Contacts of the strand formed by residues 1371 - 1379 (chain A) in PDB entry 6XAF
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 ILE1371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1369A VAL* 3.1 14.4 - - - +
1370A GLY* 1.3 82.4 - - - +
1372A ASP* 1.3 62.1 + - - +
1373A VAL* 4.0 10.5 + - + -
1393A TRP* 3.9 27.8 - - + -
1394A ASP 3.5 7.2 - - - +
1395A PHE* 4.0 9.9 - - + -
1400A GLU* 3.8 22.0 - - + +
1403A SER* 3.9 6.5 - - - +
1404A THR* 3.8 27.8 - - + -
1373B VAL* 3.8 36.1 + - + +
1391B ASN* 5.2 2.0 - - - +
1393B TRP* 3.9 17.3 - - + -
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Residues in contact with ASP1372 (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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1369A VAL* 4.1 16.5 - - + +
1371A ILE* 1.3 73.4 - - - +
1373A VAL* 1.3 67.6 + - - +
1374A LYS* 3.7 28.4 + - - +
1392A VAL 3.4 2.8 - - - +
1393A TRP* 3.6 0.7 - - - -
1394A ASP* 2.8 56.9 + - + +
1348B THR* 5.7 3.6 - - - +
1351B LEU* 5.8 1.2 - - - +
1369B VAL* 5.9 1.4 - - - +
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Residues in contact with VAL1373 (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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1371A ILE* 4.0 9.4 + - + -
1372A ASP* 1.3 81.0 + - - +
1374A LYS* 1.3 66.1 + - - +
1391A ASN* 3.9 16.8 - - - +
1392A VAL 3.2 8.5 - - - +
1393A TRP* 3.8 52.5 - - + +
1369B VAL* 3.4 24.3 - - - +
1371B ILE* 3.8 36.1 + - + +
1373B VAL* 4.8 4.5 - - + -
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Residues in contact with LYS1374 (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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1372A ASP* 3.7 27.2 + - - +
1373A VAL* 1.3 77.9 - - - +
1375A ASP* 1.3 64.9 + - - +
1391A ASN* 4.3 2.0 - - - +
1392A VAL* 2.7 43.4 + - + +
1351B LEU* 4.6 10.6 - - + +
1352B GLN* 5.8 5.9 - - - +
1355B MET* 3.7 36.0 - - + +
1369B VAL* 5.2 5.2 - - + -
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Residues in contact with ASP1375 (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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1374A LYS* 1.3 77.9 - - - +
1376A TRP* 1.3 61.1 + - - +
1377A PRO* 3.7 9.7 - - + +
1389A VAL* 3.9 20.9 - - + +
1390A LEU 3.4 2.8 - - - +
1391A ASN* 2.7 37.1 + - - +
1355B MET* 3.8 11.8 - - - +
1365B GLN* 5.6 14.1 + - + +
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Residues in contact with TRP1376 (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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1375A ASP* 1.3 74.8 - - - +
1377A PRO* 1.3 71.6 + - + +
1378A ILE* 3.5 33.5 + - + +
1388A LEU 3.5 2.1 - - - +
1389A VAL* 3.5 2.0 - - - -
1390A LEU* 2.8 45.5 + - + +
1392A VAL* 3.8 14.4 - - + -
1337B LEU* 3.9 30.3 - - + -
1351B LEU* 4.4 3.6 - - + -
1354B LEU* 3.6 38.3 + - + -
1355B MET* 3.6 41.2 + - + +
1501B ARG* 4.2 17.9 - - + -
1504B ILE* 4.2 21.8 - - + -
1505B ILE* 6.1 0.4 - - + -
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Residues in contact with PRO1377 (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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1375A ASP* 3.7 10.8 - - + +
1376A TRP* 1.3 95.8 + - + +
1378A ILE* 1.3 60.6 + - - +
1379A GLN 4.1 1.0 + - - -
1387A ASP* 4.3 8.3 - - - +
1388A LEU 3.5 4.7 - - - +
1389A VAL* 3.9 20.4 - - + -
1355B MET* 5.2 2.2 - - + -
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Residues in contact with ILE1378 (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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1376A TRP* 3.5 51.6 - - + +
1377A PRO* 1.3 73.6 - - - +
1379A GLN* 1.3 71.5 + - - +
1380A ILE* 3.6 9.3 + - + +
1387A ASP* 3.4 5.5 + - - +
1388A LEU* 2.6 42.9 + - + +
1390A LEU* 4.1 26.5 - - + -
1501B ARG* 6.5 0.4 - - + -
1504B ILE* 5.2 0.4 - - + -
1505B ILE* 3.7 39.7 - - + -
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Residues in contact with GLN1379 (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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1377A PRO 4.1 1.6 + - - -
1378A ILE* 1.3 79.2 - - - +
1380A ILE* 1.3 60.1 + - - +
1381A ARG 4.4 0.2 + - - -
1386A ARG 4.8 4.5 - - - +
1387A ASP* 4.5 5.1 + - - -
1505B ILE* 5.4 1.0 - - - +
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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