Contacts of the strand formed by residues 1340 - 1348 (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 PRO1340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1338A PRO 3.4 8.5 - - - +
1339A LYS* 1.3 102.7 + - + +
1341A ASP* 1.3 67.7 + - - +
1342A TYR* 4.1 22.1 + - + +
1364A ARG* 3.7 18.4 - - + +
1365A GLY 3.8 15.3 - - - +
1366A LYS 4.1 10.3 - - - +
1367A GLU* 4.9 1.1 - - - -
1368A TYR 4.6 0.2 - - - +
1413A PRO* 5.5 0.9 - - - +
1436A SER* 4.1 5.5 - - - +
1437A ASN* 3.6 32.3 - - - +
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Residues in contact with ASP1341 (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 LYS* 3.3 29.0 + - - +
1340A PRO* 1.3 75.6 - - - +
1342A TYR* 1.3 63.0 + - - +
1343A PHE* 3.8 14.0 - - + -
1365A GLY* 2.8 27.2 + - - -
1366A LYS 4.0 7.1 + - - -
1368A TYR* 4.1 11.7 - - - +
1369A GLU* 2.9 29.9 - - - +
1370A ARG* 5.6 0.3 - - - +
1410A THR* 4.9 6.2 - - + +
26B ASN* 3.3 18.5 + - - +
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Residues in contact with TYR1342 (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* 4.2 17.5 - - + -
1341A ASP* 1.3 72.9 - - - +
1343A PHE* 1.3 63.4 + - - +
1362A ILE* 4.3 1.3 - - + -
1363A TYR 3.2 16.6 - - - +
1364A ARG* 3.4 42.5 + - + -
1410A THR* 3.5 8.0 - - - +
1411A VAL* 2.8 45.9 + - + +
1413A PRO* 3.8 30.2 - - + +
1436A SER 2.9 29.8 + - - -
1437A ASN* 3.9 3.1 - - - -
1439A VAL* 3.7 15.0 - - + +
1442A PHE* 3.9 13.5 - + + -
1475A LEU* 3.8 25.4 + - + -
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Residues in contact with PHE1343 (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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1341A ASP* 3.8 15.7 - - + -
1342A TYR* 1.3 79.0 - - - +
1344A ALA* 1.3 60.0 + - - +
1345A VAL 3.8 0.3 + - - -
1361A PHE 3.6 0.3 - - - +
1362A ILE* 3.5 0.7 - - - -
1363A TYR* 2.8 43.1 + - - +
1365A GLY* 3.8 21.3 - - - -
1369A GLU* 3.5 29.6 - - + -
1371A ARG* 3.6 28.7 - - + -
1374A PHE* 3.5 56.3 - + + -
1408A CYS* 4.5 4.7 - - - -
1409A PHE 3.5 7.9 - - - +
1410A THR* 3.7 21.5 - - + -
1411A VAL* 4.0 4.5 - - - -
26B ASN* 4.0 5.8 - - - -
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Residues in contact with ALA1344 (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* 1.3 72.5 - - - +
1345A VAL* 1.3 61.4 + - - +
1346A GLY 4.2 0.4 - - - -
1360A VAL* 4.4 9.6 - - + -
1361A PHE 3.4 5.8 - - - +
1362A ILE* 3.5 21.1 - - + -
1407A GLN 3.6 0.7 - - - +
1408A CYS* 3.3 5.0 - - - +
1409A PHE* 2.8 53.1 + - + +
1411A VAL* 3.9 18.3 - - + +
1469A PHE* 4.5 3.6 - - + -
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Residues in contact with VAL1345 (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 4.4 0.9 - - - +
1344A ALA* 1.3 76.6 - - - +
1346A GLY* 1.3 61.4 + - - +
1347A TYR* 3.7 22.2 - - + -
1360A VAL* 3.4 3.8 - - - -
1361A PHE* 2.9 34.4 + - - -
1363A TYR* 3.6 31.4 - - + -
1374A PHE* 3.8 13.9 - - + -
1378A LEU* 3.7 33.7 - - + -
1406A ILE* 3.8 18.4 - - + -
1407A GLN 3.1 4.5 - - - +
1408A CYS* 4.4 4.0 - - + -
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Residues in contact with GLY1346 (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 4.2 0.6 - - - -
1345A VAL* 1.3 74.7 - - - +
1347A TYR* 1.3 61.8 + - - -
1348A TYR* 3.5 25.2 - - - -
1359A LYS 3.4 9.4 - - - -
1360A VAL* 4.0 6.0 - - - +
1406A ILE* 3.5 8.7 - - - +
1407A GLN* 2.9 36.1 + - - +
1409A PHE* 5.9 0.8 - - - -
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Residues in contact with TYR1347 (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 VAL* 3.7 19.5 - - + +
1346A GLY* 1.3 73.0 - - - -
1348A TYR* 1.3 54.5 + - - +
1352A PHE* 3.6 34.3 - + + -
1356A LEU* 3.7 28.9 - - + +
1358A ASN* 2.6 36.2 + - - -
1359A LYS 3.0 8.6 + - - -
1361A PHE* 3.6 38.4 - + - -
1363A TYR* 2.7 29.3 + - - -
1378A LEU* 3.9 6.0 - - + +
1382A PHE* 3.6 37.8 - + - -
1405A TYR 4.0 2.5 - - - -
1406A ILE* 3.9 13.5 - - + -
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Residues in contact with TYR1348 (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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1346A GLY* 3.5 23.7 - - - -
1347A TYR* 1.3 73.7 - - - +
1349A GLY* 1.3 62.2 + - - +
1352A PHE* 3.1 8.2 - - - -
1358A ASN* 3.3 32.5 - - - +
1359A LYS 4.8 0.7 - - - -
1360A VAL* 3.5 20.9 - - + +
1388A MET* 4.2 6.7 - - - -
1393A ALA* 4.8 4.2 - - - +
1394A PRO* 3.6 37.0 - - + +
1398A VAL* 4.2 18.2 - - + -
1399A LYS* 4.0 16.4 - - + -
1404A GLN* 3.7 0.5 - - - -
1405A TYR* 2.9 47.9 + - - +
1407A GLN* 3.3 28.5 + - + -
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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