Contacts of the helix formed by residues 1482 - 1496 (chain E) in PDB entry 6C3P
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 SER1482 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716E GLY* 3.8 3.8 - - - -
774E GLN* 5.2 1.6 - - - -
1481E PHE* 1.3 79.2 - - - +
1483E GLN* 1.3 68.4 + - - +
1484E GLY 3.3 0.2 - - - -
1485E GLN* 3.1 14.7 + - - +
1486E ARG* 2.9 23.2 + - - +
2002E MG 4.5 0.2 - - - -
2004E ATP 2.3 70.6 + - - -
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Residues in contact with GLN1483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774E GLN* 3.4 41.7 - - + +
775E LYS* 3.1 42.1 - - - +
854E ASP* 5.4 0.2 - - - +
888E HIS* 6.0 1.8 - - - +
1428E PRO* 4.0 18.4 - - - +
1482E SER* 1.3 74.7 - - - +
1484E GLY* 1.3 58.8 + - - +
1486E ARG* 2.9 35.2 + - - +
1487E GLN* 2.9 27.3 + - - +
1510E SER* 4.7 13.3 + - - +
2004E ATP 4.0 1.7 + - - +
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Residues in contact with GLY1484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715E VAL* 3.5 22.6 - - - +
1482E SER 3.3 0.4 - - - -
1483E GLN* 1.3 77.1 - - - +
1485E GLN* 1.3 59.8 + - - +
1487E GLN* 3.3 7.0 + - - +
1488E LEU* 2.9 38.6 + - - +
1510E SER* 4.2 16.6 - - - -
1511E ILE* 5.2 0.4 - - - -
2004E ATP 3.6 7.9 + - - -
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Residues in contact with GLN1485 (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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715E VAL* 3.3 34.5 + - - +
716E GLY* 3.4 9.7 - - - -
1459E LEU* 4.4 15.7 - - - +
1462E VAL* 4.4 21.5 - - - +
1481E PHE* 3.5 24.2 - - + -
1482E SER* 3.1 36.5 + - - +
1484E GLY* 1.3 74.8 - - - +
1486E ARG* 1.3 57.5 + - - +
1488E LEU* 3.1 10.7 + - - +
1489E PHE* 2.9 35.6 + - + -
2004E ATP 5.1 5.9 + - - +
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Residues in contact with ARG1486 (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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775E LYS* 5.0 5.5 - - - +
1428E PRO* 3.6 16.5 + - + +
1430E LEU* 3.5 23.5 - - + +
1477E GLY 3.5 20.8 + - - -
1478E GLY* 2.5 31.8 + - - +
1479E GLU* 4.5 6.4 + - - +
1481E PHE* 2.3 40.8 + - + +
1482E SER 2.9 11.9 + - - +
1483E GLN* 2.9 50.1 + - - +
1485E GLN* 1.3 73.5 - - - +
1487E GLN* 1.3 67.1 + - - +
1489E PHE* 3.2 11.0 + - - +
1490E CYS* 3.0 26.3 + - - -
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Residues in contact with GLN1487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424E ILE* 3.6 6.7 - - - +
1425E LEU 3.3 20.0 + - - -
1426E GLN 2.9 19.5 - - - +
1428E PRO* 3.2 27.0 - - + +
1483E GLN 2.9 14.0 + - - +
1484E GLY* 3.6 7.9 - - - +
1486E ARG* 1.3 75.0 - - - +
1488E LEU* 1.3 58.0 + - - +
1490E CYS* 3.1 6.0 + - - +
1491E LEU* 2.9 54.8 + - + +
1507E ALA* 3.3 28.9 + - - +
1510E SER* 4.2 15.1 + - - -
1511E ILE* 3.6 11.4 - - + -
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Residues in contact with LEU1488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715E VAL* 5.1 7.4 - - + -
1457E ALA* 2.9 31.5 - - + +
1458E GLN 5.7 0.9 - - - +
1459E LEU* 3.4 21.8 - - + +
1484E GLY 2.9 28.5 + - - +
1485E GLN* 3.1 12.5 + - - +
1487E GLN* 1.3 76.8 - - - +
1489E PHE* 1.3 62.4 + - - +
1491E LEU* 3.2 8.0 + - + +
1492E ALA* 2.9 23.7 + - - +
1511E ILE* 3.5 31.6 - - + -
1515E THR* 4.9 9.4 - - + -
1519E LEU* 3.4 22.0 - - + -
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Residues in contact with PHE1489 (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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1430E LEU* 4.3 19.7 - - + -
1435E ILE* 4.1 26.0 - - + -
1438E ASN* 6.5 0.4 - - + -
1439E LEU* 4.3 8.3 - - + +
1454E LEU* 5.3 7.6 - - + -
1459E LEU* 4.1 25.8 - - + -
1462E VAL* 6.4 1.1 - - + -
1463E VAL* 5.2 10.1 - - + -
1466E LEU* 6.0 1.3 - - + -
1474E ILE* 4.9 4.3 - - + -
1481E PHE* 3.8 45.8 - + + -
1485E GLN* 2.9 40.1 + - + -
1486E ARG* 3.2 11.2 + - - +
1488E LEU* 1.3 74.8 - - - +
1490E CYS* 1.3 58.2 + - - +
1492E ALA* 3.3 5.8 + - + +
1493E ARG* 2.9 31.7 + - - +
