Contacts of the strand formed by residues 1378 - 1385 (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 SER1378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1275A LEU 3.1 6.3 + - - -
1276A LEU* 3.3 9.2 - - - +
1277A ASP* 2.8 29.1 + - - +
1376A GLU 3.9 2.0 + - - -
1377A ALA* 1.3 72.5 - - - +
1379A ARG* 1.3 60.2 + - - +
1380A ILE* 4.9 0.2 - - - -
1410A ILE* 5.7 1.1 - - - -
1460A LEU* 3.5 27.2 + - - +
1461A ALA* 3.3 20.3 - - - -
1462A PRO* 3.2 20.3 - - - +
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Residues in contact with ARG1379 (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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1277A ASP* 3.6 15.7 + - + +
1369A PHE* 3.6 35.2 - - + -
1372A ILE* 3.5 29.4 - - - +
1374A ARG 3.0 22.4 + - - -
1375A PRO* 3.7 12.5 + - - +
1377A ALA 2.9 25.3 + - - -
1378A SER* 1.3 75.3 - - - +
1380A ILE* 1.3 65.8 + - - +
1407A LYS 3.3 18.2 + - - -
1408A LYS* 3.3 39.8 + - - +
1409A VAL* 3.5 8.9 - - + -
1410A ILE* 2.8 29.0 + - - +
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Residues in contact with ILE1380 (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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1276A LEU* 3.6 22.2 - - + -
1277A ASP 2.9 9.8 + - - +
1278A LEU* 3.7 20.4 - - + -
1279A VAL* 2.8 30.1 + - - +
1369A PHE* 4.3 2.6 - - - -
1379A ARG* 1.3 81.6 - - - +
1381A ALA* 1.3 68.1 + - - +
1382A LEU* 4.3 1.8 - - + +
1409A VAL* 4.5 2.2 - - - -
1410A ILE* 3.3 15.7 - - + +
1412A ILE* 3.7 23.6 - - + -
1457A LEU* 3.5 29.6 - - + +
1460A LEU* 3.8 27.8 - - + -
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Residues in contact with ALA1381 (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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1279A VAL* 3.7 7.2 - - + -
1281A LEU* 4.5 13.5 - - + -
1361A LEU* 5.3 3.1 - - + -
1364A THR* 4.4 19.1 - - + -
1369A PHE* 4.8 0.2 - - + -
1380A ILE* 1.3 73.9 - - - +
1382A LEU* 1.3 59.4 + - - +
1383A LEU 3.4 4.1 + - - -
1404A LEU* 5.4 0.4 - - + -
1409A VAL* 4.1 14.5 - - + +
1410A ILE 2.8 12.9 + - - +
1411A VAL* 3.6 14.7 - - + +
1412A ILE 2.9 26.2 + - - -
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Residues in contact with LEU1382 (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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1278A LEU* 4.3 11.0 - - + -
1279A VAL 2.7 16.1 + - - +
1280A PHE* 3.6 33.2 - - + -
1281A LEU* 2.9 29.5 + - - +
1299A PHE* 4.4 10.5 - - + -
1303A MET* 3.7 24.5 - - + -
1380A ILE* 3.9 3.3 - - + +
1381A ALA* 1.3 68.7 - - - +
1383A LEU* 1.3 58.9 + - - +
1384A LEU* 3.5 11.1 + - + +
1412A ILE* 3.6 37.7 - - + +
1414A VAL* 3.7 15.7 - - + -
1453A ILE* 4.4 10.8 - - + -
1457A LEU* 5.9 1.1 - - + -
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Residues in contact with LEU1383 (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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1281A LEU* 3.8 29.4 - - + -
1321A TYR* 3.7 20.6 - - + +
1357A THR* 4.6 9.4 - - + -
1360A VAL* 3.9 14.6 - - + -
1361A LEU* 4.3 18.4 - - + -
1381A ALA* 3.4 4.4 + - + +
1382A LEU* 1.3 69.4 - - - +
1384A LEU* 1.3 58.3 + - - +
1385A MET* 3.3 30.3 + - + +
1397A PHE* 5.4 0.4 - - + -
1411A VAL* 4.7 5.4 - - + -
1412A ILE 2.9 13.8 + - - +
1413A PRO* 3.4 4.5 - - + +
1414A VAL* 2.8 25.8 + - - -
1428A ILE* 3.9 21.8 - - + -
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Residues in contact with LEU1384 (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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1280A PHE* 4.5 8.5 - - + -
1281A LEU 3.0 16.4 + - - +
1282A LEU* 3.5 30.7 - - + -
1283A ASP* 3.1 27.8 + - - +
1296A LEU* 4.0 25.1 - - + -
1299A PHE* 3.9 24.9 - - + -
1300A VAL* 4.3 9.0 - - + -
1321A TYR* 3.4 4.1 + - - -
1382A LEU* 4.2 13.0 - - + +
1383A LEU* 1.3 70.4 - - - +
1385A MET* 1.3 60.5 + - - +
1414A VAL* 3.6 32.5 - - + -
1416A ILE* 4.5 8.1 - - + -
1446A LEU* 4.5 0.9 - - + -
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Residues in contact with MET1385 (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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1283A ASP* 3.9 3.6 - - - +
1321A TYR* 4.0 8.5 - - - +
1357A THR* 3.9 17.7 - - + -
1383A LEU* 3.5 40.6 - - + +
1384A LEU* 1.3 72.6 - - - +
1386A ALA* 1.3 55.0 + - - +
1387A SER 4.7 4.9 - - - +
1413A PRO* 4.1 10.3 - - - -
1414A VAL 2.8 12.3 + - - +
1415A GLY* 3.4 4.0 - - - -
1416A ILE* 2.6 36.0 + - - +
1420A ALA* 3.8 4.2 - - + +
1421A ASN* 3.7 41.5 - - + +
1424A GLN* 4.3 8.1 - - + +
1425A ILE* 3.7 20.9 - - + -
1428A ILE* 4.9 2.2 - - + -
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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