Contacts of the helix formed by residues 114 - 130 (chain C) in PDB entry 3E2A
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 GLY 114 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASP* 2.8 16.6 + - - -
113C LEU* 1.3 77.1 - - - +
115C LEU* 1.3 67.1 + - - +
116C ILE 3.2 2.9 - - - -
117C ASN* 3.0 19.2 + - - +
162D SER* 3.6 14.9 - - - -
82E GLN* 3.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLY* 1.3 70.6 - - - -
116C ILE* 1.3 57.1 + - - +
118C ASN* 3.0 40.4 + - - +
119C TRP 3.9 2.1 + - - -
75D PHE* 5.3 2.0 - - + -
78D LEU* 4.7 0.7 - - + -
162D SER* 4.4 2.5 - - - +
163D ILE* 6.4 0.4 - - + -
75E PHE* 3.7 32.2 - - + -
78E LEU* 4.1 35.0 - - + +
79E SER* 4.2 4.5 - - - +
82E GLN* 3.3 20.9 + - + +
163E ILE* 4.1 15.7 - - + -
115F LEU* 3.8 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 4.3 13.9 - - + -
113C LEU* 3.6 29.6 - - + +
115C LEU* 1.3 67.6 - - - +
117C ASN* 1.3 72.2 + - - +
118C ASN 3.0 2.5 + - - -
119C TRP* 3.1 20.3 + - + +
120C LEU* 3.0 32.7 + - + +
79E SER* 3.6 37.6 + - - +
82E GLN* 2.8 23.4 + - - +
83E TYR* 3.8 35.0 - - + -
87E VAL* 4.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ALA 4.9 4.4 + - - -
107C ALA* 6.1 0.4 - - - +
110C ASP 4.7 1.7 - - - +
111C LYS 3.1 18.7 + - - +
112C ASP* 3.5 13.3 - - - +
113C LEU* 3.5 41.3 - - - +
114C GLY 3.0 14.0 + - - +
116C ILE* 1.3 81.3 - - - +
118C ASN* 1.3 56.9 + - - +
120C LEU* 3.3 11.2 + - - +
121C LEU* 2.9 34.3 + - + +
124C ARG* 5.8 1.7 - - - -
160D ARG 6.1 0.7 - - - +
162D SER* 5.0 5.6 - - - +
165D LYS* 5.2 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 3.0 28.6 + - - +
117C ASN* 1.3 76.0 - - - +
119C TRP* 1.3 63.3 + - - +
121C LEU* 3.3 18.8 + - - +
122C HIS* 4.1 0.2 - - - -
72D HIS* 3.4 38.0 - - - +
73D THR* 3.7 3.2 - - - +
78D LEU* 3.8 20.0 - - - +
161D THR* 3.5 15.1 - - - +
162D SER* 2.9 45.2 + - - -
163D ILE* 5.5 0.2 - - - +
75E PHE* 3.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASN* 3.9 27.4 - - + -
66C VAL* 2.9 29.9 + - + +
69C GLN* 3.1 41.3 + - + +
71C ILE* 3.6 26.9 - - + -
74C ASP* 3.6 28.3 - - + -
115C LEU 3.9 0.4 + - - -
116C ILE* 3.1 21.5 + - + +
118C ASN* 1.3 80.3 - - - +
120C LEU* 1.3 70.9 + - + +
122C HIS* 3.3 14.7 + - - -
73D THR* 3.5 26.6 - - + +
75E PHE* 4.2 7.4 - + + -
76E ASN* 3.6 35.9 - - + -
79E SER* 3.7 20.6 - - - +
80E VAL* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 4.1 14.6 - - + -
67C ALA* 4.5 2.7 - - + -
69C GLN* 4.5 0.9 - - - +
103C GLY* 3.7 17.9 - - - +
106C ALA* 3.7 31.4 - - + +
107C ALA* 4.0 18.8 - - + +
113C LEU* 4.9 1.1 - - + -
116C ILE* 3.0 35.1 + - + +
117C ASN* 3.3 14.1 + - - +
119C TRP* 1.3 88.6 - - + +
121C LEU* 1.3 59.1 + - - +
122C HIS 3.1 2.7 - - - -
123C ILE* 2.9 33.5 + - + +
124C ARG* 3.0 15.6 + - + +
83E TYR* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASN* 2.9 16.8 + - + +
118C ASN* 3.4 25.4 - - - +
119C TRP 3.3 1.0 - - - -
120C LEU* 1.3 77.7 - - - +
122C HIS* 1.3 56.7 + - - +
124C ARG* 3.2 11.1 + - - +
125C ASP* 2.8 32.2 + - - +
72D HIS* 3.6 33.2 - - + +
157D ASN 4.9 1.3 - - - +
160D ARG* 3.6 47.3 + - + +
161D THR* 4.6 2.5 - - + +
165D LYS* 6.2 0.7 - - - -
231D SO4 3.6 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLN* 3.5 15.7 - - - +
