Contacts of the strand formed by residues 1381 - 1386 (chain B) in PDB entry 3KQ4
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 GLY1381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1293B SER* 3.2 12.6 - - - -
1296B TYR* 3.9 5.2 - - - -
1300B TYR* 3.5 16.6 - - - -
1325B PHE* 3.7 0.9 - - - -
1326B ASP* 3.0 33.9 + - - +
1327B LEU* 4.2 6.2 - - - +
1370B LEU* 6.3 0.2 - - - -
1379B GLU 3.5 1.0 - - - -
1380B LYS* 1.3 81.4 - - - +
1382B PHE* 1.3 63.2 + - - +
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Residues in contact with PHE1382 (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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1291B LEU* 3.0 34.5 - - + -
1292B GLU* 3.5 1.6 - - - -
1293B SER* 3.3 48.4 + - - -
1296B TYR* 3.4 16.6 - - - -
1308B TRP* 4.1 26.0 - + - -
1322B PHE* 4.0 7.6 - + - -
1324B ALA 3.3 13.9 - - - +
1325B PHE* 4.2 17.7 - - + -
1327B LEU* 5.6 2.2 - - + -
1338B LEU* 3.9 26.7 - - + -
1368B VAL* 5.8 1.6 - - + -
1370B LEU* 4.4 11.2 - - + -
1381B GLY* 1.3 75.9 - - - +
1383B GLN* 1.3 69.9 - - - +
1384B MET* 3.6 20.0 - - + -
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Residues in contact with GLN1383 (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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1199B HIS* 5.2 2.2 - - - -
1290B ILE* 4.3 11.4 - - + +
1291B LEU 3.2 5.4 - - - +
1292B GLU* 2.9 39.9 + - + -
1296B TYR* 3.7 26.9 + - + -
1322B PHE* 3.7 1.9 - - - -
1323B LEU* 2.9 37.5 + - + +
1324B ALA* 3.0 23.1 + - + +
1382B PHE* 1.3 74.1 - - - +
1384B MET* 1.3 64.3 + - - +
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Residues in contact with MET1384 (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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1290B ILE* 3.4 7.6 - - - +
1291B LEU* 2.8 55.3 + - - +
1310B ILE* 6.2 1.6 - - - -
1320B TYR* 3.8 27.1 - - + -
1321B THR 3.1 15.5 - - - +
1322B PHE* 3.4 48.0 - - + -
1323B LEU* 3.6 7.2 - - - -
1338B LEU* 6.1 0.2 - - + -
1340B LEU* 4.3 2.7 - - + -
1366B LEU* 6.1 1.1 - - + -
1368B VAL* 4.2 21.3 - - + -
1382B PHE* 3.6 15.5 - - + -
1383B GLN* 1.3 76.8 - - - +
1385B GLN* 1.3 71.2 + - - +
1386B TRP* 4.6 4.7 - - - -
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Residues in contact with GLN1385 (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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1289B GLY 3.6 5.4 - - - +
1290B ILE* 3.9 13.9 - - + +
1319B ASN 3.9 3.3 - - - +
1320B TYR* 4.1 2.0 - - - -
1321B THR* 2.9 50.2 + - - +
1323B LEU* 3.4 30.4 - - + +
1384B MET* 1.3 82.1 - - - +
1386B TRP* 1.3 66.3 + - - +
1387B PHE* 5.5 9.5 - - + -
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Residues in contact with TRP1386 (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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1200B GLY* 5.0 4.5 - - - -
1283B ILE* 3.9 23.1 - - + -
1286B GLN* 3.0 36.9 + - - +
1287B THR 4.3 0.9 - - - -
1288B TYR* 3.3 40.2 + - - +
1289B GLY* 3.1 34.9 + - - -
1290B ILE* 2.9 35.9 - - - -
1291B LEU* 3.8 14.8 - - + -
1310B ILE* 3.1 44.9 - - + +
1318B VAL* 4.2 6.1 - - + -
1319B ASN 3.7 9.0 - - - +
1320B TYR* 5.9 1.6 - - + -
1366B LEU* 5.7 0.7 - - + -
1384B MET* 5.5 3.6 - - - -
1385B GLN* 1.3 79.9 - - - +
1387B PHE* 1.3 79.2 + - - +
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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