Contacts of the strand formed by residues 1462 - 1475 (chain A) in PDB entry 3B13
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 MET1462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1447A PRO* 4.3 19.3 - - + -
1448A VAL 4.0 2.9 - - - +
1449A ARG* 3.8 18.6 - - + +
1458A GLU* 3.6 14.7 + - - +
1459A PHE* 3.8 17.7 + - + +
1460A ALA 3.5 3.6 + - - -
1461A SER* 1.3 76.1 - - - +
1463A TRP* 1.3 70.6 - - - +
1464A ILE* 4.6 2.6 - - + +
1493A SER 4.4 0.7 - - - -
1494A PRO* 3.4 21.5 - - - +
1497A ASN* 3.5 33.8 + - - +
33B ILE* 4.0 10.8 - - + -
34B PRO* 3.5 46.7 - - + +
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Residues in contact with TRP1463 (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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1447A PRO* 3.6 2.9 - - - +
1448A VAL* 2.9 39.6 + - + +
1450A ARG* 3.3 72.7 + - + +
1461A SER* 3.8 6.3 - - - +
1462A MET* 1.3 75.1 - - - +
1464A ILE* 1.3 66.5 + - - +
1465A GLU* 6.0 0.4 - - - +
1491A THR* 3.3 27.1 - - + -
1492A ILE 3.3 23.3 - - - -
1493A SER* 3.3 25.8 - - - -
1494A PRO* 3.3 24.5 - - + +
1496A GLU* 5.3 0.4 - - - -
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Residues in contact with ILE1464 (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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1445A SER* 3.6 29.6 - - - +
1446A ARG 3.4 8.5 - - - +
1447A PRO* 4.9 3.8 - - + -
1448A VAL* 5.2 0.7 - - - -
1462A MET* 4.6 4.0 - - + +
1463A TRP* 1.3 80.8 - - - +
1465A GLU* 1.3 70.7 + - - +
1466A ARG* 3.8 13.5 + - + +
1491A THR* 3.4 8.4 - - - +
1492A ILE* 2.8 51.6 + - + -
1497A ASN* 2.9 43.1 - - + +
1500A GLU* 4.9 0.2 - - - +
33B ILE* 4.5 20.9 - - + -
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Residues in contact with GLU1465 (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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1444A TYR* 3.2 5.5 - - - +
1445A SER* 3.4 0.5 - - - -
1446A ARG* 2.8 72.5 + - - +
1448A VAL* 4.1 12.4 - - + +
1450A ARG* 6.0 1.2 - - - -
1463A TRP* 4.3 0.4 - - - +
1464A ILE* 1.3 74.3 - - - +
1466A ARG* 1.3 57.8 + - - +
1467A THR* 4.0 1.3 + - - -
1489A GLN* 3.3 40.5 + - - +
1490A THR 3.8 1.8 - - - +
1491A THR* 3.0 31.5 + - - +
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Residues in contact with ARG1466 (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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1443A HIS* 3.9 34.2 + - + +
1444A TYR 3.1 8.1 - - - +
1445A SER* 3.0 21.9 + - - +
1464A ILE* 3.8 11.3 + - + +
1465A GLU* 1.3 73.8 - - - +
1467A THR* 1.3 68.0 + - - +
1468A SER* 4.1 2.8 + - - +
1488A SER 3.8 0.3 - - - +
1489A GLN* 3.5 5.4 - - - -
1490A THR* 2.9 50.2 + - - +
1492A ILE* 4.2 28.5 - - + +
1500A GLU* 2.8 44.2 + - - -
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Residues in contact with THR1467 (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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1442A PHE 3.6 0.9 - - - +
1443A HIS* 3.3 6.8 - - - +
1444A TYR* 2.8 41.4 + - - +
1465A GLU 4.8 0.7 + - - -
1466A ARG* 1.3 72.5 - - - +
1468A SER* 1.3 68.9 + - - +
1469A PHE* 3.7 35.6 - - + -
1487A MET* 4.5 10.1 - - + -
1488A SER 3.4 7.4 - - - +
1489A GLN* 2.9 30.5 + - - +
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Residues in contact with SER1468 (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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1441A ARG* 4.5 20.4 - - - -
1442A PHE 3.3 4.7 - - - -
1443A HIS* 3.8 21.4 + - - -
1466A ARG* 4.6 4.9 + - - +
1467A THR* 1.3 74.9 - - - +
1469A PHE* 1.3 61.3 - - - +
1470A VAL* 5.2 1.3 - - - +
