Contacts of the helix formed by residues 1488 - 1498 (chain J) in PDB entry 4XLN
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 ASP1488 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1487J VAL* 1.3 73.6 - - - +
1489J GLN* 1.3 67.3 + - - +
1490J ARG* 4.1 4.2 + - - +
1491J THR* 2.7 60.6 + - - +
1492J LEU* 2.8 9.3 + - - +
26K ARG* 3.3 40.1 + - - +
37K ASN* 3.8 8.3 - - - +
39K VAL* 3.8 9.4 - - + -
73K LEU* 3.7 9.4 - - + +
89K MET* 3.7 8.3 - - - +
93K TYR* 3.5 10.1 + - - -
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Residues in contact with GLN1489 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1487J VAL 4.2 0.6 + - - -
1488J ASP* 1.3 71.0 - - - +
1490J ARG* 1.3 69.8 + - + +
1492J LEU* 3.1 7.2 + - - +
1493J LYS* 2.9 47.6 + - + +
39K VAL* 5.0 11.9 - - + +
72K ARG* 4.3 12.5 + - + +
74K PHE* 3.6 35.5 - - + -
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Residues in contact with ARG1490 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488J ASP* 3.5 3.9 + - - +
1489J GLN* 1.3 81.7 - - + +
1491J THR* 1.3 58.6 + - - +
1493J LYS* 3.2 8.5 + - - +
1494J ALA* 2.9 26.3 + - - +
92K LEU* 4.8 3.4 - - + -
93K TYR* 4.3 15.0 - - - +
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Residues in contact with THR1491 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1487J VAL* 4.4 5.2 - - - +
1488J ASP* 2.7 52.0 + - - +
1490J ARG* 1.3 74.8 - - - +
1492J LEU* 1.3 63.7 + - - +
1494J ALA* 3.0 2.9 + - - +
1495J ILE* 2.9 26.4 + - - +
88K GLU* 5.0 3.9 - - - +
89K MET* 3.7 18.6 - - - -
92K LEU* 3.6 18.8 - - + -
93K TYR* 3.4 29.8 - - + +
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Residues in contact with LEU1492 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1487J VAL* 3.7 33.4 - - + -
1488J ASP 2.8 14.2 + - - +
1489J GLN* 3.3 20.6 - - - +
1491J THR* 1.3 78.8 + - - +
1493J LYS* 1.3 58.8 + - + +
1495J ILE* 3.2 17.6 - - + +
1496J GLU* 2.9 54.2 + - + +
74K PHE* 4.2 14.6 - - + -
79K LEU* 4.7 7.9 - - + -
80K VAL* 4.5 16.4 - - + -
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Residues in contact with LYS1493 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1489J GLN* 2.9 38.3 + - - +
1490J ARG* 3.8 6.3 - - - +
1492J LEU* 1.3 75.7 - - + +
1494J ALA* 1.3 61.1 + - - +
1496J GLU* 3.6 23.1 - - - +
1497J GLU* 2.9 28.6 + - - +
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Residues in contact with ALA1494 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490J ARG 2.9 13.0 + - - +
1491J THR 3.2 11.0 - - - +
1493J LYS* 1.3 77.1 - - - +
1495J ILE* 1.3 58.0 + - - +
1497J GLU* 3.1 8.3 + - - +
1498J ALA 2.9 18.7 + - - -
88K GLU* 2.9 14.7 - - + +
91K ARG* 3.6 26.5 - - - +
92K LEU* 4.0 11.7 - - + -
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Residues in contact with ILE1495 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1487J VAL* 5.8 0.9 - - + -
1491J THR 2.9 14.2 + - - +
1492J LEU* 3.2 29.8 - - + +
1494J ALA* 1.3 76.5 - - - +
1496J GLU* 1.3 60.6 + - - +
1498J ALA* 3.2 12.0 + - - +
1499J ARG* 3.5 7.6 + - - +
80K VAL* 3.9 35.2 - - + -
81K PRO* 4.2 6.1 - - + +
84K ARG* 3.7 41.1 - - + +
85K LEU* 3.9 10.3 - - + +
88K GLU* 3.3 26.4 + - + +
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Residues in contact with GLU1496 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1492J LEU* 2.9 39.2 + - + +
1493J LYS* 3.6 27.6 - - - +
1495J ILE* 1.3 78.4 - - - +
1497J GLU* 1.3 59.9 + - - +
1499J ARG* 3.0 44.8 + - - +
1500J LYS* 5.1 0.2 - - - -
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Residues in contact with GLU1497 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493J LYS 2.9 17.3 + - - +
1494J ALA* 3.5 6.1 - - - +
1496J GLU* 1.3 73.1 - - - +
1498J ALA* 1.3 63.9 + - - +
1499J ARG 3.0 6.5 + - - -
1500J LYS* 3.2 41.9 + - - +
1501J GLU* 3.6 9.5 + - - +
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Residues in contact with ALA1498 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1494J ALA 2.9 5.4 + - - -
1495J ILE* 3.2 10.7 + - + +
1497J GLU* 1.3 77.6 - - - +
1499J ARG* 1.3 60.4 + - - +
1501J GLU* 3.3 22.7 + - + +
1502J ALA* 3.9 5.9 + - - +
84K ARG* 4.9 17.7 + - - +
88K GLU* 3.2 37.5 - - - +
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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
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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