Contacts of the strand formed by residues 1372 - 1378 (chain B) in PDB entry 6PUO
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 LEU1372 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1353B THR* 4.0 17.3 - - + -
1354B ARG 3.3 24.7 - - - +
1355B TRP* 3.6 23.3 - - + -
1370B LYS 4.3 0.2 + - - -
1371B MET* 1.3 81.9 - - - +
1373B GLU* 1.3 58.8 + - - +
1374B VAL* 5.6 0.7 - - + -
1448B HIS* 4.0 20.6 - - + -
1477B VAL* 3.4 5.8 - - - +
1478B VAL* 2.7 55.4 + - + +
1496B ALA* 6.2 1.8 - - - -
1499B PHE* 4.8 11.9 - - + -
1501B ALA* 3.7 27.4 - - + +
1502B HIS* 5.7 0.6 - - - -
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Residues in contact with GLU1373 (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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1352B VAL 3.5 0.5 - - - +
1353B THR* 3.5 5.7 - - - -
1354B ARG* 2.5 83.9 + - + +
1355B TRP 3.1 6.8 - - - +
1356B ARG* 3.3 38.4 + - + +
1357B ARG 4.7 1.8 + - - +
1372B LEU* 1.3 77.5 - - - +
1374B VAL* 1.3 62.9 + - - +
1475B TRP* 3.6 14.6 - - + -
1476B GLN 3.3 7.0 - - - +
1477B VAL* 4.3 13.0 - - + +
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Residues in contact with VAL1374 (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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1351B MET* 5.5 4.0 - - + -
1352B VAL 3.3 18.4 - - - +
1353B THR* 4.4 14.8 - - + -
1372B LEU* 5.6 0.4 - - + -
1373B GLU* 1.3 76.8 - - - +
1375B LEU* 1.3 64.0 + - - +
1376B VAL* 5.2 4.7 - - + -
1387B LEU* 5.8 8.3 - - + -
1475B TRP* 3.3 5.8 - - - -
1476B GLN* 2.5 59.2 + - + +
1477B VAL 5.3 0.7 - - - -
1478B VAL* 4.4 17.5 - - + +
1484B LEU* 6.6 0.2 - - + -
1492B LEU* 4.4 24.9 - - + -
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Residues in contact with LEU1375 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1352B VAL* 3.6 28.7 + - + +
1374B VAL* 1.3 75.5 - - - +
1376B VAL* 1.3 60.3 + - - +
1387B LEU* 4.9 3.6 - - - +
1388B PRO* 3.9 19.3 - - - +
1473B ILE* 4.8 20.2 - - + -
1474B ARG* 3.5 28.9 - - - +
1475B TRP* 3.4 41.6 - - + +
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Residues in contact with VAL1376 (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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1374B VAL* 4.6 6.5 - - + +
1375B LEU* 1.3 76.9 - - - +
1377B VAL* 1.3 63.0 + - - +
1385B TRP* 3.4 29.8 - - + -
1386B ALA 3.3 18.6 - - - +
1387B LEU* 5.1 4.9 - - + -
1388B PRO* 4.8 2.9 - - - -
1473B ILE* 3.5 3.9 - - - +
1474B ARG 3.0 36.9 + - - +
1476B GLN* 3.7 29.4 - - + +
1484B LEU* 3.7 27.1 - - + -
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Residues in contact with VAL1377 (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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1376B VAL* 1.3 74.8 - - - +
1378B LYS* 1.3 71.3 + - - +
1379B LEU* 4.0 18.7 + - + +
1385B TRP* 3.5 4.3 - - - -
1386B ALA* 3.0 41.6 + - + +
1387B LEU 4.3 1.3 - - - +
1388B PRO* 4.1 26.0 - - + +
1406B LEU* 5.8 5.8 - - + -
1470B GLY* 5.7 4.7 - - - -
1472B SER 3.7 6.1 - - - +
1473B ILE* 3.7 22.0 - - + -
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Residues in contact with LYS1378 (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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1377B VAL* 1.3 76.3 - - - +
1379B LEU* 1.3 74.6 + - - +
1380B PRO* 5.6 0.2 - - + -
1383B GLU* 3.3 13.4 - - - +
1384B HIS* 3.0 36.9 - - - +
1385B TRP* 3.4 53.9 - - + +
1471B ALA* 3.3 23.7 + - + +
1472B SER* 2.9 21.4 + - - +
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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