Contacts of the helix formed by residues 39 - 53 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D ASP* 5.0 0.2 - - - -
36D SER* 4.7 0.4 + - - -
37D ASP* 3.2 24.5 + - - +
38D GLY* 1.3 71.7 - - - +
40D VAL* 1.3 57.4 + - - +
41D ALA* 3.1 11.8 + - - +
42D LEU* 3.1 44.3 + - - +
43D HIS* 3.2 31.2 + - - -
74D SER* 3.6 7.2 - - - +
113D MSE 5.7 0.2 - - - +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ASP* 3.2 53.2 - - + +
10D VAL* 3.5 6.5 - - - +
11D HIS* 4.6 3.4 - - + -
38D GLY 3.0 10.5 + - - +
39D ASP* 1.3 71.1 + - - +
41D ALA* 1.3 68.9 + - + +
43D HIS* 3.8 0.6 - - - +
44D ALA* 3.1 17.2 + - - +
99D ILE* 5.2 5.8 - - + -
147D ILE* 4.0 27.6 - - + +
148D ALA 3.7 9.4 - - - +
149D CYS* 3.4 25.7 - - + +
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 3.1 9.0 + - - +
40D VAL* 1.3 80.8 - - + +
42D LEU* 1.3 69.9 + - + +
44D ALA* 3.9 2.3 - - - +
45D LEU* 3.0 22.5 + - - +
97D ILE* 4.4 11.6 - - + +
99D ILE* 4.4 9.2 - - + -
113D MSE 3.7 30.1 - - + -
117D ILE* 5.8 0.4 - - + -
149D CYS* 3.5 19.3 - - - -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASP* 5.8 0.2 - - - +
39D ASP* 3.1 31.8 + - - +
41D ALA* 1.3 77.9 - - + +
43D HIS* 1.3 51.7 + - - +
45D LEU* 3.6 5.8 - - + +
46D THR* 2.7 44.6 + - - +
74D SER* 3.8 20.4 - - - -
75D ARG* 3.7 33.9 - - + +
78D LEU* 4.1 17.2 - - + +
113D MSE 6.0 1.1 - - + -
117D ILE* 3.6 37.0 - - + -
120D ASP* 5.2 0.4 - - - +
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Residues in contact with HIS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ASP* 3.5 34.3 - - - +
35D HIS* 5.5 3.3 + + - -
36D SER* 4.0 29.1 - - - -
37D ASP* 4.4 0.9 - - - -
38D GLY 6.3 0.2 - - - -
39D ASP 3.2 21.8 + - - +
40D VAL 3.9 1.6 - - - +
41D ALA 3.2 0.4 - - - -
42D LEU* 1.3 77.2 - - - +
44D ALA* 1.3 62.2 + - - +
46D THR* 3.3 7.5 + - - -
47D ASP* 3.0 27.6 + - - +
58D ILE* 3.8 33.2 - - + +
72D ALA 5.3 0.7 - - - -
74D SER* 3.1 30.4 + - - -
77D LEU* 4.3 8.2 - - + +
169D MN 4.4 7.9 - - - -
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLY* 3.4 28.0 - - - +
8D PHE 4.2 2.5 - - - +
9D ASP* 4.1 6.9 - - - +
40D VAL 3.1 17.0 + - - +
41D ALA 3.9 2.9 - - - +
43D HIS* 1.3 79.3 - - - +
45D LEU* 1.3 58.0 + - - +
47D ASP* 3.2 2.6 + - - +
48D ALA* 2.9 25.5 + - - +
149D CYS* 3.6 26.2 - - - +
151D ALA* 3.8 11.2 - - + -
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA 3.0 18.3 + - - +
42D LEU* 3.6 6.5 - - + +
44D ALA* 1.3 77.4 - - - +
46D THR* 1.3 62.5 + - - +
48D ALA* 3.0 6.7 + - + +
49D ILE* 2.9 39.7 + - + +
78D LEU* 4.3 12.6 - - + -
95D VAL* 3.7 33.2 - - + -
97D ILE* 3.6 24.7 - - + -
117D ILE* 3.5 35.7 - - + -
121D LEU* 4.1 8.7 - - + -
151D ALA* 3.9 8.7 - - + +
152D VAL 5.1 0.9 - - - +
153D ALA* 4.8 0.4 - - + -
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Residues in contact with THR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU 2.7 29.5 + - - -
43D HIS* 3.5 5.9 + - - -
45D LEU* 1.3 73.3 - - - +
47D ASP* 1.3 57.7 + - - +
49D ILE* 3.4 3.0 + - - +
50D LEU* 3.0 39.9 + - + +
58D ILE* 3.9 26.5 - - + +
61D LEU* 4.2 0.7 - - + -
