Contacts of the helix formed by residues 39 - 53 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F ASP* 2.9 23.5 + - - +
38F GLY* 1.3 73.2 - - - +
40F VAL* 1.3 60.8 + - - +
41F ALA* 3.4 12.1 + - - +
42F LEU* 3.2 38.5 + - - +
43F HIS* 3.0 27.9 + - - -
74F SER* 3.4 10.4 - - - +
75F ARG* 5.6 0.2 - - - +
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Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASP* 4.2 7.2 - - + +
10F VAL* 3.7 9.9 - - - +
11F HIS* 3.4 43.1 - - + +
38F GLY 2.9 8.8 + - - +
39F ASP* 1.3 72.5 - - - +
41F ALA* 1.3 68.0 + - + +
43F HIS* 3.8 9.4 - - + +
44F ALA* 3.1 26.7 + - - +
99F ILE* 4.9 6.7 - - + -
147F ILE* 3.8 31.0 - - + +
148F ALA 4.1 6.7 - - - +
149F CYS* 3.6 19.2 - - + +
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Residues in contact with ALA 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ASP* 3.2 10.2 + - - +
40F VAL* 1.3 84.0 - - + +
42F LEU* 1.3 67.7 + - + +
44F ALA* 4.1 1.4 - - - +
45F LEU* 3.2 23.9 + - - +
97F ILE* 4.3 11.3 - - + +
99F ILE* 4.3 24.5 - - + -
113F MSE 5.6 4.5 - - - -
117F ILE* 5.9 4.7 - - + -
130F VAL* 6.2 0.4 - - + -
149F CYS* 3.7 15.0 - - - -
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Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ASP* 3.2 26.4 + - - +
41F ALA* 1.3 79.5 - - + +
43F HIS* 1.3 58.4 + - - +
45F LEU* 3.7 5.7 - - + +
46F THR* 2.6 40.5 + - - +
74F SER* 3.7 20.6 - - - +
75F ARG* 3.5 43.7 - - + +
78F LEU* 4.0 21.7 - - + +
117F ILE* 4.0 26.2 - - + -
120F ASP* 5.1 0.2 - - - +
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Residues in contact with HIS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASP* 3.1 27.5 - - + +
10F VAL 5.7 2.9 - - - -
11F HIS* 6.3 0.2 - - + -
35F HIS* 5.7 1.5 + - - -
36F SER* 3.2 31.7 + - - -
38F GLY* 4.3 2.7 - - - -
39F ASP 3.0 27.6 + - - +
40F VAL* 3.8 9.0 - - + +
42F LEU* 1.3 77.1 - - - +
44F ALA* 1.3 57.2 + - - +
46F THR* 3.1 4.2 + - - -
47F ASP* 2.8 28.1 + - - +
58F ILE* 3.7 28.5 - - + +
72F ALA 5.5 0.2 - - - -
74F SER* 3.0 29.3 + - - -
77F LEU* 4.6 7.0 - - + -
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Residues in contact with ALA 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLY* 3.4 17.1 - - - +
8F PHE 4.2 0.2 - - - +
9F ASP* 2.9 17.7 + - - +
40F VAL 3.1 14.7 + - - +
41F ALA 4.1 2.5 - - - +
43F HIS* 1.3 75.3 - - - +
45F LEU* 1.3 58.9 + - - +
47F ASP 3.1 1.9 + - - -
48F ALA* 2.8 26.3 + - - +
149F CYS* 3.7 27.6 - - - +
151F ALA* 3.9 16.6 - - + -
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ALA 3.2 16.6 + - - +
42F LEU* 3.7 10.1 - - + +
44F ALA* 1.3 78.9 - - - +
46F THR* 1.3 63.0 + - - +
48F ALA* 3.1 3.5 + - + +
49F ILE* 2.9 31.6 + - + +
78F LEU* 3.8 20.0 - - + -
95F VAL* 3.3 42.4 - - + -
97F ILE* 3.5 13.2 - - + -
117F ILE* 3.5 40.6 - - + -
121F LEU* 4.0 1.6 - - + -
151F ALA* 3.8 7.8 - - + +
153F ALA* 4.9 4.5 - - + -
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Residues in contact with THR 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU 2.6 29.0 + - - -
43F HIS* 3.4 5.5 - - - -
45F LEU* 1.3 75.7 - - - +
47F ASP* 1.3 57.1 + - - +
49F ILE* 3.4 3.9 + - - +
50F LEU* 2.9 35.0 + - + +
58F ILE* 4.0 15.9 - - + +
61F LEU* 4.0 13.5 - - + -
