Contacts of the strand formed by residues 49 - 52 (chain S) in PDB entry 2VGL
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 PHE 49 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A ASN* 3.1 57.2 - - + -
347A TYR* 4.6 15.5 - + + -
348A LEU* 4.0 22.0 - - + -
42S ARG* 3.3 4.2 + - - -
47S THR* 2.9 30.3 + - + -
48S ASN* 1.3 93.3 - - + +
50S VAL* 1.3 68.2 + - - +
56S LYS* 5.5 2.9 - - + -
57S ILE 3.3 5.2 - - - +
58S ILE* 4.3 6.3 - - + -
77S ASN* 3.8 39.9 - - + +
78S LEU* 4.1 5.8 - - + -
81S LEU* 4.2 10.3 - - + -
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Residues in contact with VAL 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M GLN* 4.0 13.0 - - - +
38S VAL* 3.8 29.6 - - + -
42S ARG* 3.6 29.4 - - - +
49S PHE* 1.3 79.1 - - - +
51S GLU* 1.3 77.9 + - - +
52S PHE 3.6 0.2 + - - -
56S LYS* 3.3 4.4 - - - +
57S ILE* 2.8 47.8 + - + +
59S TYR* 4.6 8.7 - - + -
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Residues in contact with GLU 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A TYR* 4.7 9.7 + - - +
186M SER* 4.3 13.4 - - - -
187M PRO* 5.6 1.0 - - - +
188M GLN* 3.7 20.4 + - - -
190M GLN* 3.0 35.8 + - - +
192M LEU* 3.7 16.0 - - + +
434M ARG* 3.7 22.7 + - - +
38S VAL* 5.5 3.3 - - - +
50S VAL* 1.3 83.8 - - - +
52S PHE* 1.3 61.3 + - - +
55S PHE 3.6 9.6 - - - +
56S LYS* 4.0 7.9 - - + -
73S VAL* 5.5 3.8 - - + +
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Residues in contact with PHE 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M LEU* 4.2 0.8 - - - +
4S PHE* 4.0 8.5 - + - -
31S LEU* 3.6 30.7 - - + -
34S GLU* 3.9 31.2 - - + -
35S VAL* 3.4 32.8 - - + -
38S VAL* 4.6 16.4 - - + -
50S VAL* 4.2 1.8 - - + +
51S GLU* 1.3 76.8 - - - +
53S ARG* 1.3 68.9 + - + +
54S ASN 3.1 0.3 + - - -
55S PHE* 2.7 41.4 + + + +
56S LYS* 4.3 0.9 - - - -
57S ILE* 3.4 35.7 - - + -
70S CYS* 4.3 11.2 - - - -
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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