Contacts of the helix formed by residues 1514 - 1534 (chain A) in PDB entry 6J8H
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 ASN1514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1510A ASP 3.5 9.5 + - - +
1511A LEU* 3.4 15.4 + - - +
1512A VAL 3.2 4.1 - - - +
1513A THR* 1.3 80.6 - - - +
1515A GLN* 1.3 92.7 + - - +
1516A ALA* 2.9 30.2 - - - +
1517A PHE* 3.2 19.5 + - + +
1518A ASP* 3.6 5.2 + - - +
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Residues in contact with GLN1515 (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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1513A THR 3.3 5.0 + - - +
1514A ASN* 1.3 81.4 + - - +
1516A ALA* 1.3 78.6 + - - +
1518A ASP* 3.0 19.6 + - + +
1519A ILE* 3.1 33.3 + - + +
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Residues in contact with ALA1516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1514A ASN* 2.9 22.2 - - - +
1515A GLN* 1.3 89.9 + - - +
1517A PHE* 1.3 63.6 + - - +
1519A ILE* 3.2 18.8 + - - +
1520A SER* 3.3 11.8 + - - -
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Residues in contact with PHE1517 (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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1511A LEU* 3.2 44.2 - - + +
1512A VAL* 4.0 28.3 - - + -
1514A ASN* 3.2 14.3 + - + +
1515A GLN 3.1 0.6 - - - -
1516A ALA* 1.3 80.2 - - - +
1518A ASP* 1.3 68.6 + - + +
1520A SER* 3.1 22.3 + - - -
1521A ILE* 3.3 35.1 + - + +
1561A GLU* 4.7 16.2 - - + -
1564A LEU* 4.9 10.3 - - + -
1565A LYS* 5.1 9.6 - - + -
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Residues in contact with ASP1518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512A VAL 5.8 0.9 - - - +
1514A ASN 3.6 4.5 + - - +
1515A GLN* 3.0 13.9 + - - +
1517A PHE* 1.3 87.5 - - + +
1519A ILE* 1.3 65.6 + - - +
1521A ILE* 3.1 18.0 + - - +
1522A MET* 3.1 21.8 + - - +
1625A LYS* 4.9 17.3 - - - +
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Residues in contact with ILE1519 (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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1515A GLN* 3.1 35.2 + - + +
1516A ALA* 3.2 11.6 + - - +
1518A ASP* 1.3 77.1 - - - +
1520A SER* 1.3 66.1 + - - +
1522A MET* 3.1 14.2 + - + +
1523A VAL* 3.0 23.2 + - + +
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Residues in contact with SER1520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516A ALA 3.3 10.0 + - - -
1517A PHE* 3.1 15.5 + - - -
1519A ILE* 1.3 80.6 - - - +
1521A ILE* 1.3 59.3 + - - +
1523A VAL* 2.7 33.1 - - - +
1524A LEU* 3.0 11.9 + - - +
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Residues in contact with ILE1521 (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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1517A PHE* 3.3 34.5 + - + +
1518A ASP* 3.1 16.1 + - - +
1520A SER* 1.3 75.2 - - - +
1522A MET* 1.3 65.9 + - - +
1524A LEU* 3.1 19.6 + - + +
1525A ILE* 3.0 36.9 + - + +
1557A LEU 5.6 1.1 - - - +
1558A PHE* 4.3 10.8 - - + -
1561A GLU* 3.7 43.1 - - + +
1622A ARG* 4.4 3.1 - - - +
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Residues in contact with MET1522 (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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1518A ASP* 3.1 26.6 + - - +
1519A ILE* 3.1 17.5 + - + +
1521A ILE* 1.3 76.9 - - - +
1523A VAL* 1.3 62.9 + - - +
1525A ILE* 3.4 12.5 + - + +
1526A CYS* 3.3 23.3 + - - -
1622A ARG 4.5 6.1 - - - +
1623A LEU* 2.6 45.5 - - + +
1625A LYS* 5.7 4.5 - - - -
1626A GLY* 4.1 28.0 - - - -
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Residues in contact with VAL1523 (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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1519A ILE* 3.0 13.1 + - + +
1520A SER* 2.7 35.4 - - - +
1522A MET* 1.3 78.9 - - - +
1524A LEU* 1.3 65.2 + - + +
1526A CYS* 3.3 9.6 + - + +
1527A LEU* 3.0 34.3 + - + +
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Residues in contact with LEU1524 (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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1520A SER 3.0 14.5 + - - +
1521A ILE* 3.1 20.6 + - + +
1523A VAL* 1.3 82.2 - - + +
1525A ILE* 1.3 57.6 + - - +
1527A LEU* 3.2 21.1 + - + +
1528A ASN* 2.9 25.6 + - - +
1554A PHE* 3.8 21.2 - - + -
1557A LEU* 4.2 35.4 - - + -
1558A PHE* 4.1 19.3 - - + -
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Residues in contact with ILE1525 (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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1521A ILE* 3.0 29.1 + - + +
1522A MET* 3.8 21.5 - - + +