74F SER 4.7 1.4 + - - -
77F LEU 3.9 9.0 - - - +
78F LEU* 3.5 26.9 + - - +
81F ALA* 3.6 24.7 - - + -
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Residues in contact with ASP 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LYS* 3.7 21.4 - - + +
133D THR* 5.2 3.6 + - - -
6F HIS 4.0 1.8 - - - -
7F GLY* 3.9 11.9 - - - -
8F PHE 4.2 3.0 - - - +
9F ASP* 2.9 28.2 - - - +
43F HIS 2.8 10.8 + - - +
44F ALA 3.5 7.9 - - - +
46F THR* 1.3 77.2 - - - +
48F ALA* 1.3 52.4 + - - +
50F LEU* 3.9 3.4 - - - +
51F GLY* 2.7 33.4 + - - -
56F GLY 5.0 0.2 - - - +
57F ASP* 3.2 11.2 - - - +
58F ILE* 2.8 42.2 + - - +
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F GLY* 3.3 19.2 - - - +
6F HIS 3.5 13.9 - - - +
7F GLY* 3.5 16.7 - - - +
44F ALA 2.8 10.6 + - - +
45F LEU* 3.1 9.8 + - + +
47F ASP* 1.3 77.2 - - - +
49F ILE* 1.3 57.4 + - - +
51F GLY 3.3 0.3 + - - -
52F ALA* 2.8 26.5 + - - +
151F ALA* 3.8 13.0 - - + +
152F VAL 4.2 0.4 - - - +
153F ALA* 4.0 14.6 - - + +
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Residues in contact with ILE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 2.9 37.0 + - + +
46F THR* 3.8 4.5 - - - +
48F ALA* 1.3 78.3 - - - +
50F LEU* 1.3 63.0 + - - +
52F ALA* 3.5 10.6 + - - +
53F ALA 3.6 7.3 + - - -
78F LEU* 4.3 6.3 - - + +
81F ALA* 4.4 12.8 - - + +
82F PHE* 4.8 2.7 - - + -
85F VAL* 3.3 33.7 - - + +
92F ILE* 4.7 5.6 - - + -
95F VAL* 4.7 2.9 - - + -
121F LEU* 3.6 34.1 - - + -
153F ALA* 3.9 19.7 - - + -
155F LEU* 3.9 14.8 - - + +
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F THR* 2.9 24.4 + - + +
47F ASP 3.9 2.9 - - - +
49F ILE* 1.3 76.6 - - - +
51F GLY* 1.3 61.2 + - - +
53F ALA* 3.5 1.9 + - - -
54F ALA 3.3 3.1 + - - -
55F LEU* 2.8 61.2 + - + +
56F GLY 4.6 0.2 - - - -
57F ASP* 3.4 38.4 - - - +
58F ILE* 3.4 6.7 - - - +
61F LEU* 3.5 31.4 - - + -
81F ALA* 3.5 28.3 - - + +
84F GLN* 4.3 2.9 - - - +
85F VAL* 4.9 1.8 - - + -
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Residues in contact with GLY 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASN* 4.7 2.3 + - - -
96D ASP* 3.4 21.4 - - - +
129D ASN* 3.2 37.8 - - - +
131D LYS* 4.3 0.2 - - - -
3F ARG* 5.2 0.2 + - - -
47F ASP 2.7 19.3 + - - -
50F LEU* 1.3 73.4 - - - +
52F ALA* 1.3 64.2 + - - +
54F ALA 3.0 10.2 + - - -
56F GLY 4.2 1.0 + - - -
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASN* 3.3 9.2 + - - -
3F ARG* 2.9 32.3 + - + +
4F ILE 3.2 16.4 - - - +
5F GLY* 3.5 16.7 - - - +
48F ALA 2.8 18.1 + - - +
49F ILE* 3.7 7.9 - - - +
50F LEU 3.3 0.4 - - - -
51F GLY* 1.3 76.3 - - - +
53F ALA* 1.3 56.9 + - - +
54F ALA 3.3 0.2 - - - -
153F ALA 4.4 2.7 - - - +
155F LEU* 3.8 21.8 - - + -
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Residues in contact with ALA 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D GLU* 4.5 0.3 - - - +
3F ARG* 3.9 6.5 + - - +
49F ILE 3.6 5.5 + - - +
50F LEU 3.5 2.2 + - - -
51F GLY 3.2 0.2 - - - -
52F ALA* 1.3 77.4 - - - +
54F ALA* 1.3 66.5 + - - +
55F LEU* 3.3 19.7 + - + +
85F VAL* 4.5 3.6 - - + -
88F LYS* 2.8 32.5 + - + +
90F TYR* 4.1 22.2 - - + -
155F LEU* 3.8 20.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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