Contacts of the helix formed by residues 39 - 53 (chain C) in PDB entry 1VHA
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 ASP 39 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP* 3.1 25.6 + - - +
38C GLY* 1.3 71.7 - - - +
40C VAL* 1.3 57.6 + - - +
41C ALA* 3.3 12.1 + - - +
42C LEU* 3.1 39.9 + - - +
43C HIS* 3.1 34.3 + - - -
74C SER* 3.6 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASP* 3.2 24.4 - - - +
10C VAL* 3.7 4.3 - - - -
11C HIS* 3.5 40.4 - - + +
38C GLY 2.9 8.2 + - - +
39C ASP* 1.3 69.8 + - - +
41C ALA* 1.3 65.7 + - + +
44C ALA* 2.9 32.4 + - - +
99C ILE* 5.0 7.0 - - + -
147C ILE* 3.8 27.4 - - + +
148C ALA 4.0 7.6 - - - +
149C CYS* 3.5 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASP* 3.3 9.3 + - - +
40C VAL* 1.3 83.5 - - + +
42C LEU* 1.3 64.8 + - + +
44C ALA* 3.9 1.9 - - - +
45C LEU* 3.0 28.8 + - - +
97C ILE* 4.4 11.9 - - + +
99C ILE* 4.3 20.4 - - + -
113C MSE 5.4 6.3 - - - -
117C ILE* 5.8 4.9 - - + -
130C VAL* 6.1 1.1 - - + -
149C CYS* 3.6 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASP* 3.1 26.4 + - - +
41C ALA* 1.3 77.9 - - + +
43C HIS* 1.3 58.3 + - - +
45C LEU* 3.6 5.3 - - + +
46C THR* 2.7 38.2 + - - +
74C SER* 3.7 27.4 - - - +
75C ARG* 3.6 35.4 - - + +
78C LEU* 4.3 15.5 - - + +
116C LYS* 6.4 1.1 - - + -
117C ILE* 3.9 32.8 - - + -
120C ASP* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASP* 3.2 37.7 - - + +
36C SER* 3.3 31.5 + - - -
37C ASP* 4.2 2.2 + - - -
38C GLY* 4.8 1.6 - - - -
39C ASP 3.1 18.9 + - - +
41C ALA 3.3 0.2 - - - -
42C LEU* 1.3 75.6 - - - +
44C ALA* 1.3 64.8 + - - +
46C THR* 3.1 6.5 + - - -
47C ASP* 2.9 28.6 + - - +
58C ILE* 3.5 28.4 - - + +
71C ASN 5.3 0.2 - - - -
74C SER* 3.0 30.7 + - - -
77C LEU* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLY* 3.3 22.7 - - - +
8C PHE 4.2 3.1 - - - +
9C ASP* 3.9 5.1 - - - +
40C VAL 2.9 18.4 + - - +
41C ALA 3.9 2.7 - - - +
43C HIS* 1.3 75.3 - - - +
45C LEU* 1.3 63.5 + - - +
47C ASP* 3.2 3.3 + - - +
48C ALA 3.0 18.5 + - - -
149C CYS* 3.7 27.8 - - + +
151C ALA* 3.6 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA 3.0 18.7 + - - +
42C LEU* 3.6 6.5 - - + +
44C ALA* 1.3 77.5 - - - +
46C THR* 1.3 61.8 + - - +
48C ALA* 3.2 2.5 + - + +
49C ILE* 3.0 31.3 + - + +
78C LEU* 3.8 26.7 - - + -
95C VAL* 3.8 36.1 - - + -
97C ILE* 3.9 13.9 - - + -
117C ILE* 3.6 39.9 - - + -
121C LEU* 4.3 2.7 - - + -
151C ALA* 3.7 9.6 - - + +
152C VAL 5.2 2.2 - - - +
153C ALA* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU 2.7 25.0 + - - -
43C HIS* 3.4 5.3 - - - -
45C LEU* 1.3 77.9 - - - +
47C ASP* 1.3 61.7 + - - +
49C ILE* 3.4 3.6 + - - +
50C LEU* 3.1 32.4 + - + +
58C ILE* 3.7 32.9 - - + +
61C LEU* 4.1 4.9 - - + -
