Contacts of the strand formed by residues 1409 - 1416 (chain A) in PDB entry 4C2A
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 VAL1409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1369A PHE* 3.5 52.7 - - + -
1379A ARG* 3.5 16.2 - - + +
1381A ALA* 4.1 11.0 - - + +
1404A LEU* 2.8 40.5 + - + +
1405A LYS* 4.1 5.4 + - - -
1407A LYS* 3.6 16.6 - - + +
1408A LYS* 1.3 77.7 - - - +
1410A ILE* 1.3 72.9 + - - +
1411A VAL* 3.7 6.7 + - + +
1435A ASN* 4.5 2.4 + - - +
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Residues in contact with ILE1410 (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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1378A SER* 5.7 1.6 - - - -
1379A ARG 2.8 16.8 + - - +
1380A ILE* 3.3 7.5 - - + +
1381A ALA 2.8 27.0 + - - +
1408A LYS 5.0 4.7 - - - +
1409A VAL* 1.3 73.1 - - - +
1411A VAL* 1.3 62.6 + - - +
1412A ILE* 4.0 20.4 - - + -
1434A GLU* 3.6 47.8 - - + +
1435A ASN* 3.8 7.4 - - - +
1460A LEU* 3.6 39.7 - - + -
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Residues in contact with VAL1411 (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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1361A LEU* 4.7 11.9 - - + -
1381A ALA* 3.6 13.9 - - + +
1383A LEU* 4.7 9.2 - - + -
1401A VAL* 4.8 8.3 - - + +
1404A LEU* 3.9 30.5 - - + -
1409A VAL* 4.2 9.2 - - + +
1410A ILE* 1.3 75.2 - - - +
1412A ILE* 1.3 64.4 - - - +
1413A PRO* 3.2 11.1 - - + +
1428A ILE* 3.8 34.5 - - + -
1435A ASN* 3.0 36.8 + - - +
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Residues in contact with ILE1412 (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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1380A ILE* 3.7 16.8 - - + -
1381A ALA 2.9 10.1 + - - +
1382A LEU* 3.6 26.2 - - + +
1383A LEU* 2.9 24.0 + - - -
1410A ILE* 4.0 15.3 - - + -
1411A VAL* 1.3 76.8 - - - +
1413A PRO* 1.3 60.1 - - - +
1414A VAL* 3.6 1.1 + - + -
1436A LYS 3.3 19.5 - - - +
1438A PHE* 3.8 24.5 - - + -
1453A ILE* 5.2 1.3 - - + -
1456A TYR* 4.0 20.6 - - + -
1457A LEU* 3.5 32.1 - - + -
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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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1383A LEU* 3.4 9.9 - - + +
1385A MET* 4.1 15.3 - - - -
1411A VAL* 3.2 13.2 - - + +
1412A ILE* 1.3 84.0 - - - +
1414A VAL* 1.3 61.1 + - - +
1415A GLY 3.9 0.7 - - - -
1425A ILE* 3.9 15.8 - - + +
1428A ILE* 3.9 37.2 - - + -
1429A GLU* 5.2 0.4 - - + -
1435A ASN 4.9 0.9 - - - +
1436A LYS 3.5 10.9 - - - +
1437A ALA* 3.5 18.9 - - + +
1438A PHE 3.0 24.8 + - - +
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Residues in contact with VAL1414 (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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1382A LEU* 3.7 29.4 - - + -
1383A LEU 2.8 10.0 + - - +
1384A LEU* 3.6 27.5 - - + -
1385A MET* 2.8 28.5 + - - +
1412A ILE* 4.0 5.6 - - + +
1413A PRO* 1.3 75.2 - - - +
1415A GLY* 1.3 60.7 + - - +
1416A ILE* 3.5 10.7 + - + +
1438A PHE* 3.3 13.7 - - + +
1440A LEU* 4.0 24.2 - - + -
1446A LEU* 4.6 2.2 - - + -
1453A ILE* 4.4 17.7 - - + -
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Residues in contact with GLY1415 (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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1385A MET* 3.4 5.6 - - - -
1413A PRO 3.9 1.6 - - - -
1414A VAL* 1.3 71.7 - - - +
1416A ILE* 1.3 58.3 + - - -
1417A GLY 5.0 0.7 - - - -
1420A ALA* 3.9 9.0 - - - -
1425A ILE* 3.8 23.6 - - - +
1438A PHE 2.7 13.4 + - - +
1439A VAL* 4.5 5.6 - - - -
1440A LEU* 2.6 37.3 + - - +
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Residues in contact with ILE1416 (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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1288A LEU* 4.5 9.1 - - + +
1296A LEU* 4.2 22.2 - - + -
1384A LEU* 4.5 11.0 - - + -
1385A MET 2.6 16.7 + - - +
1386A ALA* 3.3 31.3 - - + +
1414A VAL* 3.7 16.6 - - + +
1415A GLY* 1.3 76.9 - - - +
1417A GLY* 1.3 67.7 + - - +
1420A ALA* 3.8 2.2 - - - +
1440A LEU* 3.6 4.9 - - + -
1442A SER* 3.5 30.5 - - - +
1443A VAL* 3.7 17.3 - - + +
1446A LEU* 4.0 26.9 - - + -
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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