Contacts of the helix formed by residues 76 - 89 (chain C) in PDB entry 1IVH
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 TYR 76 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C THR* 4.2 13.9 - - + -
75C GLY* 1.3 68.7 - - - -
77C LEU* 1.3 59.7 + - - +
79C HIS* 3.6 6.1 - - - +
80C VAL* 2.8 35.1 + - - +
102C ASN* 4.5 4.5 - - - -
106C ASN* 3.4 33.3 + - - -
110C ARG* 4.4 6.6 + - - +
253C LEU* 3.2 39.2 - - + +
256C LEU* 4.0 20.0 - - + -
257C VAL* 3.9 20.0 - - + -
315C ALA* 4.3 3.1 - - + +
318C CYS* 4.5 18.2 - - + -
319C ASP* 2.8 27.3 + - - +
323C CYS* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.4 9.4 - - + -
17C GLN* 3.4 34.8 - - - +
75C GLY 3.2 1.2 + - - -
76C TYR* 1.3 75.6 - - - +
78C GLU* 1.3 67.0 + - - +
80C VAL* 3.2 4.3 + - + +
81C LEU* 3.0 31.0 + - + +
312C TYR* 3.9 46.2 - - + +
315C ALA* 3.9 11.8 - - + +
316C LYS* 4.0 23.8 - - + +
319C ASP* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN* 3.0 41.6 + - + +
20C LEU* 3.9 21.3 - - + +
63C ILE* 3.9 12.3 - - + -
74C LEU* 4.2 21.2 - - + +
75C GLY* 3.0 29.2 + - - +
77C LEU* 1.3 80.2 - - - +
79C HIS* 1.3 58.2 + - - +
81C LEU* 3.1 11.2 + - + +
82C VAL* 2.9 33.9 + - - +
319C ASP* 4.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 3.3 27.8 - - + +
64C THR* 3.7 14.7 + - + +
75C GLY 3.2 9.3 + - - +
76C TYR* 3.2 14.3 + - - +
78C GLU* 1.3 80.7 - - - +
80C VAL* 1.3 56.9 + - - +
82C VAL* 4.0 2.7 - - - +
83C MET* 3.1 20.6 + - - +
97C TYR* 3.6 17.8 - + - -
98C GLY* 5.4 0.6 - - - -
101C SER* 2.7 50.2 + - - -
102C ASN* 3.8 14.8 + - + -
257C VAL* 3.6 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR 2.8 22.8 + - - +
77C LEU* 3.5 6.7 - - + +
79C HIS* 1.3 74.9 - - - +
81C LEU* 1.3 60.7 + - - +
83C MET* 3.5 5.4 + - - +
84C GLU* 2.8 31.9 + - - +
256C LEU* 3.9 22.4 - - + +
257C VAL* 4.0 14.4 - - + -
260C GLY* 4.1 15.6 - - - -
263C LEU* 4.7 1.6 - - + -
311C VAL* 4.3 16.8 - - + +
312C TYR* 4.3 24.5 - - + -
315C ALA* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.6 28.9 - - + -
17C GLN* 3.7 29.6 - - + +
20C LEU* 4.8 9.2 - - + -
21C ARG* 4.2 16.3 + - + +
77C LEU* 3.0 25.4 + - + +
78C GLU* 3.2 15.7 - - - +
80C VAL* 1.3 75.5 - - - +
82C VAL* 1.3 64.0 + - - +
84C GLU* 3.0 8.9 + - - +
85C GLU* 2.9 28.3 + - - +
312C TYR* 3.6 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.8 25.4 - - + -
24C MET* 4.3 11.7 - - + -
60C VAL* 3.7 28.5 - - + -
63C ILE* 4.5 7.2 - - + -
78C GLU 2.9 17.7 + - - +
79C HIS* 4.1 2.0 - - - +
81C LEU* 1.3 75.3 - - - +
83C MET* 1.3 61.8 + - - +
85C GLU* 3.2 7.1 + - - +
86C ILE* 3.0 33.4 + - + +
97C TYR* 2.9 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C HIS 3.1 20.6 + - - +
80C VAL 3.6 4.0 - - - +
82C VAL* 1.3 76.7 - - - +
