Contacts of the strand formed by residues 1439 - 1449 (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 VAL1439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1342A TYR* 3.7 33.9 - - + +
1413A PRO* 4.1 9.4 - - + -
1414A VAL 3.5 24.2 - - - +
1416A ASP* 4.8 5.2 - - - +
1434A TYR 3.7 11.4 - - - +
1435A LYS 4.1 6.3 - - - +
1436A SER 4.3 0.2 - - - +
1437A ASN 3.4 17.3 - - - +
1438A TYR* 1.3 79.3 - - - +
1440A GLN* 1.3 60.1 + - - +
1441A ARG 3.7 2.0 - - - +
1442A PHE* 3.4 21.8 - - + -
1471A THR* 4.3 0.3 + - - -
1474A LYS* 3.5 4.9 - - - +
1475A LEU 2.9 25.1 + - - +
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Residues in contact with GLN1440 (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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1414A VAL 5.5 0.2 + - - -
1416A ASP* 4.3 26.7 + - - +
1439A VAL* 1.3 73.0 - - - +
1441A ARG* 1.3 59.6 + - + +
1442A PHE* 3.5 7.1 - - - -
1470A VAL* 3.3 16.0 - - + +
1471A THR* 3.1 53.3 + - - +
1472A ALA 4.1 6.9 - - - +
1473A TYR* 4.3 0.3 - - - -
1474A LYS* 3.9 27.7 + - + +
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Residues in contact with ARG1441 (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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1413A PRO* 3.6 0.5 - - - +
1414A VAL* 2.9 57.3 + - + +
1416A ASP* 5.3 8.2 + - - +
1439A VAL* 3.7 2.5 - - - +
1440A GLN* 1.3 78.7 - - + +
1442A PHE* 1.3 73.8 + - - +
1443A HIS* 4.7 8.4 + - + +
1468A SER* 4.5 17.4 - - - -
1469A PHE 3.4 7.4 - - - +
1470A VAL* 3.4 32.8 - - + +
1486A HIS* 4.5 12.1 + - - -
1488A SER* 5.5 3.0 + - - -
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Residues in contact with PHE1442 (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* 3.9 24.9 - + + -
1362A ILE* 3.7 35.4 - - + -
1411A VAL* 4.0 15.9 - - + -
1412A GLN 3.1 6.5 - - - +
1413A PRO* 3.8 14.6 - - + -
1414A VAL* 4.5 0.7 - - - -
1439A VAL* 3.4 35.7 - - + -
1440A GLN 3.5 17.5 - - - -
1441A ARG* 1.3 80.0 - - - +
1443A HIS* 1.3 64.9 + - - +
1468A SER* 3.3 4.7 - - - -
1469A PHE* 2.8 49.7 + - + +
1471A THR* 3.6 21.1 - - + -
1475A LEU* 4.3 9.4 - - + -
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Residues in contact with HIS1443 (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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1411A VAL* 3.6 7.9 - - - +
1412A GLN* 2.7 45.4 + - + +
1414A VAL* 3.5 28.5 - - + +
1441A ARG* 4.7 8.8 + - + -
1442A PHE* 1.3 81.6 - - - +
1444A TYR* 1.3 61.3 + - - +
1445A SER* 5.1 1.6 - - - +
1466A ARG* 3.9 33.1 + - + +
1467A THR 3.3 2.5 - - - +
1468A SER* 3.8 25.6 + - - -
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Residues in contact with TYR1444 (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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1391A THR* 3.3 32.4 - - + +
1409A PHE* 3.5 34.3 - + + -
1410A THR 3.4 25.4 - - - -
1411A VAL* 4.1 0.9 - - + -
1443A HIS* 1.3 74.5 - - - +
1445A SER* 1.3 75.8 + - - +
1446A ARG* 3.9 16.4 - - + -
1465A GLU 3.2 2.8 - - - +
1466A ARG* 3.1 6.2 - - - -
1467A THR* 2.8 45.7 + - - +
1469A PHE* 3.9 11.6 - - + -
28B PHE* 3.7 8.6 + - + +
31B GLU* 2.0 38.7 + - - +
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Residues in contact with SER1445 (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* 4.3 3.0 - - - +
1444A TYR* 1.3 92.0 + - - +
1446A ARG* 1.3 60.2 + - - +
1447A PRO* 4.3 1.9 - - - +
1464A ILE* 3.6 17.0 - - - -
1465A GLU 3.4 3.4 - - - -
1466A ARG* 3.0 33.3 + - - +
31B GLU 4.4 3.1 - - - +
33B ILE* 3.8 26.6 - - - +
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Residues in contact with ARG1446 (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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1391A THR* 4.1 3.9 + - - -
1392A SER* 3.1 38.4 - - - +
1444A TYR* 3.9 12.1 - - + -
1445A SER* 1.3 75.6 - - - +
1447A PRO* 1.3 76.3 - - + +
1448A VAL* 4.0 15.8 - - - +
1464A ILE* 3.4 5.9 - - - -
1465A GLU* 2.8 64.3 + - + +
1489A GLN* 5.2 1.6 - - - +
31B GLU* 3.6 34.1 + - + -
33B ILE* 5.0 0.4 - - - -
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Residues in contact with PRO1447 (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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1446A ARG* 1.3 97.2 - - + +
1448A VAL* 1.3 64.4 + - - +
1449A ARG* 6.1 1.8 - - + +
1462A MET* 4.3 20.6 - - + -
1463A TRP 3.6 6.7 - - - +
1464A ILE* 4.7 2.7 - - + -
30B GLY 5.0 2.0 - - - +
31B GLU* 3.2 26.2 - - + +
32B TYR 3.3 26.0 - - - +
33B ILE* 3.6 15.0 - - + -
34B PRO* 5.5 0.2 - - + -
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Residues in contact with VAL1448 (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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1446A ARG* 4.0 28.7 - - - +
1447A PRO* 1.3 80.6 - - - +
1449A ARG* 1.3 73.5 + - - +
1450A ARG* 4.1 15.5 - - + -
1461A SER 3.7 0.3 - - - +
1462A MET* 3.9 2.1 - - - +
1463A TRP* 2.9 43.6 + - + +
1465A GLU* 4.1 17.9 - - + +
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Residues in contact with ARG1449 (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* 6.1 1.7 - - + +
1448A VAL* 1.3 78.5 - - - +
1450A ARG* 1.3 63.0 + - - +
1451A GLY 4.4 7.8 - - - +
1453A VAL* 4.2 27.3 - - + +
1458A GLU* 3.1 55.2 + - - +
1461A SER* 3.6 22.1 + - - +
1462A MET* 3.8 26.5 - - - +
34B PRO* 5.4 0.8 - - - +
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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