Contacts of the helix formed by residues 39 - 53 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASP* 2.8 25.5 + - - +
38A GLY* 1.3 72.0 - - - +
40A VAL* 1.3 58.4 + - - +
41A ALA* 3.3 10.9 + - - +
42A LEU* 3.1 44.4 + - - +
43A HIS* 2.9 34.6 + - - -
74A SER* 3.6 8.6 - - - +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 3.2 48.6 - - - +
10A VAL* 3.6 13.9 - - - +
11A HIS* 3.8 6.5 - - + +
38A GLY 2.7 9.4 + - - +
39A ASP* 1.3 70.1 + - - +
41A ALA* 1.3 70.0 + - + +
43A HIS* 4.0 0.3 - - - +
44A ALA* 3.1 27.0 + - - +
99A ILE* 4.8 6.1 - - + -
147A ILE* 3.9 23.3 - - + +
148A ALA* 3.6 9.9 - - - +
149A CYS* 3.0 22.8 - - + +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASP* 3.3 7.5 + - - +
40A VAL* 1.3 82.5 - - + +
42A LEU* 1.3 63.6 + - + +
44A ALA* 4.1 1.4 - - - +
45A LEU* 3.1 28.2 + - - +
97A ILE* 4.1 19.0 - - + +
99A ILE* 4.4 16.4 - - + -
113A MSE 5.4 7.9 - - - -
117A ILE* 5.9 2.2 - - + -
130A VAL* 5.8 1.3 - - + -
149A CYS* 3.6 18.4 - - - -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASP* 3.1 38.0 + - - +
41A ALA* 1.3 77.6 - - + +
43A HIS* 1.3 58.6 + - - +
45A LEU* 3.7 4.8 - - + +
46A THR* 2.7 40.4 + - - +
74A SER* 3.8 27.8 - - - +
75A ARG* 3.6 31.9 - - + -
78A LEU* 3.9 14.8 - - + +
116A LYS* 6.5 0.4 - - + -
117A ILE* 3.9 31.9 - - + -
120A ASP* 5.8 0.4 - - - +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 3.3 35.2 - - - +
36A SER* 3.2 34.0 + - - -
38A GLY* 4.3 2.2 - - - -
39A ASP 2.9 30.7 + - - +
40A VAL 4.0 0.2 - - - +
42A LEU* 1.3 76.8 - - - +
44A ALA* 1.3 63.1 + - - +
46A THR* 3.1 3.8 + - - -
47A ASP* 2.9 28.7 + - - +
58A ILE* 3.2 31.5 - - + +
74A SER* 3.1 26.3 + - - -
77A LEU* 4.2 8.3 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY* 3.3 28.2 - - - +
8A PHE 4.0 3.8 - - - +
9A ASP* 4.0 6.6 - - - +
40A VAL 3.1 17.3 + - - +
41A ALA 4.1 2.2 - - - +
43A HIS* 1.3 76.8 - - - +
45A LEU* 1.3 57.1 + - - +
47A ASP* 3.1 2.6 + - - -
48A ALA* 2.9 25.5 + - - +
149A CYS* 3.6 28.7 - - - +
151A ALA* 3.9 10.1 - - + -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 3.1 19.5 + - - +
42A LEU* 3.7 6.1 - - + +
43A HIS 3.3 0.2 - - - -
44A ALA* 1.3 76.2 - - - +
46A THR* 1.3 61.0 - - - +
48A ALA* 3.3 4.6 + - + +
49A ILE* 3.2 37.3 + - + +
78A LEU* 4.0 24.0 - - + -
95A VAL* 3.9 26.5 - - + -
97A ILE* 3.8 22.4 - - + -
117A ILE* 3.5 34.8 - - + -
121A LEU* 4.3 2.2 - - + -
151A ALA* 3.8 11.4 - - + +
152A VAL 5.2 0.2 - - - +
153A ALA* 4.9 0.7 - - + -
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU 2.7 24.9 + - - -
43A HIS* 3.4 4.4 - - - -
45A LEU* 1.3 75.5 - - - +
47A ASP* 1.3 63.8 + - - +
49A ILE* 3.6 3.6 + - - +
50A LEU* 3.2 26.1 + - + +
58A ILE* 3.7 33.9 - - + +
61A LEU* 3.9 9.0 - - + -
74A SER 4.7 1.4 + - - -
77A LEU 4.3 2.2 - - - +
78A LEU* 3.3 30.1 + - - +
81A ALA* 3.9 21.3 - - + +