74D SER* 4.8 1.9 + - - -
77D LEU* 4.1 7.1 - - - +
78D LEU* 3.6 28.2 + - - +
81D ALA* 3.7 24.5 - - + -
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Residues in contact with ASP 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D HIS 3.7 1.7 - - - +
7D GLY* 3.9 12.6 - - - -
8D PHE 4.2 13.9 + - - +
9D ASP* 4.9 5.2 - - - +
43D HIS* 3.0 17.6 + - - +
44D ALA* 3.2 7.6 + - - +
46D THR* 1.3 78.5 - - - +
48D ALA* 1.3 56.7 + - - +
50D LEU* 4.2 3.1 - - - +
51D GLY* 2.8 26.9 + - - -
57D ASP* 3.2 7.5 - - - +
58D ILE* 2.8 42.9 + - - +
131E LYS* 3.4 26.1 - - + +
133E THR* 5.2 4.9 + - - -
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLY* 3.4 13.2 - - - +
6D HIS 3.6 13.2 - - - +
7D GLY* 3.7 13.4 - - - +
44D ALA 2.9 13.2 + - - +
45D LEU* 3.0 11.0 + - + +
47D ASP* 1.3 75.6 - - - +
49D ILE* 1.3 60.5 + - - +
52D ALA* 2.9 30.7 + - - +
151D ALA* 3.9 13.0 - - + +
152D VAL 4.3 0.7 - - - -
153D ALA* 4.0 15.6 - - + +
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 2.9 25.1 + - + +
46D THR* 3.8 4.3 - - - +
48D ALA* 1.3 74.6 - - - +
50D LEU* 1.3 67.2 + - - +
52D ALA* 3.3 4.5 + - - +
53D ALA* 3.3 21.1 + - - +
78D LEU* 3.8 18.8 - - + +
81D ALA* 4.5 6.3 - - + +
82D PHE* 4.7 3.6 - - + -
85D VAL* 3.2 34.5 - - + -
92D ILE* 4.3 9.2 - - + -
95D VAL* 5.0 0.4 - - + -
121D LEU* 3.3 41.7 - - + -
153D ALA* 4.3 13.5 - - + -
155D LEU* 3.8 8.3 - - + +
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR* 3.0 27.1 + - + +
47D ASP 4.2 2.0 - - - +
49D ILE* 1.3 76.2 - - - +
51D GLY* 1.3 55.9 + - - +
53D ALA* 3.2 4.7 + - - -
54D ALA 3.0 7.8 + - - -
55D LEU* 2.7 56.1 + - + +
56D GLY 4.5 0.7 - - - -
57D ASP* 3.3 41.3 - - - +
58D ILE* 3.4 11.9 - - - +
61D LEU* 4.1 14.1 - - + -
81D ALA* 3.4 36.8 - - + +
84D GLN* 5.1 2.5 - - + +
85D VAL* 4.8 0.2 - - + -
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Residues in contact with GLY 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ARG* 5.2 0.2 + - - -
47D ASP 2.8 18.0 + - - -
50D LEU* 1.3 74.7 - - - +
52D ALA* 1.3 65.0 + - - +
54D ALA* 3.1 8.3 + - - +
56D GLY 4.1 1.9 + - - -
94E ASN* 5.0 0.7 + - - -
95E VAL 4.8 1.0 - - - +
96E ASP* 3.3 19.9 - - - +
129E ASN* 3.2 39.2 - - - +
131E LYS* 4.4 0.4 - - - -
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ARG* 2.9 38.3 + - + +
4D ILE 3.4 15.0 - - - +
5D GLY* 3.5 19.0 - - - +
48D ALA 2.9 18.3 + - - +
49D ILE* 3.7 0.9 - - - +
50D LEU 3.3 0.2 - - - -
51D GLY* 1.3 77.2 - - - +
53D ALA* 1.3 56.9 + - - +
54D ALA 3.1 0.2 - - - -
153D ALA 4.5 2.5 - - - +
155D LEU* 3.6 28.0 - - + -
94E ASN* 3.7 2.6 + - - -
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Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ARG* 4.0 3.1 - - - +
49D ILE 3.3 8.6 + - - +
50D LEU 3.2 4.5 + - - +
52D ALA* 1.3 76.5 - - - +
54D ALA* 1.3 69.7 + - - +
55D LEU* 3.2 20.3 + - + -
85D VAL* 4.3 6.5 - - + -
88D LYS* 3.4 24.4 + - + +
90D TYR* 4.2 19.0 - - + -
155D LEU* 3.6 19.5 - - + +
126E GLU* 3.6 1.0 - - - +
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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