Contacts of the strand formed by residues 1405 - 1408 (chain A) in PDB entry 2VK7
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 ASP1405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1321A PRO* 5.6 0.2 - - - +
1400A THR* 3.1 25.6 - - - -
1401A ASN* 2.9 34.0 + - - +
1403A LEU* 4.5 9.8 - - - +
1404A GLY* 1.3 80.0 - - - +
1406A LEU* 1.4 58.3 + - - +
1407A PHE* 3.6 16.0 - - + -
1412A LYS* 3.3 33.5 + - + +
1414A ASP 3.7 2.9 - - - -
1415A ASN* 2.9 20.3 + - - +
1612B ALA* 5.2 3.5 - - - +
1613B ARG* 5.2 6.9 + - - +
1614B SER* 4.8 1.9 + - - -
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Residues in contact with LEU1406 (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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1373A LEU* 4.9 0.2 - - + -
1388A VAL* 4.7 1.6 - - + -
1398A TYR* 3.9 30.5 - - + -
1399A THR 3.6 13.7 - - - +
1400A THR* 4.2 7.0 - - + -
1405A ASP* 1.4 72.7 - - - +
1407A PHE* 1.3 59.5 + - - +
1412A LYS* 3.6 1.4 - - - -
1413A ILE* 2.8 34.5 + - + +
1414A ASP* 2.8 22.8 + - + +
1415A ASN 4.2 0.2 - - - +
1416A ILE* 4.1 20.9 - - + -
1421A ALA* 4.4 3.4 - - + -
1422A PRO* 3.9 35.0 - - + -
1423A LEU* 4.0 28.7 - - + +
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Residues in contact with PHE1407 (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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1397A GLU 3.6 1.2 - - - +
1398A TYR* 3.2 10.4 - - - -
1399A THR* 2.9 58.5 + - - +
1400A THR 4.0 2.9 - - - -
1401A ASN* 3.6 32.1 - - + -
1405A ASP* 3.6 28.0 - - + -
1406A LEU* 1.3 73.6 - - - +
1408A LYS* 1.3 60.5 + - - +
1409A ASN 3.9 0.4 + - - -
1410A GLY* 4.1 11.4 - - - -
1411A THR 3.2 6.5 - - - +
1412A LYS* 3.5 33.2 - - + -
1413A ILE* 4.8 0.2 - - - -
1611B ASN 4.2 5.6 - - - -
1612B ALA* 4.4 5.4 - - + -
1617B ASN* 3.5 43.1 - - + -
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Residues in contact with LYS1408 (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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1397A GLU* 3.5 15.9 - - + +
1398A TYR* 3.4 36.5 + - + -
1406A LEU 4.2 0.8 + - - -
1407A PHE* 1.3 70.7 - - - +
1409A ASN* 1.3 87.3 + - - +
1411A THR* 2.8 23.6 + - - -
1413A ILE* 3.9 34.3 - - + +
1422A PRO* 5.9 0.2 - - - +
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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