71C ILE* 3.4 31.9 - - + +
118C ASN 4.1 3.1 - - - -
119C TRP 3.3 19.7 - - - +
120C LEU 3.1 0.6 - - - -
121C LEU* 1.3 75.8 - - - +
123C ILE* 1.3 64.9 + - - +
125C ASP* 3.4 8.6 + - - +
126C ILE* 3.2 27.0 + - + +
72D HIS* 3.5 31.3 - + + +
73D THR* 2.8 31.4 + - + -
122D HIS* 4.0 22.5 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ALA* 4.4 7.9 - - + -
69C GLN* 3.2 39.9 - - + +
104C ILE* 4.0 11.0 - - + -
107C ALA* 3.7 24.9 - - + -
120C LEU* 2.9 19.5 + - + +
122C HIS* 1.3 76.7 - - - +
124C ARG* 1.3 58.3 + - - +
126C ILE* 3.1 7.7 + - + +
127C TRP* 2.9 26.4 + - + +
146C LEU* 3.9 24.7 - - + -
150C ASN* 3.2 32.8 - - + +
154C GLN* 4.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA* 2.8 46.2 + - + +
108C MET 3.5 8.9 + - - -
109C ALA 3.2 19.2 + - - -
110C ASP* 4.1 14.6 + - - -
117C ASN* 5.8 1.6 - - - -
120C LEU* 3.0 16.1 + - - +
121C LEU* 3.2 18.4 + - - +
123C ILE* 1.3 77.9 - - - +
125C ASP* 1.3 56.9 + - - +
127C TRP* 3.4 29.6 - - + +
128C PHE* 3.0 26.5 + - - +
160D ARG* 4.4 1.7 + - - +
231D SO4 2.7 54.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU 2.8 14.3 + - - -
122C HIS* 3.6 10.8 + - - +
123C ILE 3.2 0.2 - - - -
124C ARG* 1.3 77.3 - - - +
126C ILE* 1.3 57.8 + - + +
128C PHE* 3.4 8.8 + - - +
129C LYS* 3.0 27.0 + - - +
72D HIS* 2.6 29.3 + - - -
129D LYS* 5.9 1.2 + - - -
160D ARG* 2.8 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C HIS* 3.2 16.0 + - + +
123C ILE* 3.1 11.9 + - + +
125C ASP* 1.3 72.3 - - + +
127C TRP* 1.3 66.5 + - - +
129C LYS* 3.2 8.0 + - + -
130C HIS* 3.1 25.7 + - + +
146C LEU* 4.2 10.3 - - + -
149C ILE* 3.7 18.2 - - + -
150C ASN* 3.6 14.1 - - + +
153C GLU* 3.7 39.0 - - + +
154C GLN* 3.3 29.6 - - - +
157C ASN* 5.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA 5.2 0.2 - - - -
108C MET* 3.6 63.4 - - + +
123C ILE* 2.9 12.3 + - + +
124C ARG* 3.4 40.8 - - + +
126C ILE* 1.3 75.8 - - - +
128C PHE* 1.3 64.2 + - - +
130C HIS 3.2 3.5 + - - -
131C GLY* 2.9 21.9 + - - -
134C LEU* 3.3 32.1 - - + +
135C GLY 5.6 0.4 - - - +
142C ARG* 5.3 13.2 - - - +
146C LEU* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ARG 3.0 14.3 + - - +
125C ASP* 3.6 12.6 - - - +
126C ILE 3.3 0.2 - - - -
127C TRP* 1.3 76.2 - - - +
129C LYS* 1.3 69.8 + - - +
131C GLY* 3.0 15.6 + - - +
129D LYS* 3.7 39.9 - - + -
160D ARG* 6.4 0.4 - - - +
205D TYR* 6.2 4.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ASP 3.0 14.8 + - - +
126C ILE* 3.2 12.8 + - + +
128C PHE* 1.3 85.1 - - + +
130C HIS* 1.3 67.8 + - + +
131C GLY 3.7 1.2 + - - -
132C HIS 5.3 0.2 + - - -
153C GLU* 3.1 24.5 + - - +
156C TYR* 4.9 7.9 - - - -
160C ARG* 6.0 1.0 - - - +
205C TYR* 2.8 31.1 + - - -
128D PHE* 3.8 35.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ILE* 3.1 21.1 + - + +
127C TRP 3.3 3.6 - - - -
129C LYS* 1.3 90.8 + - + +
131C GLY* 1.3 58.2 + - - +
132C HIS* 3.2 4.0 + - - +
133C LEU* 3.4 14.2 + - + +
134C LEU* 3.0 30.5 + - + +
149C ILE* 3.4 39.9 - - + +
153C GLU* 2.5 29.5 + - - -
205C TYR* 4.4 2.9 - - - -
209C ILE* 3.6 40.6 - - + +
----------------------------------------------------------
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