1523A VAL 3.3 0.2 - - - -
1524A LEU* 1.3 72.5 - - - +
1526A CYS* 1.3 61.0 + - - +
1528A ASN* 3.0 6.8 + - + +
1529A MET* 2.9 26.4 + - + +
1558A PHE* 3.4 26.2 - - + -
1619A ARG* 3.8 22.0 - - + +
1620A ILE* 4.3 8.9 - - + +
1622A ARG* 4.2 29.2 - - + +
1623A LEU* 3.9 23.3 - - + +
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Residues in contact with CYS1526 (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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1522A MET* 3.3 15.7 + - - +
1523A VAL* 3.5 13.2 - - + +
1524A LEU 3.3 0.2 - - - -
1525A ILE* 1.3 78.5 - - - +
1527A LEU* 1.3 65.9 + - + +
1529A MET* 3.2 10.4 + - - +
1530A VAL* 3.2 22.1 + - - +
1623A LEU* 4.1 26.9 - - - -
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Residues in contact with LEU1527 (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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1523A VAL* 3.0 27.1 + - + +
1524A LEU* 3.3 27.8 - - + +
1526A CYS* 1.3 79.9 - - + +
1528A ASN* 1.3 59.0 + - - +
1530A VAL* 2.6 31.1 - - + +
1531A THR* 3.4 9.5 + - - -
1554A PHE* 3.9 12.4 - - + -
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Residues in contact with ASN1528 (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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1524A LEU 2.9 13.3 + - - +
1525A ILE* 3.0 15.0 + - + +
1527A LEU* 1.3 77.9 - - - +
1529A MET* 1.3 62.2 + - - +
1531A THR* 3.1 18.7 + - - -
1532A MET* 3.5 25.3 + - - +
1551A ASN* 4.8 3.2 - - - +
1554A PHE* 3.5 41.4 - - + +
1558A PHE* 3.6 9.7 - - + -
1619A ARG* 3.1 30.7 + - - +
1620A ILE* 5.5 2.9 - - + -
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Residues in contact with MET1529 (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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254A PHE* 4.7 9.2 - - + -
257A SER* 3.8 25.6 - - - -
258A VAL 5.0 0.2 - - - +
261A LEU* 4.2 11.7 - - + -
1525A ILE 2.9 11.9 + - - +
1526A CYS* 3.2 12.7 + - - +
1528A ASN* 1.3 78.2 - - - +
1530A VAL* 1.3 61.3 + - - +
1532A MET* 3.2 13.1 + - - +
1533A MET* 3.0 44.2 + - + +
1620A ILE* 4.1 43.5 - - + +
1623A LEU* 4.4 17.7 - - + -
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Residues in contact with VAL1530 (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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1526A CYS 3.2 9.4 + - - +
1527A LEU* 2.6 43.5 - - + +
1529A MET* 1.3 77.3 - - - +
1531A THR* 1.3 62.1 + - - +
1533A MET* 3.3 23.1 + - + +
1534A VAL* 3.5 18.5 + - + +
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Residues in contact with THR1531 (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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1527A LEU 3.4 11.3 + - - -
1528A ASN* 3.1 11.0 + - - -
1530A VAL* 1.3 81.3 - - - +
1532A MET* 1.3 57.0 - - - +
1534A VAL* 2.4 31.8 - - + +
1535A GLU* 4.0 5.9 + - - +
1547A LEU* 3.5 26.6 - - + +
1550A ILE* 4.3 13.8 - - + +
1551A ASN* 3.6 26.9 - - - +
1554A PHE* 3.6 14.3 - - - -
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Residues in contact with MET1532 (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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261A LEU* 3.7 25.0 - - + +
264A LEU* 4.3 4.7 - - - +
1528A ASN* 3.5 25.7 + - - +
1529A MET* 3.2 8.6 + - - +
1531A THR* 1.3 80.0 - - + +
1533A MET* 1.3 62.1 + - - +
1535A GLU* 3.3 28.8 + - - +
1551A ASN* 6.0 0.2 - - - +
1616A ARG* 2.8 67.8 - - + +
1617A ILE* 4.3 4.9 - - + +
1619A ARG* 4.1 4.3 - - - +
1620A ILE* 3.0 38.8 - - + -
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Residues in contact with MET1533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A SER* 4.8 2.0 - - - +
261A LEU* 4.2 10.7 - - + +
264A LEU* 5.0 0.6 - - - +
346A THR* 5.5 1.6 - - - +
347A PHE* 3.6 64.6 + - + +
1529A MET* 3.0 59.5 - - + +
1530A VAL* 3.5 18.4 - - + +
1531A THR 3.2 0.2 - - - -
1532A MET* 1.3 76.0 - - - +
1534A VAL* 1.3 61.9 + - + +
1535A GLU 3.2 9.0 + - - +
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Residues in contact with VAL1534 (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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1530A VAL* 3.5 12.5 + - + +
1531A THR* 2.4 44.2 - - - +
1533A MET* 1.3 72.9 - - + +
1535A GLU* 1.3 62.9 + - - +
1536A LYS* 3.4 11.8 + - - +
1539A GLN* 4.5 3.1 - - - +
1543A MET* 4.9 15.1 - - + +
1547A LEU* 3.9 21.5 - - + -
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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
------------------------------------------------------------
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