Contacts of the helix formed by residues 52 - 57 (chain A) in PDB entry 2VM6
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 LEU 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.0 38.4 + - + +
49A GLU 3.9 2.0 - - - -
50A LYS 3.1 0.2 - - - -
51A ASN* 1.3 82.5 - - - +
53A LYS* 1.3 53.9 + - - +
54A SER 3.2 3.1 - - - -
55A CYS* 3.1 7.9 + - + +
56A LEU* 2.7 50.3 + - + +
98A ILE* 5.7 0.2 - - + -
147B TRP* 3.4 35.4 - - + +
148B ILE* 3.8 35.4 - - + +
151B GLU* 3.6 26.0 - - + -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU 3.3 16.3 + - - +
50A LYS* 3.6 11.4 + - - +
51A ASN 3.7 0.4 - - - -
52A LEU* 1.3 74.8 - - - +
54A SER* 1.3 62.1 + - - +
56A LEU* 4.6 4.0 - - - +
57A ASP* 2.9 60.7 + - - +
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN 5.4 0.4 + - - -
52A LEU* 3.2 1.0 - - - -
53A LYS* 1.3 85.7 + - - +
55A CYS* 1.3 64.8 + - - +
57A ASP* 5.0 1.1 - - - -
58A ASN* 3.3 21.3 - - - +
142B MET* 4.7 2.1 - - - +
147B TRP* 3.9 22.8 - - - -
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Residues in contact with CYS 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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52A LEU* 3.1 10.9 + - + +
54A SER* 1.3 78.8 - - - +
56A LEU* 1.3 55.7 + - - +
58A ASN* 2.9 28.4 + - - +
59A VAL* 3.4 12.7 - - - +
142B MET* 4.3 5.3 - - - +
144B PRO* 3.9 25.4 - - - -
147B TRP* 3.4 59.7 - - + +
148B ILE* 3.9 16.8 - - - -
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Residues in contact with LEU 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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49A GLU* 4.4 15.5 - - + +
52A LEU* 2.7 42.0 + - + +
53A LYS* 4.3 2.7 - - - +
55A CYS* 1.3 68.7 - - + +
57A ASP* 1.3 65.0 + - - +
58A ASN 3.1 1.8 - - - -
59A VAL* 3.1 19.2 + - + -
70A LEU* 6.0 0.9 - - + -
95A PHE* 4.9 4.3 - - + -
98A ILE* 4.0 42.4 - - + -
102A LYS* 2.9 37.7 + - + +
148B ILE* 4.1 28.7 - - + -
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Residues in contact with ASP 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 LYS* 2.9 52.5 + - - +
54A SER* 4.4 1.1 - - - +
56A LEU* 1.3 77.5 - - - +
58A ASN* 1.3 67.0 + - - +
59A VAL 3.4 2.8 + - - +
60A ASN* 5.7 0.5 - - - +
102A LYS* 4.8 3.4 + - - +
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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