Contacts of the strand formed by residues 744 - 748 (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 GLN 744 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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999I HIS* 4.5 2.6 - - - -
1004I LYS* 4.0 46.7 + - + +
628J ARG* 2.5 47.3 + - - +
629J SER* 3.3 14.5 - - - +
630J VAL* 4.5 6.5 - - + -
703J ASN 4.9 0.3 - - - +
704J ARG* 4.1 13.7 + - - +
705J ALA 5.0 2.1 + - - +
742J GLY 3.7 8.9 + - - +
743J ASP* 1.3 79.4 - - - +
745J MET* 1.3 66.9 + - - +
14S G 5.0 0.2 - - - +
3T G 4.1 30.8 + - - +
4T A 5.4 3.0 + - - +
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Residues in contact with MET 745 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628J ARG* 3.0 21.1 - - - +
629J SER 2.8 20.1 + - - +
631J ILE* 3.6 31.5 - - + +
702J LEU* 3.5 36.3 - - + -
703J ASN 3.3 28.0 - - - +
704J ARG* 3.7 18.2 - - + +
726J ILE* 3.8 8.3 - - + +
728J LEU* 3.6 28.5 - - - -
736J PHE* 3.8 16.6 - - + -
738J ALA* 4.9 0.2 - - - -
744J GLN* 1.3 77.3 - - - +
746J ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 746 (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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1030I GLN* 4.8 4.7 - - + -
627J GLY 3.9 5.2 - - - +
628J ARG* 3.4 19.4 - - + +
702J LEU* 3.3 8.0 - - - +
703J ASN* 2.9 48.1 + - + +
745J MET* 1.3 73.4 - - - +
747J VAL* 1.3 65.6 + - - +
748J HIS* 4.2 19.5 - - + -
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Residues in contact with VAL 747 (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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626J SER* 3.2 7.3 - - - -
627J GLY 2.8 39.1 + - - +
644J LEU* 4.4 13.2 - - + -
648J MET* 4.8 3.4 - - - -
652J LEU* 4.2 20.0 - - + -
700J VAL* 3.6 32.3 - - + -
701J LEU 3.2 4.9 - - - +
702J LEU* 3.6 15.3 - - + -
726J ILE* 3.6 28.9 - - + -
746J ALA* 1.3 79.5 - - - +
748J HIS* 1.3 64.9 + - - +
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Residues in contact with HIS 748 (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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1030I GLN* 4.3 14.0 + - + +
1031I ARG 5.2 2.5 - - - -
1032I PHE* 3.5 26.7 - + - +
1052I MET* 3.6 28.5 - - + -
623J VAL* 3.4 32.5 - - + +
625J TYR 3.9 4.9 - - - +
626J SER* 3.7 12.6 + - - +
652J LEU* 5.7 0.4 - - - -
700J VAL* 3.2 7.5 - - - +
701J LEU* 2.9 42.1 + - + +
703J ASN* 5.3 7.4 - - + +
746J ALA* 4.2 20.2 - - + +
747J VAL* 1.3 81.1 + - - +
749J VAL* 1.3 61.1 - - - +
750J PRO* 3.8 0.8 - - - +
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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