Contacts of the helix formed by residues 115 - 130 (chain C) in PDB entry 5U03
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 PRO 115 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B MET* 4.2 37.7 - - + -
233B PHE* 5.3 2.7 - - + -
235B HIS* 6.3 0.7 - - - +
112C GLN* 4.9 2.7 - - + +
113C VAL 3.4 4.5 - - - -
114C VAL* 1.3 89.9 - - + +
116C HIS* 1.3 84.8 + - + +
118C THR* 2.9 17.4 + - - +
119C ASP* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C VAL* 5.9 1.1 - - + +
106C TYR* 3.9 27.4 + + + +
109C LYS* 6.3 0.2 - - - +
110C THR 3.8 10.5 + - - -
111C VAL* 3.6 33.1 - - + +
112C GLN* 2.9 38.0 + - + +
115C PRO* 1.3 100.0 - - + +
117C ILE* 1.3 59.3 + - + +
119C ASP* 3.4 7.2 + - - +
120C ALA* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 5.0 9.9 - - + -
93C ILE* 4.5 17.3 - - + -
94C TYR* 6.1 5.8 - - + -
97C VAL* 3.9 36.3 - - + -
111C VAL* 4.9 7.9 - - + -
112C GLN 3.1 5.8 + - - +
113C VAL* 2.8 34.7 + - + +
116C HIS* 1.3 72.0 - - + +
118C THR* 1.3 56.7 + - - +
120C ALA* 3.0 5.4 + - - +
121C ILE* 2.7 48.7 + - + +
158C PRO* 4.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C VAL* 2.9 23.8 + - + +
114C VAL* 3.8 10.5 - - + +
115C PRO* 2.9 22.2 + - - +
117C ILE* 1.3 77.2 - - - +
119C ASP* 1.3 59.3 + - - +
121C ILE* 3.4 10.5 + - + +
122C GLN* 3.1 34.7 + - - +
158C PRO 3.5 22.2 - - - +
161C GLU* 3.8 23.1 - - + +
162C ALA* 3.8 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PRO* 2.9 41.2 + - - +
116C HIS* 3.6 7.3 - - - +
118C THR* 1.3 78.2 + - - +
120C ALA* 1.3 59.4 + - - +
122C GLN* 3.0 19.8 + - - +
123C GLU* 2.8 40.0 + - + +
169C LYS* 4.1 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 5.1 3.6 - - + -
96C TYR* 5.2 5.2 - - + -
97C VAL* 4.6 18.6 - - + -
106C TYR* 5.7 3.8 - - - +
116C HIS 3.0 13.2 + - - +
117C ILE* 3.0 13.1 + - - +
119C ASP* 1.3 74.9 - - - +
121C ILE* 1.3 57.5 + - - +
123C GLU* 3.0 20.2 + - - +
124C TRP* 2.8 46.3 + - + +
127C ARG* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ILE* 5.4 2.2 - - + -
93C ILE* 4.4 9.2 - - + -
117C ILE* 2.7 33.1 + - + +
118C THR* 3.5 12.6 - - - +
119C ASP 3.1 0.2 - - - -
120C ALA* 1.3 76.1 - - + +
122C GLN* 1.3 63.5 + - - +
124C TRP* 3.0 14.0 + - + +
125C VAL* 3.0 29.3 + - + +
158C PRO* 3.7 28.3 - - + +
159C PHE* 3.6 42.8 - - + -
162C ALA* 3.6 14.8 - - + -
163C PHE* 5.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C THR* 3.1 19.9 + - - +
119C ASP* 3.0 12.8 + - - +
121C ILE* 1.3 74.6 - - - +
123C GLU* 1.3 62.9 + - + +
125C VAL* 3.2 13.8 + - - +
126C MET* 3.2 23.9 + - - +
162C ALA* 3.0 33.6 + - + +
165C GLN* 4.0 9.7 - - - +
