Contacts of the helix formed by residues 1461 - 1481 (chain B) in PDB entry 5NPK
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 ASP1461 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1457B THR* 3.3 8.0 + - + +
1458B ILE 3.0 15.8 - - - +
1459B LEU 3.5 1.1 - - - -
1460B ALA* 1.3 81.0 - - + +
1462B GLU* 1.3 64.2 + - - +
1463B GLU* 2.9 29.2 + - - +
1464B VAL* 3.1 30.7 + - + +
1465B LEU 3.1 10.7 + - - -
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Residues in contact with GLU1462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360B LYS* 6.5 0.9 - - - -
1364B ARG* 5.5 11.0 + - - +
1460B ALA 4.2 0.8 - - - -
1461B ASP* 1.3 74.5 + - - +
1463B GLU* 1.3 56.9 + - - +
1465B LEU* 3.3 12.8 + - + +
1466B LEU* 2.9 30.0 + - - +
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Residues in contact with GLU1463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1461B ASP* 2.9 14.5 + - - +
1462B GLU* 1.3 75.8 - - - +
1464B VAL* 1.3 61.1 + - + +
1466B LEU* 3.2 14.1 + - - +
1467B GLN* 2.9 33.1 + - + +
1470B ARG* 2.9 33.7 + - - -
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Residues in contact with VAL1464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457B THR* 4.0 18.6 - - + +
1458B ILE* 3.7 31.2 - - + +
1461B ASP* 3.1 34.6 + - + +
1463B GLU* 1.3 78.0 - - + +
1465B LEU* 1.3 61.3 + - - +
1467B GLN* 3.4 6.0 + - - +
1468B LEU* 3.1 21.7 + - - +
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Residues in contact with LEU1465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360B LYS* 4.1 35.9 - - + +
1363B VAL* 4.7 5.8 - - + +
1364B ARG* 3.6 52.5 - - + +
1458B ILE* 3.8 34.5 + - + +
1459B LEU* 5.0 3.8 - - + -
1461B ASP 3.1 7.1 + - - +
1462B GLU* 3.6 14.4 - - + +
1464B VAL* 1.3 78.3 - - - +
1466B LEU* 1.3 67.8 + - + +
1468B LEU* 3.1 6.0 + - - +
1469B VAL* 3.1 22.9 + - + +
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Residues in contact with LEU1466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199B SER* 3.7 26.0 - - - +
1356B LEU* 4.4 9.6 - - + -
1360B LYS* 4.2 34.3 - - + +
1462B GLU 2.9 18.9 + - - +
1463B GLU* 3.7 15.3 - - - +
1465B LEU* 1.3 80.3 - - + +
1467B GLN* 1.3 58.2 + - - +
1469B VAL* 3.2 9.1 + - + +
1470B ARG* 3.0 58.4 + - + +
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Residues in contact with GLN1467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1463B GLU* 2.9 19.4 + - + +
1464B VAL* 3.8 6.7 - - - +
1466B LEU* 1.3 74.2 - - - +
1468B LEU* 1.3 61.2 + - - +
1470B ARG* 2.9 39.2 + - - +
1471B ASP* 2.8 65.6 + - - +
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Residues in contact with LEU1468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363B VAL* 3.7 14.8 - - + -
1366B ARG* 3.6 19.5 - - - +
1367B THR* 4.5 2.2 - - - +
1458B ILE* 3.7 33.9 - - + -
1464B VAL* 3.1 14.3 + - + +
1465B LEU* 3.1 10.3 + - - +
1467B GLN* 1.3 75.4 - - - +
1469B VAL* 1.3 62.2 + - - +
1471B ASP* 3.3 10.6 + - + +
1472B GLU* 3.0 50.7 + - + +
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Residues in contact with VAL1469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163B ARG* 5.1 2.6 + - - +
1199B SER* 6.5 0.2 - - - -
1356B LEU* 4.2 15.0 - - + -
1359B GLN* 4.1 24.2 - - + +
1360B LYS* 4.3 11.7 - - + -
1363B VAL* 3.8 32.1 - - + -
1465B LEU* 3.1 18.1 + - + +
1466B LEU* 3.2 12.3 + - + +
1468B LEU* 1.3 76.5 - - - +
1470B ARG* 1.3 57.3 + - + +
1472B GLU* 3.3 5.6 + - - +
1473B LEU* 2.9 48.5 + - + +
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Residues in contact with ARG1470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196B LEU* 3.8 18.5 - - + +
1199B SER* 2.9 53.2 + - - +
1200B LYS* 3.6 32.4 - - - +
1463B GLU* 2.9 27.5 + - - -
1466B LEU* 3.0 32.3 + - + +
1467B GLN* 2.9 43.6 + - - +
1469B VAL* 1.3 78.8 - - + +
1471B ASP* 1.3 57.7 + - - +
1473B LEU* 3.4 2.9 + - + +
1474B THR* 2.8 34.2 + - - +
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Residues in contact with ASP1471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467B GLN* 2.8 50.9 + - - +
1468B LEU* 3.3 12.8 + - + +
1470B ARG* 1.3 75.5 - - - +
1472B GLU* 1.3 60.2 + - + +
1474B THR* 3.3 7.2 + - - -
1475B GLU* 3.0 28.1 + - - +
