Contacts of the strand formed by residues 700 - 703 (chain J) in PDB entry 4XLR
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 VAL 700 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642J CYS* 4.4 11.0 - - - -
644J LEU* 5.2 6.3 - - + -
652J LEU* 5.4 0.4 - - + -
653J PHE* 3.9 23.3 - - + -
698J LYS 5.7 0.2 - - - +
699J VAL* 1.3 77.4 - - - +
701J LEU* 1.3 66.3 + - - +
702J LEU* 4.5 2.0 - - + +
715J ALA* 3.2 5.7 - - - +
716J PHE 2.9 32.8 + - - +
718J PRO* 3.7 20.8 - - + +
747J VAL* 4.1 16.8 - - + -
748J HIS 3.3 20.2 - - - +
749J VAL* 3.9 17.5 - - + -
750J PRO* 4.2 3.4 - - - -
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Residues in contact with LEU 701 (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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1040I LEU* 4.7 3.8 - - + -
1048I THR* 4.6 15.7 - - + -
1056I LYS* 5.6 0.9 - - - +
700J VAL* 1.3 78.6 - - - +
702J LEU* 1.3 65.5 + - - +
713J ILE* 4.4 13.7 - - + -
714J GLN 3.2 11.0 - - - +
715J ALA* 4.6 3.8 - - + -
746J ALA 3.9 0.4 - - - +
747J VAL* 3.3 29.1 - - - +
748J HIS* 3.4 11.5 + - + -
749J VAL* 3.8 15.9 - - - +
750J PRO* 3.6 30.5 - - + -
759J ALA* 5.1 3.4 - - + -
763J MET* 3.6 39.5 - - + -
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Residues in contact with LEU 702 (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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642J CYS* 4.0 22.9 - - + -
700J VAL* 4.5 6.1 - - + +
701J LEU* 1.3 83.3 - - - +
703J ASN* 1.3 60.7 + - - +
713J ILE* 3.3 3.4 - - - -
714J GLN 2.9 31.8 + - - -
716J PHE* 3.5 28.9 - - + -
726J ILE* 3.8 29.4 - - + -
728J LEU* 3.9 19.3 - - + -
736J PHE* 3.2 5.0 - - - -
745J MET* 3.7 21.8 - - + -
746J ALA 3.4 3.8 - - - +
747J VAL* 3.8 17.5 - - + -
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Residues in contact with ASN 703 (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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1032I PHE* 5.8 2.0 - - + -
1036I GLU* 3.7 18.3 - - + +
702J LEU* 1.3 74.6 - - - +
704J ARG* 1.3 69.0 + - - +
705J ALA* 4.0 9.2 + - - +
707J THR* 3.0 24.4 + - - +
712J GLY 2.9 23.1 + - - -
713J ILE* 3.2 27.9 - - + +
744J GLN 4.9 0.3 - - - +
745J MET* 3.6 7.0 - - - -
746J ALA* 3.0 42.6 + - + +
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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