166C PHE* 3.5 38.8 - - + +
169C LYS* 2.7 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 4.8 2.1 + - - -
100C LYS* 5.9 2.4 - - - -
119C ASP* 2.8 24.5 + - + +
120C ALA* 3.2 19.1 - - - +
122C GLN* 1.3 75.9 - - + +
124C TRP* 1.3 51.5 + - - +
126C MET* 2.9 10.7 + - - +
127C ARG* 2.7 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 5.3 0.2 - - - -
85C ASP* 5.8 3.4 - - - -
88C LEU* 3.6 26.7 - - + -
92C LYS* 3.7 34.3 - - + -
93C ILE* 4.0 25.0 - - + +
96C TYR* 3.8 48.7 - + + -
120C ALA* 2.8 36.6 + - + +
121C ILE* 3.0 12.8 + - + +
123C GLU* 1.3 74.9 - - - +
125C VAL* 1.3 64.6 + - + +
127C ARG* 2.8 43.0 + - - +
128C GLN* 2.6 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C TYR* 3.4 33.9 - - + -
37C ILE* 4.0 14.5 - - + +
39C ILE* 5.6 4.0 - - + -
121C ILE* 3.0 24.6 + - + +
122C GLN* 3.2 14.6 - - + +
124C TRP* 1.3 76.6 - - + +
126C MET* 1.3 51.7 + - - +
128C GLN* 3.4 0.9 + - - -
129C ALA* 2.7 34.8 + - - +
145C ILE* 4.7 8.7 - - + -
163C PHE* 4.3 24.5 - - + -
166C PHE* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C TYR* 3.1 29.6 - - - +
122C GLN 3.2 10.9 + - - +
123C GLU* 2.9 11.2 + - - +
125C VAL* 1.3 76.8 - - + +
127C ARG* 1.3 66.2 + - - +
129C ALA* 3.7 4.7 - - + -
130C LEU* 3.0 58.5 + - + +
139C GLU* 4.6 4.9 - - - +
166C PHE* 4.8 9.4 - - + -
170C VAL* 6.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 2.9 34.0 + - - -
120C ALA 3.6 2.2 + - - -
123C GLU* 2.7 51.7 + - + +
124C TRP* 2.8 68.3 + - - +
126C MET* 1.3 73.8 - - + +
128C GLN* 1.3 68.9 + - - +
130C LEU* 4.0 8.6 + - - +
131C ILE* 3.3 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 4.9 6.8 + - - +
37C ILE* 3.6 28.2 - - + +
85C ASP* 3.1 50.3 + - + +
86C ASN* 4.3 11.0 + - - +
88C LEU* 3.5 18.4 - - - +
124C TRP* 2.6 40.6 + - - +
127C ARG* 1.3 97.0 - - - +
129C ALA* 1.3 67.7 + - - +
130C LEU 3.1 2.5 - - - -
131C ILE* 3.0 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.0 34.7 - - + +
3C TYR* 3.8 26.2 - - + +
35C THR* 5.4 2.5 - - - -
37C ILE* 4.7 3.1 - - + +
125C VAL 2.7 19.2 + - - +
126C MET* 3.1 16.8 + - + +
128C GLN* 1.3 77.5 - - - +
130C LEU* 1.3 60.1 + - - +
131C ILE 3.3 1.6 + - - -
139C GLU* 3.3 10.0 - - - +
140C PRO* 3.3 5.0 - - - +
143C CYS* 5.5 1.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
126C MET* 3.0 39.9 + - + +
127C ARG* 4.2 7.4 - - - +
128C GLN 3.1 0.4 - - - -
129C ALA* 1.3 76.4 - - - +
131C ILE* 1.4 58.5 + - + +
132C PRO* 3.4 10.9 - - - +
139C GLU* 3.7 35.1 + - + +
140C PRO* 4.7 1.8 - - - -
----------------------------------------------------------
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