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Residues in contact with GLU1472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137B ARG* 3.7 21.3 + - - +
1163B ARG* 2.6 48.4 + - - +
1363B VAL* 4.0 2.2 - - - +
1366B ARG* 2.7 35.2 + - - -
1468B LEU* 3.0 35.0 + - + +
1469B VAL 3.9 0.9 - - - +
1470B ARG 3.3 0.2 - - - -
1471B ASP* 1.3 75.2 - - + +
1473B LEU* 1.3 64.3 + - - +
1475B GLU* 3.5 7.3 + - - +
1476B ILE* 3.2 29.4 + - + +
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Residues in contact with LEU1473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163B ARG* 3.5 26.0 - - - +
1165B PRO* 4.4 1.3 - - + -
1192B ILE* 3.5 38.0 - - + +
1195B VAL* 3.7 30.3 - - + -
1196B LEU* 4.7 10.3 - - + -
1355B TYR* 3.8 21.3 - - + +
1356B LEU* 5.0 1.3 - - + -
1359B GLN* 5.1 4.7 - - + +
1469B VAL* 2.9 39.4 + - + +
1470B ARG* 3.8 4.7 - - - +
1472B GLU* 1.3 76.5 - - - +
1474B THR* 1.3 58.0 + - - +
1476B ILE* 3.3 5.9 + - + +
1477B ARG 2.9 23.0 + - - -
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Residues in contact with THR1474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B ILE* 4.8 2.0 - - - -
1196B LEU* 3.7 18.2 - - - +
1470B ARG* 2.8 23.6 + - - +
1471B ASP* 3.6 7.2 - - - -
1472B GLU 3.3 0.2 - - - -
1473B LEU* 1.3 73.6 - - - +
1475B GLU* 1.3 61.7 + - - +
1477B ARG* 3.3 31.7 + - - +
1478B ASP* 2.9 37.9 + - - +
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Residues in contact with GLU1475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137B ARG* 4.4 7.0 + - - +
1471B ASP 3.0 16.9 + - - +
1472B GLU* 3.8 7.9 - - - +
1473B LEU 3.3 0.2 - - - -
1474B THR* 1.3 77.8 - - - +
1476B ILE* 1.3 64.0 + - - +
1478B ASP* 3.5 8.0 + - + +
1479B ARG* 2.8 65.0 + - - +
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Residues in contact with ILE1476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131B ILE* 6.0 0.2 - - + -
1134B GLU* 3.6 33.0 - - + +
1137B ARG* 3.9 10.3 - - - +
1163B ARG* 3.2 38.1 - - + +
1164B PHE* 4.0 17.3 - - + -
1188B LEU* 4.6 5.8 - - + +
1192B ILE* 4.0 15.9 - - + -
1472B GLU 3.2 17.3 + - - +
1473B LEU* 3.6 7.4 - - - +
1474B THR 3.2 0.6 - - - -
1475B GLU* 1.3 77.7 - - - +
1477B ARG* 1.3 60.5 + - - +
1479B ARG* 3.2 2.4 + - - +
1480B PHE* 2.8 45.7 + - + +
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Residues in contact with ARG1477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188B LEU* 5.4 0.4 - - - -
1189B THR* 3.9 39.4 - - + +
1192B ILE* 3.7 21.8 - - + -
1193B ASN* 3.0 30.4 + - - +
1196B LEU* 4.0 15.0 - - - +
1473B LEU 2.9 15.9 + - - +
1474B THR* 3.3 22.6 + - - +
1476B ILE* 1.3 76.6 - - - +
1478B ASP* 1.3 80.7 + - - +
1481B GLY* 2.7 34.0 + - - +
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Residues in contact with ASP1478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474B THR* 2.9 31.0 + - - +
1475B GLU* 3.9 7.4 - - + +
1477B ARG* 1.3 102.1 + - - +
1479B ARG* 1.3 60.6 + - - +
1481B GLY 4.5 4.2 + - - +
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Residues in contact with ARG1479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130B LYS 5.4 0.8 + - - -
1133B LEU* 6.3 1.0 - - - +
1134B GLU* 2.9 35.1 + - - -
1137B ARG* 4.2 4.4 - - - +
1475B GLU* 2.8 50.5 + - - +
1476B ILE* 3.2 5.6 + - - +
1478B ASP* 1.3 79.0 - - - +
1480B PHE* 1.3 94.1 + - + +
1481B GLY 5.2 0.8 - - - +
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Residues in contact with PHE1480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101B TYR* 4.3 9.0 - - - -
1130B LYS* 3.8 31.6 - - + -
1131B ILE* 3.8 38.6 - - + -
1134B GLU* 3.7 13.9 - - + -
1188B LEU* 3.9 20.6 - - + +
1476B ILE* 2.8 26.6 + - + +
1479B ARG* 1.3 124.7 - - + +
1481B GLY* 1.3 69.3 + - - +
1482B ASP* 3.5 6.2 + - - +
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Residues in contact with GLY1481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188B LEU* 4.4 6.5 - - - +
1189B THR* 3.1 27.1 - - - -
1476B ILE 3.9 0.6 + - - -
1477B ARG* 2.7 27.6 + - - +
1478B ASP 4.9 3.5 - - - +
1479B ARG 5.2 0.7 - - - +
1480B PHE* 1.3 75.6 - - - +
1482B ASP* 1.3 59.3 + - - +
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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
------------------------------------------------------------
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