Contacts of the strand formed by residues 62 - 66 (chain I) in PDB entry 2VLR
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 62 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47I LEU* 4.1 22.4 - - + -
57I LYS 4.1 0.2 - - - +
58I LYS* 3.5 4.5 + - - +
59I LEU* 2.9 36.2 + - + +
60I LYS* 3.4 2.9 - - + +
61I ARG* 1.3 85.6 - - + +
63I THR* 1.3 65.5 + - - +
64I PHE* 3.7 31.4 - - + -
75I LEU* 4.2 7.6 - - + -
76I HIS 3.4 5.2 - - - +
77I ILE* 3.7 36.8 - - + -
84I ASP* 4.3 11.2 - - - +
88I TYR* 4.6 11.9 - - + +
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Residues in contact with THR 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I VAL* 3.9 26.2 - - + -
57I LYS 3.4 5.8 - - - +
58I LYS* 4.0 20.6 + - + +
61I ARG 4.9 2.3 + - - -
62I LEU* 1.3 75.9 + - - +
64I PHE* 1.3 64.3 - - - +
65I GLN* 5.6 3.1 - - + -
74I SER* 3.8 1.0 + - - +
75I LEU* 3.6 2.3 - - - -
76I HIS* 2.8 55.5 + - + +
78I THR* 5.1 3.5 + - - -
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Residues in contact with PHE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I TRP* 3.6 36.3 - + + +
47I LEU* 4.1 15.5 - - + -
48I VAL* 3.7 25.6 - - + -
50I VAL* 4.7 11.3 - - + +
55I GLU 3.9 0.7 - - - +
56I VAL* 3.4 7.3 - - - +
57I LYS* 3.0 39.2 + - + +
59I LEU* 3.6 29.8 - - + -
62I LEU* 3.7 33.7 - - + -
63I THR* 1.3 73.7 - - - +
65I GLN* 1.3 63.2 + - - +
73I SER* 5.4 0.7 - - - +
74I SER 3.3 6.1 - - - +
75I LEU* 3.7 33.7 - - + -
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Residues in contact with GLN 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I VAL* 5.4 2.2 - - - -
54I GLY* 3.4 25.3 + - - -
55I GLU 3.5 6.5 + - - -
56I VAL* 3.4 26.2 - - + +
63I THR* 5.6 2.9 - - + -
64I PHE* 1.3 75.5 - - - +
66I PHE* 1.3 68.9 + - - +
73I SER* 2.9 22.0 + - - -
74I SER* 3.0 34.6 + - - +
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Residues in contact with PHE 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I PHE* 3.8 24.0 - - + -
31I SER 4.8 1.6 - - - -
33I LEU* 4.1 30.7 - - + -
50I VAL* 3.8 30.2 - - + +
51I VAL* 3.6 27.6 - - - -
52I THR 3.5 27.4 - - - +
54I GLY* 3.0 21.3 + - - -
55I GLU* 3.1 13.2 + - + +
65I GLN* 1.3 77.6 + - - +
67I GLY* 1.3 68.1 + - - +
70I ARG* 3.9 29.8 - - + -
72I ASP 3.3 19.3 - - - -
73I SER* 4.3 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