84C GLU* 1.3 57.3 + - - +
86C ILE* 3.5 1.7 + - - +
87C SER* 2.9 48.9 + - - +
94C GLY 3.3 28.3 - - - +
95C LEU* 4.1 2.2 - - - +
97C TYR* 3.7 15.8 - - + -
98C GLY* 4.0 17.9 - - - -
257C VAL* 3.4 27.6 - - + +
258C LEU* 4.5 12.8 - - + +
260C GLY* 3.9 0.7 - - - -
261C GLY* 3.8 14.1 - - - +
371C TYR* 3.2 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASP* 4.0 1.7 - - - +
21C ARG* 3.1 14.3 + - - -
80C VAL 2.8 18.8 + - - +
81C LEU* 3.0 5.7 + - - +
83C MET* 1.3 78.0 - - - +
85C GLU* 1.3 61.4 + - - +
87C SER 3.3 1.0 + - - -
88C ARG* 3.0 24.2 + - + +
260C GLY* 3.3 13.9 - - - +
263C LEU* 3.6 16.6 - - + +
264C GLY* 3.2 31.3 - - - +
267C GLN* 4.8 2.9 - - - +
308C ARG* 2.6 32.9 + - - -
312C TYR* 2.7 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASP* 3.7 6.6 - - - +
21C ARG* 3.1 43.5 + - - +
24C MET* 4.0 30.5 - - + -
25C ALA* 3.8 13.2 - - - +
28C LEU* 4.5 5.3 - - + +
81C LEU 2.9 16.1 + - - +
82C VAL 3.7 7.0 - - - +
84C GLU* 1.3 76.9 - - - +
86C ILE* 1.3 67.0 + - + +
88C ARG* 3.0 55.3 + - - +
89C ALA* 3.1 8.8 + - - +
267C GLN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C MET* 5.4 1.1 - - - -
28C LEU* 3.9 25.1 - - + -
32C LEU* 4.2 6.1 - - + -
51C PHE* 5.2 0.7 - - + -
55C LEU* 4.3 21.8 - - + -
60C VAL* 5.0 0.4 - - + -
82C VAL* 3.0 26.9 + - + +
83C MET 4.0 2.7 - - - +
85C GLU* 1.3 75.9 - - + +
87C SER* 1.3 51.9 + - - +
89C ALA* 3.1 3.6 + - - +
90C SER 2.7 34.5 + - - +
93C VAL* 3.8 19.1 - - + +
94C GLY* 3.5 26.9 - - - +
97C TYR* 3.7 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C MET* 2.9 44.3 + - - +
84C GLU 3.6 4.7 - - - -
86C ILE* 1.3 76.9 - - - +
88C ARG* 1.3 61.9 + - - +
89C ALA 3.5 0.2 + - - -
90C SER 3.4 21.0 + - - -
91C GLY* 3.6 8.7 + - - -
94C GLY* 3.7 5.5 - - - -
261C GLY* 3.5 26.6 - - - -
264C GLY* 4.2 3.4 - - - -
265C LEU* 3.8 14.6 - - - +
268C ALA* 5.1 0.7 - - - +
364C PHE* 6.1 0.3 - - - -
371C TYR* 4.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 5.1 9.3 - - - +
7C ASP* 3.4 23.1 + - - +
21C ARG* 5.7 1.0 - - - +
25C ALA* 4.3 13.5 - - - +
84C GLU* 3.0 13.1 + - + +
85C GLU* 3.0 45.7 + - - +
87C SER* 1.3 77.1 - - - +
89C ALA* 1.3 60.2 + - - +
264C GLY* 3.7 21.5 - - - +
267C GLN* 3.5 16.3 - - + +
268C ALA* 3.8 15.7 - - - +
271C ASP* 3.1 37.2 + - - +
363C ARG* 5.2 0.7 + - - -
364C PHE* 5.2 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.8 33.2 - - + -
32C LEU* 4.0 6.5 - - + -
33C ALA* 4.1 24.7 - - + +
36C ALA* 3.3 22.7 - - - +
85C GLU 3.1 6.1 + - - +
86C ILE 3.1 7.7 + - - +
87C SER 4.2 0.2 - - - -
88C ARG* 1.3 80.5 - - - +
90C SER* 1.3 58.5 + - - +
363C ARG* 3.8 6.0 + - - -
----------------------------------------------------------
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