74C SER 4.7 1.4 + - - -
77C LEU 4.3 1.1 - - - +
78C LEU* 3.4 29.6 + - - +
81C ALA* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 6.1 0.2 - - - +
131A LYS* 3.6 26.1 - - + +
133A THR* 4.9 7.3 + - - -
6C HIS 3.9 1.6 - - - -
7C GLY* 3.9 11.9 - - - -
8C PHE 4.0 15.2 - - - +
9C ASP* 5.5 1.9 - - - +
43C HIS* 2.9 16.7 + - - +
44C ALA 3.2 7.8 + - - +
46C THR* 1.3 77.1 - - - +
48C ALA* 1.3 54.4 + - - +
50C LEU* 3.8 1.5 - - - +
51C GLY* 2.7 32.2 + - - -
56C GLY 4.8 0.2 - - - +
57C ASP* 3.5 5.9 - - - +
58C ILE* 2.8 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLY* 3.4 21.1 - - - +
6C HIS 3.6 26.9 + - - +
7C GLY 3.6 3.6 - - - +
44C ALA 3.0 10.0 + - - +
45C LEU* 3.7 8.1 - - + +
47C ASP* 1.3 75.1 - - - +
49C ILE* 1.3 65.2 + - - +
52C ALA* 3.0 20.4 + - - +
151C ALA* 3.8 11.9 - - + +
152C VAL 4.2 0.2 - - - -
153C ALA* 3.9 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 3.0 25.7 + - + +
46C THR* 3.9 4.3 - - - +
48C ALA* 1.3 78.6 - - - +
50C LEU* 1.3 61.2 + - - +
52C ALA* 3.5 6.4 + - - -
53C ALA* 3.6 4.2 + - - +
78C LEU* 4.2 11.7 - - + -
81C ALA* 4.4 14.6 - - + +
82C PHE* 4.8 0.9 - - + -
85C VAL* 4.1 30.4 - - + +
92C ILE* 4.5 4.9 - - + -
95C VAL* 4.8 2.2 - - + -
121C LEU* 3.4 44.0 - - + -
153C ALA* 4.2 18.2 - - + -
155C LEU* 3.5 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 3.1 29.6 + - + +
47C ASP 4.1 2.0 - - - +
49C ILE* 1.3 74.1 - - + +
51C GLY* 1.3 65.1 + - - +
53C ALA 3.3 1.9 + - - -
54C ALA 3.2 3.3 + - - -
55C LEU* 2.8 68.8 + - + +
56C GLY 4.6 1.3 - - - -
57C ASP* 3.6 34.3 - - - +
58C ILE 3.8 3.4 - - - +
61C LEU* 3.7 23.6 - - + -
81C ALA* 3.9 27.4 - - + +
84C GLN* 4.8 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASN* 4.7 2.4 + - - -
96A ASP* 3.1 28.2 - - - +
129A ASN* 3.1 40.2 - - - +
131A LYS* 4.3 0.2 - - - -
3C ARG* 5.2 0.2 + - - -
47C ASP 2.7 20.3 + - - -
50C LEU* 1.3 75.8 - - - +
52C ALA* 1.3 60.6 + - - +
54C ALA 3.3 1.7 + - - -
56C GLY 4.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASN* 3.4 2.6 + - - -
96A ASP* 3.9 0.6 + - - -
3C ARG* 2.6 45.6 + - + +
4C ILE 3.3 30.3 - - - +
5C GLY 3.7 1.8 - - - +
48C ALA 3.0 16.8 + - - +
50C LEU 3.2 0.4 - - - -
51C GLY* 1.3 76.1 - - - +
53C ALA* 1.3 52.8 + - - +
54C ALA 3.2 0.4 - - - -
153C ALA* 4.6 1.6 - - + +
155C LEU* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ARG* 4.0 4.7 - - - +
49C ILE 3.6 2.8 + - - +
50C LEU 3.3 4.9 + - - +
52C ALA* 1.3 77.8 - - - +
54C ALA* 1.3 66.3 + - - +
55C LEU* 3.2 19.0 + - + -
85C VAL* 4.0 26.7 - - + -
88C LYS* 2.8 40.9 + - + +
90C TYR* 4.4 9.9 - - + -
155C LEU* 4.2 3.1 - - + -
----------------------------------------------------------
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