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Residues in contact with CYS1490 (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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512E TYR* 4.7 2.5 + - - +
1424E ILE* 4.5 8.3 - - + +
1425E LEU* 5.7 3.1 - - + +
1427E ASP 4.8 1.6 - - - +
1428E PRO* 3.6 8.5 - - + -
1429E VAL 3.4 40.8 - - - -
1430E LEU* 4.1 3.6 - - - -
1486E ARG 3.0 18.7 + - - -
1487E GLN* 3.1 16.4 + - - +
1489E PHE* 1.3 73.4 - - - +
1491E LEU* 1.3 67.1 + - - +
1493E ARG* 3.2 28.2 + - - +
1494E ALA* 3.0 23.0 + - - +
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Residues in contact with LEU1491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424E ILE* 3.6 22.7 - - + -
1487E GLN* 2.9 54.9 + - + +
1488E LEU* 3.4 13.2 - - + +
1490E CYS* 1.3 77.5 - - - +
1492E ALA* 1.3 57.8 + - - +
1494E ALA* 3.2 2.6 + - - +
1495E PHE* 2.9 45.7 + - + -
1504E MET* 5.7 2.0 - - - -
1507E ALA* 3.6 18.6 - - + +
1508E THR* 6.3 0.2 - - - -
1511E ILE* 4.9 6.5 - - + -
1519E LEU* 3.6 42.6 - - + -
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Residues in contact with ALA1492 (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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1439E LEU* 4.2 9.0 - - + -
1453E ALA* 3.9 24.9 - - + +
1454E LEU* 4.7 9.6 - - + +
1457E ALA* 3.9 6.9 - - + +
1459E LEU* 5.0 2.9 - - + -
1488E LEU 2.9 15.4 + - - +
1489E PHE* 3.7 7.2 - - + +
1491E LEU* 1.3 75.8 - - - +
1493E ARG* 1.3 57.3 + - - +
1495E PHE* 2.8 30.3 + - - +
1496E VAL* 2.8 19.0 + - - +
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Residues in contact with ARG1493 (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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508E LEU* 3.2 30.1 - - - +
512E TYR* 3.9 21.6 + - + -
514E TRP* 3.4 37.5 - - + -
1425E LEU* 6.4 0.4 - - - +
1429E VAL 3.6 14.1 + - - -
1430E LEU* 4.9 4.9 - - - +
1431E PHE* 4.4 9.3 - - - -
1438E ASN* 3.4 25.8 + - - +
1439E LEU* 3.5 22.1 - - + +
1489E PHE* 2.9 19.3 + - - +
1490E CYS* 3.2 35.4 + - - +
1492E ALA* 1.3 75.2 - - - +
1494E ALA* 1.3 63.9 + - - +
1496E VAL* 3.1 18.3 + - - +
1497E ARG* 4.2 4.9 + - - +
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Residues in contact with ALA1494 (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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512E TYR* 4.4 12.5 - - + +
1422E SER* 4.2 14.3 + - - -
1423E ILE 3.9 13.9 - - - +
1424E ILE* 3.5 29.2 - - + -
1490E CYS 3.0 8.6 + - - +
1491E LEU 3.4 8.1 - - - +
1493E ARG* 1.3 75.9 - - - +
1495E PHE* 1.3 66.2 + - + +
1496E VAL 3.1 1.2 + - - -
1497E ARG* 3.1 24.0 + - - +
1499E THR* 5.1 0.3 + - - -
1502E PHE* 5.6 5.3 - - + -
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Residues in contact with PHE1495 (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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1424E ILE* 3.8 6.5 - - + -
1453E ALA* 4.4 7.0 - - + +
1456E ILE* 3.4 35.0 - - + -
1457E ALA* 4.2 9.9 - - + -
1491E LEU* 2.9 52.9 + - + -
1492E ALA* 2.8 18.7 + - - +
1494E ALA* 1.3 71.8 - - + +
1496E VAL* 1.3 63.8 + - - +
1497E ARG 3.1 9.7 + - - +
1502E PHE* 4.3 5.8 - + - -
1504E MET* 3.6 32.5 - - + -
1519E LEU* 5.0 5.8 - - + -
1523E VAL* 4.3 11.2 - - + -
1527E PHE* 3.9 31.7 - + + -
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Residues in contact with VAL1496 (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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1439E LEU* 4.0 28.3 - - + +
1440E ASP* 3.8 20.6 - - - +
1445E CYS* 4.1 15.6 - - + -
1449E THR* 5.7 7.3 - - - +
1450E LEU* 4.7 8.1 - - + -
1453E ALA* 4.2 15.0 - - + -
1492E ALA 2.8 19.1 + - - +
1493E ARG* 3.3 18.4 - - - +
1494E ALA 3.1 0.6 - - - -
1495E PHE* 1.3 78.2 - - - +
1497E ARG* 1.3 64.2 + - + +
1498E LYS* 3.5 2.4 + - - +
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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
------------------------------------------------------------
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