1486A HIS* 3.6 1.1 - - - +
1487A MET* 3.1 10.9 - - - +
1488A SER* 2.9 50.1 + - - -
1490A THR* 4.7 4.0 + - - -
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Residues in contact with PHE1469 (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 ALA* 4.5 2.0 - - + -
1360A VAL* 4.6 12.1 - - + -
1362A ILE* 4.3 12.8 - - + -
1409A PHE* 3.8 27.8 - + - -
1411A VAL* 3.6 27.8 - - + -
1440A GLN 3.7 0.5 - - - +
1441A ARG* 3.4 5.9 - - - +
1442A PHE* 2.8 47.2 + - + +
1444A TYR* 3.9 13.0 - - + -
1467A THR* 3.7 23.1 - - + -
1468A SER* 1.3 71.7 - - - +
1470A VAL* 1.3 64.4 + - - +
1471A THR 4.2 0.4 - - - -
1484A VAL* 3.8 24.7 - - + -
1486A HIS 3.4 4.9 - - - -
1487A MET* 3.7 31.2 - - + -
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Residues in contact with VAL1470 (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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1440A GLN* 3.3 19.3 - - + +
1441A ARG* 3.4 40.6 - - + +
1468A SER 5.2 0.9 - - - -
1469A PHE* 1.3 80.7 - - - +
1471A THR* 1.3 63.7 + - - +
1484A VAL* 3.2 3.3 - - - +
1485A VAL* 2.6 40.1 + - + +
1486A HIS* 2.8 37.1 + - + +
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Residues in contact with THR1471 (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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1362A ILE* 3.6 26.9 - - + +
1439A VAL 4.3 0.7 + - - -
1440A GLN* 3.1 36.5 + - - +
1442A PHE* 3.6 22.9 - - + -
1470A VAL* 1.3 81.2 - - - +
1472A ALA* 1.3 65.7 + - - +
1473A TYR 3.0 22.1 + - - -
1475A LEU* 5.5 2.4 - - + +
1482A PHE* 3.9 19.1 - - + +
1483A GLU 3.4 5.6 - - - -
1484A VAL* 4.0 2.9 - - + +
1485A VAL* 4.1 3.5 - - - +
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Residues in contact with ALA1472 (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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1440A GLN* 4.1 4.9 - - - +
1471A THR* 1.3 73.8 - - - +
1473A TYR* 1.3 86.7 + - + +
1482A PHE* 4.6 1.7 - - + +
1483A GLU* 3.0 21.5 + - + +
1485A VAL* 3.9 24.7 - - + +
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Residues in contact with TYR1473 (chain A).
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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1440A GLN* 4.2 3.4 - - - -
1471A THR* 3.0 17.7 + - - -
1472A ALA* 1.3 96.1 - - + +
1474A LYS* 1.3 65.6 + - + +
1475A LEU* 3.9 0.3 + - - +
1482A PHE* 3.3 47.7 - + + +
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Residues in contact with LYS1474 (chain A).
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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1242A TYR* 5.5 5.2 - - - -
1296A GLU* 4.7 9.5 + - - -
1416A ASP* 5.8 3.4 - - - +
1438A TYR* 4.2 39.3 - - + +
1439A VAL 3.5 24.0 - - - +
1440A GLN* 3.9 23.2 + - + +
1473A TYR* 1.3 78.9 - - + +
1475A LEU* 1.3 59.4 + - - +
1476A PRO 3.4 14.6 - - - +
1477A GLY* 4.4 0.7 - - - -
1482A PHE* 3.3 14.0 - - - -
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Residues in contact with LEU1475 (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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1342A TYR* 3.8 37.2 + - + -
1362A ILE* 3.7 28.5 - - + +
1364A ARG* 3.9 13.2 - - + +
1438A TYR* 3.1 5.3 + - - -
1439A VAL* 2.9 35.5 + - - +
1442A PHE* 4.3 4.7 - - + -
1471A THR* 5.5 1.8 - - + +
1473A TYR 4.8 1.3 - - - +
1474A LYS* 1.3 73.2 - - - +
1476A PRO* 1.3 69.8 - - + +
1479A LEU 3.8 14.8 - - - +
1480A ARG* 3.9 13.5 - - - +
1481A TRP* 4.0 1.1 - - - +
1482A PHE* 3.3 33.2 - - + +
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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