Contacts of the strand formed by residues 1413 - 1420 (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 ALA1413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1336A LYS* 3.4 10.5 - - + +
1338A MET* 3.7 25.4 - - + -
1408A PHE 4.8 0.4 - - - +
1409A MET 4.3 15.9 - - - +
1410A THR 5.1 1.1 - - - +
1411A GLN 3.0 4.9 + - - +
1412A ARG* 1.3 79.1 - - - +
1414A LEU* 1.3 59.5 + - - +
1415A TYR* 4.0 7.2 - - + -
1445A SER* 2.7 33.7 + - - +
1446A PRO* 3.8 6.8 - - - +
1511A PHE* 4.1 8.2 - - - -
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Residues in contact with LEU1414 (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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1336A LYS 2.9 11.1 + - - +
1337A LEU* 3.4 23.0 - - + +
1338A MET* 2.8 25.8 + - - +
1413A ALA* 1.3 73.7 - - - +
1415A TYR* 1.3 74.9 + - - +
1446A PRO* 3.6 36.3 - - + +
1448A ILE* 4.1 19.7 - - + -
1504A ILE* 3.8 13.2 - - + +
1507A GLU* 4.3 9.9 - - + +
1508A SER* 3.3 39.3 - - - +
1511A PHE* 5.7 4.3 - - + -
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Residues in contact with TYR1415 (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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1338A MET* 3.3 37.7 - - + +
1340A VAL* 4.2 7.9 - - + -
1409A MET 4.4 4.3 + - - -
1413A ALA* 4.0 8.3 - - + -
1414A LEU* 1.3 78.4 - - - +
1416A LEU* 1.3 60.9 + - - +
1438A ILE* 3.7 39.9 - - + -
1441A ARG* 4.1 6.9 - - - +
1442A ALA* 3.7 19.0 - - + +
1445A SER* 3.6 33.7 - - - -
1446A PRO 3.0 14.0 + - - +
1447A VAL* 3.3 13.9 - - + -
1448A ILE* 2.8 31.7 + - - -
1401B PHE* 3.8 29.4 - + - -
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Residues in contact with LEU1416 (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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1337A LEU* 4.0 19.1 - - + -
1338A MET 2.8 12.0 + - - +
1339A ILE* 3.6 20.8 - - + -
1340A VAL* 2.8 32.2 + - - +
1350A LEU* 4.1 16.4 - - + -
1354A LEU* 4.1 13.9 - - + -
1414A LEU 4.1 0.2 + - - -
1415A TYR* 1.3 72.3 - - - +
1417A ALA* 1.3 60.6 + - - +
1418A VAL* 3.8 8.4 + - + +
1448A ILE* 3.4 33.4 - - + +
1450A VAL* 4.5 6.5 - - + -
1504A ILE* 3.6 38.1 - - + -
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Residues in contact with ALA1417 (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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1340A VAL* 3.5 14.8 - - + -
1415A TYR 4.0 1.6 - - - -
1416A LEU* 1.3 71.0 - - - +
1418A VAL* 1.3 58.5 + - - +
1419A TYR 4.2 0.2 + - - -
1431A MET* 4.0 18.5 - - - +
1434A TRP* 5.3 3.4 - - + -
1435A LEU* 4.9 5.2 - - + -
1438A ILE* 4.8 5.8 - - + -
1447A VAL* 3.9 20.9 - - + -
1448A ILE 3.0 7.1 + - - -
1449A LEU* 3.5 15.2 - - + +
1450A VAL 3.0 24.0 + - - +
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Residues in contact with VAL1418 (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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1339A ILE* 4.0 11.2 - - + -
1340A VAL 2.8 16.6 + - - +
1341A GLY* 3.5 11.4 - - - -
1342A ASN 4.3 0.3 + - - -
1345A SER* 3.7 23.5 + - - +
1346A GLY 4.3 0.7 - - - -
1347A LYS* 3.7 23.3 - - + +
1350A LEU* 4.0 22.9 - - + -
1416A LEU* 4.1 8.1 - - + +
1417A ALA* 1.3 75.8 - - - +
1419A TYR* 1.3 67.6 + - - +
1431A MET* 3.5 13.9 - - - +
1450A VAL* 3.4 6.7 - - + +
1452A THR* 3.7 26.9 - - + -
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Residues in contact with TYR1419 (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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1345A SER* 4.1 8.1 - - - -
1417A ALA 4.4 2.5 - - - -
1418A VAL* 1.3 77.3 - - - +
1420A ASP* 1.3 56.3 + - - +
1421A LEU* 3.8 24.2 - - + +
1427A GLU* 4.0 27.4 - - + +
1428A VAL* 3.8 24.3 - - + +
1431A MET* 3.9 30.7 - - + -
1449A LEU* 4.5 11.2 - - + -
1450A VAL 3.0 18.4 + - - -
1451A GLY* 3.3 23.0 + - - -
1452A THR* 2.8 34.0 + - - -
1465A CYS* 4.3 1.3 - - - +
1469A ILE* 3.5 17.2 - - + +
1486A HIS 4.7 0.7 + - - -
1487A PHE* 3.2 28.1 - - - -
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Residues in contact with ASP1420 (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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1344A GLY 4.5 3.8 - - - +
1345A SER* 4.2 13.8 - - - -
1419A TYR* 1.3 72.4 - - - +
1421A LEU* 1.3 63.3 + - - +
1422A SER* 2.6 32.6 + - - -
1423A LYS* 3.1 37.0 + - + +
1424A GLY 4.1 0.2 + - - -
1427A GLU* 3.3 21.9 + - + +
1452A THR* 3.8 6.1 - - - -
1453A HIS* 3.1 34.9 + - + +
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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