Contacts of the strand formed by residues 1359 - 1367 (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 LYS1359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1345A VAL 4.1 0.2 - - - +
1346A GLY* 3.4 2.3 - - - -
1347A TYR* 3.0 24.9 + - - +
1348A TYR* 4.8 0.9 - - - -
1354A SER 3.7 19.2 + - - -
1355A PHE* 4.0 19.3 + - - +
1356A LEU 3.0 12.6 + - - +
1357A ARG 3.4 11.2 - - - +
1358A ASN* 1.3 79.6 - - - +
1360A VAL* 1.3 66.2 - - - +
1361A PHE* 3.8 11.2 - - + -
1483A GLU* 3.1 42.4 + - + +
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Residues in contact with VAL1360 (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* 4.4 10.8 - - + -
1345A VAL 3.4 19.1 - - - +
1346A GLY* 4.0 2.9 - - - +
1348A TYR* 3.5 24.5 - - + +
1358A ASN 5.4 0.7 - - - +
1359A LYS* 1.3 80.7 - - - +
1361A PHE* 1.3 65.5 + - - +
1407A GLN* 5.6 0.7 - - - +
1409A PHE* 6.1 1.6 - - + -
1469A PHE* 4.6 9.6 - - + -
1483A GLU* 3.6 3.5 - - - +
1484A VAL* 2.7 56.4 + - + +
1487A MET* 4.5 17.9 - - + +
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Residues in contact with PHE1361 (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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1343A PHE 3.6 0.9 - - - +
1344A ALA* 3.4 3.6 - - - -
1345A VAL 2.9 32.4 + - - +
1347A TYR* 3.6 25.1 - + - -
1355A PHE* 3.4 24.7 - + - -
1356A LEU* 3.5 23.6 - - + -
1359A LYS* 3.8 23.1 - - + -
1360A VAL* 1.3 76.6 - - - +
1362A ILE* 1.3 65.8 + - - +
1363A TYR* 3.9 20.1 + - + -
1481A TRP* 3.8 22.0 - + + -
1482A PHE 3.2 9.0 - - - +
1483A GLU* 3.6 34.1 - - + -
1484A VAL* 4.3 0.2 - - - -
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Residues in contact with ILE1362 (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* 4.3 0.7 - - + -
1343A PHE 3.5 2.7 - - - +
1344A ALA* 3.5 30.3 - - + -
1361A PHE* 1.3 73.7 - - - +
1363A TYR* 1.3 70.8 + - - +
1411A VAL* 3.9 15.0 - - + -
1442A PHE* 3.7 41.1 - - + -
1469A PHE* 4.3 11.2 - - + -
1471A THR* 3.6 18.2 - - + -
1475A LEU* 3.7 8.0 - - + +
1481A TRP* 3.2 2.4 - - - -
1482A PHE 2.9 31.3 + - - -
1484A VAL* 3.4 24.2 - - + +
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Residues in contact with TYR1363 (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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1198A ASP* 3.7 19.0 + - - -
1342A TYR* 3.2 13.3 - - - +
1343A PHE* 2.8 37.1 + - + +
1345A VAL* 3.6 27.8 - - + -
1347A TYR* 2.7 26.6 + + - -
1356A LEU* 5.7 1.2 - - - +
1361A PHE* 3.9 17.9 - + + -
1362A ILE* 1.3 75.9 - - - +
1364A ARG* 1.3 59.9 + - - +
1365A GLY 3.8 0.4 + - - -
1374A PHE* 3.6 34.8 - + + -
1378A LEU* 4.6 3.8 - - + +
1475A LEU* 4.1 0.7 - - - -
1480A ARG* 3.4 8.5 - - + -
1481A TRP* 3.6 51.1 + + + -
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Residues in contact with ARG1364 (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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1238A THR* 4.3 9.7 + - - +
1239A GLU* 4.4 3.1 + - - -
1291A GLY 5.3 1.8 + - - -
1293A MET* 4.2 16.6 - - - -
1340A PRO* 3.7 13.2 - - + +
1342A TYR* 3.4 35.4 + - + -
1363A TYR* 1.3 74.5 - - - +
1365A GLY* 1.3 63.4 + - - +
1374A PHE* 5.8 1.2 - - - -
1437A ASN* 3.0 25.3 + - - -
1475A LEU* 3.9 7.6 - - + +
1476A PRO* 3.6 43.6 - - - +
1480A ARG* 2.8 74.0 + - - +
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Residues in contact with GLY1365 (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 PRO* 3.8 14.6 - - - +
1341A ASP 2.8 21.9 + - - -
1343A PHE* 3.8 11.8 - - - -
1363A TYR 3.8 2.4 + - - -
1364A ARG* 1.3 81.1 - - - +
1366A LYS* 1.3 69.7 + - - +
1369A GLU* 3.2 13.7 - - - -
1374A PHE* 5.2 2.0 - - - -
1480A ARG* 4.2 5.5 + - - -
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Residues in contact with LYS1366 (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 PRO* 4.1 0.8 - - - +
1341A ASP 4.0 5.9 + - - -
1365A GLY* 1.3 79.7 - - - +
1367A GLU* 1.3 65.1 + - + +
1368A TYR 3.3 1.2 + - - -
1369A GLU* 2.8 50.0 + - + +
1480A ARG* 4.8 22.0 - - - +
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Residues in contact with GLU1367 (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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1292A LYS* 4.9 10.7 + - - +
1338A PRO* 3.6 45.2 - - + +
1339A LYS 4.4 4.3 - - - -
1340A PRO* 4.9 2.7 - - - -
1366A LYS* 1.3 71.5 - - + +
1368A TYR* 1.3 68.9 + - - +
1369A GLU* 3.0 6.2 + - - -
45B MET* 3.5 25.0 + - - +
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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