Contacts of the strand formed by residues 1368 - 1374 (chain B) 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 LYS1368 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1364B ASN* 3.4 4.2 - - - -
1365B ILE 2.9 29.8 + - - +
1366B ASP 3.4 1.3 - - - +
1367B GLY* 1.3 80.3 - - - +
1369B GLU* 1.3 74.9 + - - +
1370B TYR* 3.4 36.4 - - + +
1385B GLU* 2.5 35.6 + - - +
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Residues in contact with GLU1369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360B SER* 4.9 1.6 + - - -
1362B PHE* 3.5 27.4 - - + +
1363B LYS* 3.5 11.3 + - - -
1364B ASN* 2.8 34.2 + - - +
1368B LYS* 1.3 86.9 - - - +
1370B TYR* 1.3 61.8 + - - +
1451B PHE* 3.7 46.8 - - + +
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Residues in contact with TYR1370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362B PHE* 3.1 6.6 - - - -
1363B LYS* 2.8 36.0 + - - +
1365B ILE* 3.7 37.2 + - + -
1368B LYS* 3.4 60.8 - - + +
1369B GLU* 1.3 76.1 - - - +
1371B LEU* 1.3 63.8 + - - +
1372B CYS* 3.4 1.7 + - - -
1382B THR* 3.9 14.5 - - + +
1383B VAL 3.2 22.0 - - - +
1384B ARG* 3.6 37.3 - - + +
1385B GLU* 4.0 7.7 + - - -
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Residues in contact with LEU1371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361B GLY 3.6 15.5 - - - +
1362B PHE* 3.4 23.5 - - + -
1370B TYR* 1.3 71.8 - - - +
1372B CYS* 1.3 70.7 + - - +
1373B LEU* 4.5 4.3 - - + -
1382B THR* 3.4 2.0 - - - -
1383B VAL* 2.8 44.5 + - + +
1416B ILE* 3.9 28.9 - - + -
1425B ALA* 4.8 5.2 - - + -
1430B TYR* 4.0 15.0 - - + +
1448B ASN* 3.9 25.1 - - - +
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Residues in contact with CYS1372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361B GLY 2.9 19.4 + - - +
1362B PHE 4.0 2.2 - - - -
1363B LYS* 3.5 39.5 - - - -
1370B TYR 4.2 0.2 - - - -
1371B LEU* 1.3 79.5 - - - +
1373B LEU* 1.3 71.6 + - - +
1374B TYR* 3.4 26.2 - - + +
1380B GLU* 3.7 21.3 - - + -
1381B PHE 3.2 8.7 - - - +
1382B THR* 4.5 1.6 - - - -
1425B ALA* 3.7 12.8 - - - -
1426B LYS 4.2 3.6 + - - -
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Residues in contact with LEU1373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371B LEU* 4.5 2.2 - - + -
1372B CYS* 1.3 84.1 - - - +
1374B TYR* 1.3 66.1 + - - +
1380B GLU* 3.4 4.2 - - - +
1381B PHE* 2.7 46.9 + - + +
1383B VAL* 3.6 26.5 - - + -
1388B VAL* 3.9 23.6 - - + -
1400B THR* 4.4 2.0 - - + -
1406B LEU* 4.8 0.7 - - + -
1416B ILE* 3.9 33.9 - - + -
1423B LEU* 4.0 24.9 - - + -
1424B LYS* 3.3 5.2 - - - +
1425B ALA* 3.7 20.4 - - - +
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Residues in contact with TYR1374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361B GLY 5.8 0.3 - - - -
1372B CYS* 3.4 29.0 - - + +
1373B LEU* 1.3 78.0 - - - +
1375B ASP* 1.3 68.8 + - - +
1378B GLY* 3.7 23.6 - - - -
1379B LYS 3.3 5.8 - - - +
1380B GLU* 2.7 39.3 + - + -
1422B PRO 3.8 0.5 - - - +
1423B LEU* 3.4 7.2 - - - -
1424B LYS* 2.8 42.7 + - + +
1425B ALA 4.5 0.2 - - - -
1426B LYS* 3.7 53.0 + - + -
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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