.9 - - - +
132C ARG* 1.3 86.8 - - + +
134C ALA* 1.3 64.0 - - - +
136C LYS* 3.5 16.7 - - - +
137C ALA* 4.1 4.5 + - - +
275C LYS 5.3 2.4 - - - +
278C ASP* 4.0 38.5 + - + +
279C ILE* 4.3 12.9 - - + +
414C GLU* 3.1 21.7 + - + -
416C PRO* 4.1 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU 3.2 22.9 + - - +
131C TYR 3.4 4.2 + - - +
132C ARG 2.7 4.4 + - - -
133C LYS* 1.3 79.7 - - - +
135C ASN* 1.3 58.8 + - - +
137C ALA* 4.9 0.2 - - - +
138C SER* 2.9 35.2 + - - +
140C LEU* 3.8 25.1 - - + -
221C PHE* 4.8 8.7 - - + -
279C ILE* 4.2 17.2 - - + +
421C ILE* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TYR* 2.9 64.3 + - + +
132C ARG* 2.8 5.8 + - - +
134C ALA* 1.3 72.8 - - - +
136C LYS* 1.3 68.7 + - - +
137C ALA 3.0 1.2 + - - -
138C SER 2.7 20.6 + - - +
139C LYS* 3.4 4.5 - - - +
140C LEU* 2.6 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ARG* 2.6 23.4 + - + +
133C LYS* 3.5 15.3 - - - +
134C ALA 3.2 0.2 - - - -
135C ASN* 1.3 73.2 - - - +
137C ALA* 1.3 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LYS 4.1 2.6 + - - +
134C ALA 3.6 2.6 + - - +
135C ASN 3.8 0.9 - - - -
136C LYS* 1.3 80.2 - - + +
138C SER* 1.3 63.5 + - - +
224C LEU* 3.6 20.4 - - + +
275C LYS* 3.4 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ALA 2.9 16.8 + - - -
135C ASN* 2.7 26.3 - - - +
137C ALA* 1.3 83.1 - - - +
139C LYS* 1.3 63.3 + - - +
221C PHE* 4.8 7.4 - - - -
222C LYS 3.9 12.1 - - - -
223C GLY* 4.0 4.8 - - - -
224C LEU* 3.5 25.9 + - - +
274C PHE* 4.2 11.6 - - - +
275C LYS 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il