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A HIS 3.9 1.6 - - - -
7A GLY* 3.9 12.3 - - - -
8A PHE 4.1 13.3 - - - +
9A ASP* 5.4 2.6 - - - +
43A HIS* 2.9 17.9 + - - +
44A ALA 3.1 7.2 + - - +
46A THR* 1.3 76.3 - - - +
48A ALA* 1.3 58.2 + - - +
50A LEU* 4.1 3.4 - - - +
51A GLY 2.9 23.0 + - - -
57A ASP* 3.1 14.1 - - - +
58A ILE* 2.7 43.9 + - - +
131B LYS* 3.5 23.9 - - + +
133B THR* 5.1 7.3 + - - -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLY* 3.1 19.7 - - - +
6A HIS 3.6 12.5 + - - -
7A GLY 3.7 12.3 - - - +
44A ALA 2.9 13.2 + - - +
45A LEU* 3.5 11.9 - - + +
46A THR 3.2 0.2 - - - -
47A ASP* 1.3 77.6 - - - +
49A ILE* 1.3 58.6 + - - +
51A GLY 3.4 0.3 + - - -
52A ALA* 3.0 23.7 + - - +
151A ALA* 3.7 14.8 - - + +
152A VAL 4.3 0.2 - - - -
153A ALA* 4.0 13.2 - - + +
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.2 30.0 + - + +
46A THR* 4.1 3.8 - - - +
48A ALA* 1.3 72.9 - - - +
50A LEU* 1.3 66.5 - - - +
51A GLY 3.3 0.2 + - - -
52A ALA* 3.4 3.4 + - - -
53A ALA* 3.4 20.8 + - - +
78A LEU* 4.5 4.9 - - + -
81A ALA* 4.7 12.6 - - + +
82A PHE* 5.0 3.1 - - + +
85A VAL* 3.2 28.5 - - + -
92A ILE* 4.4 8.1 - - + -
95A VAL* 4.6 2.0 - - + -
121A LEU* 3.7 34.8 - - + -
153A ALA* 4.0 18.2 - - + -
155A LEU* 3.8 18.8 - - + +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A THR* 3.2 20.6 + - + +
47A ASP 4.1 2.2 - - - +
49A ILE* 1.3 77.3 - - - +
51A GLY* 1.3 55.5 + - - +
53A ALA 3.4 1.2 + - - -
54A ALA 3.1 6.2 + - - -
55A LEU* 2.7 64.3 + - + +
56A GLY 4.3 8.7 - - - +
57A ASP* 3.3 34.3 - - - +
58A ILE* 3.4 10.5 - - - +
61A LEU* 3.8 19.3 - - + -
81A ALA* 3.6 29.8 - - + +
84A GLN* 4.9 2.5 - - - +
85A VAL* 4.9 1.8 - - + -
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ARG* 5.0 0.5 + - - -
47A ASP 2.9 14.3 + - - -
49A ILE 3.2 0.2 - - - -
50A LEU* 1.3 76.1 - - - +
52A ALA* 1.3 63.4 + - - +
54A ALA* 3.1 8.8 + - - +
56A GLY 4.2 0.6 + - - -
94B ASN* 4.5 3.1 + - - -
96B ASP* 3.3 21.8 - - - +
129B ASN* 3.1 40.1 - - - +
131B LYS* 4.5 0.2 - - - -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ARG* 2.6 48.4 + - - +
4A ILE 3.2 34.3 - - - -
5A GLY* 3.3 6.6 - - - +
48A ALA 3.0 10.7 + - - +
49A ILE* 3.4 5.4 + - - +
51A GLY* 1.3 76.3 - - - +
53A ALA* 1.3 51.6 + - - +
54A ALA 3.3 0.7 - - - -
153A ALA 4.4 2.2 - - - +
155A LEU* 3.9 20.9 - - + -
94B ASN* 3.7 1.6 + - - +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ARG* 3.8 5.2 - - - +
49A ILE 3.4 13.4 + - - +
50A LEU 3.4 3.6 + - - +
51A GLY 3.2 0.2 - - - -
52A ALA* 1.3 78.3 - - - +
54A ALA* 1.3 64.6 + - - +
55A LEU* 3.3 11.2 + - + +
85A VAL* 4.0 13.9 - - + -
88A LYS* 2.8 32.6 + - + +
90A TYR* 4.3 17.3 - - + -
155A LEU* 3.8 14.4 - - + -
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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