Contacts of the helix formed by residues 1502 - 1514 (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 ASN1502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1499A ARG* 5.8 0.3 + - - -
1500A PRO* 3.3 4.9 - - - +
1501A GLY* 1.3 78.0 + - - +
1503A LYS* 1.3 56.3 + - - +
1504A ILE* 2.9 28.5 - - + +
1505A GLN* 3.5 18.6 + - + +
1506A GLY* 2.5 32.7 + - - -
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Residues in contact with LYS1503 (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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1499A ARG* 5.9 3.1 - - - +
1501A GLY 3.3 4.6 + - - +
1502A ASN* 1.3 72.5 - - + +
1504A ILE* 1.3 79.0 + - + +
1506A GLY* 4.0 2.2 - - - +
1507A CYS* 2.6 45.9 + - - +
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Residues in contact with ILE1504 (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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1502A ASN* 2.9 38.4 - - + +
1503A LYS* 1.3 96.1 - - + +
1505A GLN* 1.3 71.2 + - + +
1507A CYS* 3.8 3.4 + - - +
1508A ILE* 3.0 31.6 + - + +
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Residues in contact with GLN1505 (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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1500A PRO* 2.9 35.0 - - + +
1502A ASN* 3.3 22.2 + - + +
1503A LYS 3.2 0.2 - - - -
1504A ILE* 1.3 86.6 - - + +
1506A GLY* 1.3 56.8 + - - +
1508A ILE* 3.5 6.7 + - - +
1509A PHE* 3.0 24.3 + - - +
1567A ILE* 2.8 41.4 + - + +
1568A SER* 3.4 7.6 + - - -
1570A ARG* 4.5 10.9 - - - +
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Residues in contact with GLY1506 (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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1499A ARG* 4.1 21.0 + - - -
1500A PRO* 4.2 8.7 - - - -
1502A ASN 2.5 21.9 + - - -
1503A LYS* 3.1 3.1 + - - -
1505A GLN* 1.3 71.3 - - - +
1507A CYS* 1.3 54.0 + - - +
1509A PHE* 3.0 10.0 + - - +
1510A ASP* 2.4 37.1 + - - +
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Residues in contact with CYS1507 (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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1499A ARG* 6.3 0.2 - - - -
1503A LYS* 2.6 29.7 + - - +
1504A ILE* 4.4 4.3 - - - +
1506A GLY* 1.3 71.6 - - - +
1508A ILE* 1.3 54.1 + - + +
1510A ASP* 2.9 10.8 + - - +
1511A LEU* 2.5 37.9 + - - +
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Residues in contact with ILE1508 (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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1504A ILE* 3.0 22.0 - - + +
1505A GLN* 3.7 2.5 - - - +
1506A GLY 3.2 0.4 - - - -
1507A CYS* 1.3 76.3 - - + +
1509A PHE* 1.3 58.1 + - - +
1511A LEU* 3.2 9.4 + - + +
1512A VAL* 2.8 35.6 + - + +
1564A LEU* 2.9 50.3 - - + +
1567A ILE* 4.4 18.2 - - + -
1568A SER* 2.9 12.6 - - - +
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Residues in contact with PHE1509 (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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1496A PRO 5.0 3.1 - - - -
1497A ILE* 4.3 26.2 - - + -
1498A PRO 4.8 0.2 - - - -
1499A ARG* 3.2 51.1 - - + -
1500A PRO* 4.2 3.4 - - + -
1505A GLN 3.0 7.6 + - - +
1506A GLY* 3.0 10.4 + - - +
1508A ILE* 1.3 75.6 - - - +
1510A ASP* 1.3 68.4 + - - +
1512A VAL* 3.8 1.6 - - - +
1513A THR* 2.9 54.3 + - + -
1568A SER* 2.4 46.8 + - - -
1569A LEU* 3.7 21.5 - - + -
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Residues in contact with ASP1510 (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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1499A ARG* 4.8 13.3 + - - +
1506A GLY 2.4 26.9 + - - +
1507A CYS* 3.2 12.4 - - - +
1509A PHE* 1.3 83.5 - - + +
1511A LEU* 1.3 62.0 + - - +
1513A THR* 3.7 4.2 + - - -
1514A ASN* 3.5 17.7 + - - +
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Residues in contact with LEU1511 (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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1507A CYS 2.5 19.7 + - - +
1508A ILE* 3.5 8.3 - - + +
1510A ASP* 1.3 74.3 - - - +
1512A VAL* 1.3 71.8 + - + +
1514A ASN* 3.4 19.2 + - - +
1517A PHE* 3.2 42.7 - - + +
1564A LEU* 4.7 13.7 - - + -
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Residues in contact with VAL1512 (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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1508A ILE 2.8 30.3 + - - +
1509A PHE* 3.8 5.6 - - - +
1511A LEU* 1.3 83.9 - - + +
1513A THR* 1.3 66.2 + - - +
1514A ASN 3.4 6.9 + - - +
1517A PHE* 4.0 17.8 - - + -
1518A ASP* 5.8 1.0 - - - +
1564A LEU* 3.9 34.3 - - + +
1565A LYS* 3.3 37.0 - - + -
1568A SER* 4.3 2.0 - - - +
1569A LEU* 5.2 10.3 - - + -
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Residues in contact with THR1513 (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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1509A PHE* 2.9 53.3 + - + -
1510A ASP* 3.9 6.5 - - - +
1511A LEU 3.4 0.2 - - - -
1512A VAL* 1.3 77.6 - - - +
1514A ASN* 1.3 64.9 + - - +
1515A GLN* 3.3 3.6 + - - +
1569A LEU* 5.2 3.5 - - - +
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Residues in contact with ASN1514 (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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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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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