Contacts of the strand formed by residues 1404 - 1413 (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 GLN1404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1351A GLY* 3.0 34.1 + - - -
1352A PHE* 3.4 39.8 - - + +
1353A PRO* 4.7 4.2 - - - +
1382A PHE* 4.5 10.4 - - - +
1383A PRO* 5.9 0.2 - - - +
1384A ASN* 3.6 32.9 + - + +
1385A ALA* 3.1 16.3 + - - +
1386A GLU* 2.8 26.7 + - - +
1403A GLY* 1.3 75.9 - - - -
1405A TYR* 1.3 65.0 + - - +
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Residues in contact with TYR1405 (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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1348A TYR* 2.9 54.5 + - - +
1349A GLY* 4.4 0.9 - - - -
1352A PHE* 3.6 0.8 - - - -
1386A GLU* 3.7 40.6 + - + +
1388A MET* 3.4 30.1 - - + -
1398A VAL* 4.3 12.6 - - + -
1401A ALA* 3.7 32.1 - - + +
1402A PRO* 4.9 2.1 - - - +
1403A GLY* 3.6 29.8 + - - -
1404A GLN* 1.3 74.2 - - - +
1406A ILE* 1.3 61.6 + - - +
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Residues in contact with ILE1406 (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* 3.8 19.7 - - + -
1346A GLY 3.5 7.9 - - - +
1347A TYR* 3.9 9.0 - - + -
1352A PHE* 3.5 25.6 - - + -
1375A GLN* 4.6 4.7 + - - +
1378A LEU* 4.6 6.3 - - + -
1379A MET* 4.3 20.4 - - - -
1382A PHE* 3.8 29.6 - - + -
1385A ALA* 3.6 24.2 - - + -
1386A GLU 2.9 13.7 + - - +
1387A LYS* 4.0 1.9 - - - -
1388A MET* 3.0 29.2 + - - +
1405A TYR* 1.3 71.8 - - - +
1407A GLN* 1.3 65.5 + - - +
1408A CYS* 4.0 4.6 + - + -
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Residues in contact with GLN1407 (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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1344A ALA 3.6 0.8 - - - +
1345A VAL* 3.1 8.3 - - - +
1346A GLY* 2.9 33.2 + - - +
1348A TYR* 3.3 34.0 + - + -
1360A VAL* 5.6 0.7 - - - +
1388A MET* 4.0 13.1 - - + -
1390A THR* 3.2 30.7 + - - +
1391A THR 3.7 8.0 - - - +
1392A SER 3.0 31.7 + - - -
1393A ALA* 4.1 2.8 - - - +
1394A PRO* 4.1 12.0 - - - +
1405A TYR 4.2 0.8 + - - -
1406A ILE* 1.3 71.9 - - - +
1408A CYS* 1.3 61.9 + - - +
1409A PHE* 3.8 19.4 - - + -
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Residues in contact with CYS1408 (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* 4.5 3.6 - - - -
1344A ALA 3.3 7.6 - - - +
1345A VAL* 4.4 6.5 - - + -
1371A ARG* 3.4 28.7 - - - -
1374A PHE* 3.8 35.4 - - - -
1375A GLN* 3.7 31.4 + - + +
1378A LEU* 5.0 2.2 - - + -
1388A MET 5.2 2.8 + - - -
1390A THR 5.1 0.8 + - - -
1406A ILE* 4.0 6.9 + - + -
1407A GLN* 1.3 77.6 - - - +
1409A PHE* 1.3 68.7 + - - +
28B PHE* 3.4 14.3 - - - -
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Residues in contact with PHE1409 (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* 3.5 4.4 - - - -
1344A ALA* 2.8 43.4 + - + -
1360A VAL* 6.1 1.3 - - + -
1371A ARG* 3.9 8.1 - - - +
1391A THR* 3.6 50.9 - - + -
1407A GLN* 3.8 23.1 - - + -
1408A CYS* 1.3 79.7 - - - +
1410A THR* 1.3 63.4 + - - +
1411A VAL* 3.9 6.5 - - + -
1444A TYR* 3.5 47.3 - + + -
1469A PHE* 3.8 24.7 - + - -
28B PHE* 3.7 6.3 - - + -
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Residues in contact with THR1410 (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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1341A ASP* 4.9 8.5 - - + +
1342A TYR 3.5 13.2 - - - +
1343A PHE* 3.7 7.9 - - + -
1371A ARG* 3.0 28.4 + - - +
1409A PHE* 1.3 75.3 - - - +
1411A VAL* 1.3 69.5 + - - +
1412A GLN* 4.7 12.1 - - - +
1444A TYR* 3.4 25.5 - - - -
25B THR 5.3 1.1 - - - +
26B ASN* 3.4 40.1 + - + +
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Residues in contact with VAL1411 (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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1342A TYR* 2.8 46.4 + - + +
1344A ALA* 3.9 23.8 - - + +
1362A ILE* 3.9 16.4 - - + -
1409A PHE* 3.9 7.9 - - + -
1410A THR* 1.3 80.1 - - - +
1412A GLN* 1.3 70.4 + - - +
1413A PRO* 3.9 6.8 - - - +
1442A PHE* 4.0 14.4 - - + -
1443A HIS 3.6 10.1 - - - +
1444A TYR* 4.1 1.3 - - + -
1469A PHE* 3.6 31.0 - - + -
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Residues in contact with GLN1412 (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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1339A LYS* 5.3 10.5 - - - +
1410A THR* 4.7 11.9 - - - +
1411A VAL* 1.3 81.6 + - - +
1413A PRO* 1.3 75.9 - - - +
1414A VAL* 4.3 0.9 - - - +
1442A PHE* 3.1 6.5 - - - -
1443A HIS* 2.7 48.8 + - + +
25B THR 5.4 5.3 + - - -
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Residues in contact with PRO1413 (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* 5.9 5.4 - - - -
1340A PRO 5.5 2.0 - - - +
1342A TYR* 3.8 35.4 - - + +
1411A VAL 3.9 6.7 - - - +
1412A GLN* 1.3 95.1 - - + +
1414A VAL* 1.3 61.4 + - - +
1415A LEU 4.0 0.7 + - - -
1435A LYS 3.8 20.6 - - - +
1436A SER* 4.1 10.3 - - - -
1439A VAL* 4.1 15.7 - - + -
1441A ARG 3.6 6.1 - - - +
1442A PHE* 3.8 4.9 - - + -
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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