Contacts of the strand formed by residues 1378 - 1385 (chain E) in PDB entry 4C2B
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1275E LEU 2.9 11.7 + - - -
1276E LEU* 3.3 17.4 - - - +
1277E ASP* 2.5 35.3 + - - +
1377E ALA* 1.3 74.2 - - - +
1379E ARG* 1.3 56.2 + - - +
1380E ILE* 4.8 4.5 - - - -
1408E LYS* 5.7 8.7 + - - +
1410E ILE* 6.0 2.7 - - - -
1460E LEU 2.8 28.1 + - - -
1461E ALA* 4.2 2.0 - - - -
1462E PRO* 3.2 15.9 - - - +
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Residues in contact with ARG1379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277E ASP* 3.6 19.5 + - - +
1315E ARG* 5.0 1.2 - - - +
1331E LEU* 5.2 1.6 - - - +
1368E ILE 4.6 3.8 + - - -
1369E PHE* 3.2 46.5 - - + +
1371E LYS 2.8 24.0 + - - -
1372E ILE* 3.5 20.7 - - - +
1373E ASP* 2.7 33.1 + - - +
1374E ARG 3.4 18.8 + - - +
1377E ALA 3.8 7.9 - - - +
1378E SER* 1.3 79.1 - - - +
1380E ILE* 1.3 61.5 + - - +
1407E LYS 4.4 9.0 - - - -
1408E LYS* 4.1 16.0 + - - +
1409E VAL* 3.3 16.7 - - + +
1410E ILE* 3.2 22.1 + - - +
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Residues in contact with ILE1380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276E LEU* 3.6 26.6 - - + +
1277E ASP 3.2 10.4 + - - +
1278E LEU* 3.7 7.4 - - + +
1279E VAL* 3.0 26.6 + - - +
1369E PHE* 4.8 1.8 - - - -
1378E SER* 4.8 4.0 - - - -
1379E ARG* 1.3 78.2 - - - +
1381E ALA* 1.3 62.3 + - - +
1382E LEU* 3.9 10.0 + - - +
1409E VAL* 4.8 0.4 - - - -
1410E ILE* 3.3 34.5 - - + +
1412E ILE* 4.4 8.1 - - + -
1457E LEU* 3.8 46.4 - - + +
1460E LEU* 4.4 16.4 - - + -
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Residues in contact with ALA1381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279E VAL* 3.7 12.3 - - + -
1281E LEU* 4.5 10.3 - - + -
1361E LEU* 5.9 1.8 - - + -
1364E THR* 4.1 26.0 - - + -
1369E PHE* 4.5 1.6 - - + -
1380E ILE* 1.3 76.5 - - - +
1382E LEU* 1.3 60.8 + - - +
1383E LEU* 3.1 9.7 + - - +
1404E LEU* 5.9 1.6 - - + -
1409E VAL* 4.3 14.9 - - + +
1410E ILE 3.2 6.0 + - - +
1411E VAL* 3.9 14.0 - - + +
1412E ILE 3.5 13.9 + - - -
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Residues in contact with LEU1382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278E LEU* 4.8 9.6 - - + -
1279E VAL 2.9 14.5 + - - +
1280E PHE* 4.1 25.2 - - + -
1281E LEU* 3.1 25.1 + - - -
1299E PHE* 4.5 5.8 - - + -
1303E MET* 4.5 18.6 - - + -
1380E ILE* 3.8 5.9 + - + +
1381E ALA* 1.3 69.0 - - - +
1383E LEU* 1.3 59.6 + - - +
1384E LEU* 3.4 22.8 + - + +
1412E ILE* 3.4 41.5 - - + +
1414E VAL* 3.7 12.6 - - + -
1453E ILE* 4.7 12.1 - - + -
1457E LEU* 5.1 7.0 - - + -
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Residues in contact with LEU1383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281E LEU* 3.7 29.8 - - + -
1321E TYR* 3.7 25.4 - - + +
1357E THR* 5.0 7.0 - - - -
1360E VAL* 4.2 6.5 - - + -
1361E LEU* 4.2 21.8 - - + -
1381E ALA 3.1 8.0 + - - +
1382E LEU* 1.3 68.9 - - - +
1384E LEU* 1.3 55.7 + - - +
1385E MET* 3.4 29.9 + - + +
1397E PHE* 5.6 0.4 - - + -
1411E VAL* 4.6 4.7 - - + -
1412E ILE 2.9 13.9 + - - +
1413E PRO* 3.4 4.6 - - + +
1414E VAL* 2.6 33.6 + - - -
1428E ILE* 4.1 18.2 - - + -
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Residues in contact with LEU1384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1280E PHE* 4.6 8.1 - - + -
1281E LEU 2.8 16.1 + - - +
1282E LEU* 3.7 36.6 - - + -
1283E ASP* 3.0 26.8 + - - +
1296E LEU* 3.7 23.6 - - + -
1299E PHE* 4.3 13.7 - - + -
1300E VAL* 4.2 10.5 - - + -
1321E TYR* 3.7 4.1 + - - -
1382E LEU* 4.0 22.4 - - + +
1383E LEU* 1.3 69.6 - - - +
1385E MET* 1.3 60.2 + - - +
1414E VAL* 3.7 35.7 - - + -
1416E ILE* 4.5 5.2 - - + -
1446E LEU* 5.2 0.9 - - + -
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Residues in contact with MET1385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283E ASP* 4.1 0.9 - - - +
1321E TYR* 4.1 13.0 - - - +
1357E THR* 4.6 9.9 - - + -
1383E LEU* 3.4 30.2 + - + -
1384E LEU* 1.3 73.2 - - - +
1386E ALA* 1.3 61.6 + - - +
1387E SER 4.8 4.3 - - - +
1397E PHE* 5.8 0.4 - - + -
1413E PRO* 4.2 15.3 - - + -
1414E VAL 2.8 38.2 + - - +
1415E GLY* 3.8 3.8 - - - -
1416E ILE* 3.0 16.8 + - - +
1420E ALA* 4.4 3.6 - - + -
1421E ASN* 3.7 21.5 - - - +
1424E GLN* 4.4 16.4 - - + +
1425E ILE* 3.6 27.6 - - + -
1428E ILE* 4.6 7.4 - - + -
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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