Contacts of the helix formed by residues 51 - 61 (chain A) in PDB entry 5VXA
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.8 5.7 - - + +
50A THR* 1.3 75.1 + - - +
52A ILE* 1.3 64.9 + - - +
53A VAL* 2.9 26.0 + - - +
54A VAL* 3.1 28.9 + - + +
55A LEU* 3.0 22.9 + - - +
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Residues in contact with ILE 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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4A GLU* 3.5 43.7 - - + +
7A GLN* 3.7 38.4 - - + +
8A LEU* 3.6 27.4 - - + +
50A THR 3.1 8.4 + - - +
51A ASP* 1.3 73.2 + - - +
53A VAL* 1.3 67.5 + - + +
55A LEU* 3.7 5.2 - - + +
56A GLN* 2.8 38.2 + - - +
5B ALA* 5.4 2.0 - - + -
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Residues in contact with VAL 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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51A ASP* 2.9 14.1 + - - +
52A ILE* 1.3 82.6 - - + +
54A VAL* 1.3 68.3 + - + +
56A GLN* 3.9 4.3 - - - +
57A ALA* 3.0 23.4 + - - +
81A GLN* 4.0 49.4 - - + +
82A VAL* 4.0 26.2 - - + +
85A LEU* 4.1 11.0 - - + -
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Residues in contact with VAL 54 (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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43A LEU* 4.2 7.6 - - + -
49A ILE* 4.2 11.2 - - + -
51A ASP* 3.1 34.9 + - + +
53A VAL* 1.3 78.8 - - + +
55A LEU* 1.3 56.6 + - - +
57A ALA* 3.2 3.5 + - - +
58A ALA* 2.9 26.7 + - - +
85A LEU* 3.9 17.0 - - + -
114A GLY* 4.2 15.5 - - - +
117A LEU* 4.2 27.8 - - + -
118A VAL* 4.0 18.9 - - + +
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Residues in contact with LEU 55 (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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8A LEU* 3.8 18.2 - - + -
40A ALA* 4.0 7.7 - - - +
43A LEU* 3.7 31.6 - - + -
44A THR* 3.6 29.2 - - + -
49A ILE* 4.0 18.4 - - + +
50A THR 4.2 7.2 - - - +
51A ASP 3.0 20.3 + - - +
52A ILE* 3.9 4.3 - - - +
53A VAL 3.3 0.2 - - - -
54A VAL* 1.3 71.5 - - - +
56A GLN* 1.3 66.0 + - - +
58A ALA* 3.2 6.1 + - - +
59A LEU* 3.1 26.2 + - - +
5B ALA* 3.6 23.8 - - + -
9B LEU* 4.4 7.4 - - + -
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Residues in contact with GLN 56 (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 GLN* 3.0 40.8 + - - +
8A LEU* 4.3 5.1 - - + +
10A GLU* 5.0 1.0 - - - +
11A ALA* 3.8 18.4 - - + -
52A ILE* 2.8 38.3 + - + +
53A VAL* 3.9 5.1 - - - +
55A LEU* 1.3 73.2 - - - +
57A ALA* 1.3 62.3 + - - +
59A LEU* 3.2 4.7 + - - +
60A LEU* 3.0 32.4 + - + +
78A PHE* 3.7 26.7 - - - +
82A VAL* 3.6 21.8 - - + +
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Residues in contact with ALA 57 (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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53A VAL 3.0 19.2 + - - +
54A VAL 3.2 5.1 + - - +
56A GLN* 1.3 75.8 - - - +
58A ALA* 1.3 53.4 + - - +
60A LEU 3.2 1.2 + - - -
61A HIS* 2.8 38.8 + - - +
82A VAL* 4.5 6.0 - - + +
85A LEU* 3.6 34.1 - - + -
86A VAL* 4.2 17.0 - - + +
89A VAL* 5.4 1.1 - - + +
118A VAL* 4.5 6.5 - - + -
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Residues in contact with ALA 58 (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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36A PRO* 3.8 7.7 - - - +
39A VAL* 4.2 6.2 - - + +
40A ALA* 3.9 16.8 - - + +
43A LEU* 3.7 25.8 - - + -
54A VAL 2.9 13.1 + - - +
55A LEU 3.5 9.0 - - - +
57A ALA* 1.3 73.7 - - - +
59A LEU* 1.3 63.1 + - - +
61A HIS* 2.7 30.7 + - - -
118A VAL* 4.2 10.9 - - + +
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Residues in contact with LEU 59 (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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8A LEU* 3.6 39.7 - - + +
11A ALA* 3.8 19.1 - - + +
12A ALA* 3.7 18.6 - - + +
15A ALA* 3.4 16.0 - - + +
19A HIS* 5.0 0.2 + - - -
33A ILE* 6.0 0.9 - - + -
36A PRO* 3.2 23.4 - - + +
37A ILE* 3.9 30.1 - - + +
40A ALA* 3.8 19.5 - - + -
55A LEU 3.1 18.6 + - - +
56A GLN 3.2 5.1 + - - +
58A ALA* 1.3 76.3 - - - +
60A LEU* 1.3 58.9 + - - +
63A THR* 4.8 0.7 - - - +
9B LEU* 4.4 12.8 - - + -
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Residues in contact with LEU 60 (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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11A ALA* 3.8 24.7 - - + +
14A PHE* 3.5 34.5 - - + -
15A ALA* 4.4 1.1 - - + -
56A GLN* 3.0 23.5 + - + +
57A ALA 3.4 3.1 - - - +
59A LEU* 1.3 77.2 - - - +
61A HIS* 1.3 62.6 + - - +
62A ASP 2.9 3.6 + - - -
63A THR* 2.8 35.5 + - + +
74A VAL* 4.6 6.5 - - + -
78A PHE* 3.7 32.5 - - + -
82A VAL* 3.8 20.2 - - + -
86A VAL* 4.1 15.0 - - + +
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Residues in contact with HIS 61 (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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35A HIS* 3.5 10.3 - + - -
36A PRO* 4.2 7.1 - - + +
39A VAL* 3.9 16.9 - - + +
57A ALA 2.8 18.9 + - - +
58A ALA* 2.7 23.9 + - - -
59A LEU 3.5 1.0 - - - -
60A LEU* 1.3 72.1 - - - +
62A ASP* 1.3 74.0 + - - +
65A GLU* 4.7 4.0 + - - +
86A VAL* 4.6 6.3 - - - +
89A VAL* 3.7 39.6 - - + +
90A THR* 4.4 8.1 + - - -
118A VAL* 3.8 15.3 - - + -
122A ASP* 3.1 15.2 + - - -
201A ZN 2.0 37.7 - - - -
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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