Contacts of the strand formed by residues 895 - 900 (chain A) in PDB entry 2XT6
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 LEU 895 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A ASP* 4.7 12.1 - - + +
623A LEU* 6.0 1.6 - - + -
893A GLY 4.0 1.2 + - - -
894A LYS* 1.3 74.9 - - - +
896A VAL* 1.3 64.7 + - - +
897A ARG* 4.0 10.3 - - + +
940A GLY 5.1 0.6 + - - -
941A GLY 4.9 0.2 - - - -
942A LYS* 3.6 21.1 - - + +
944A LEU* 3.8 27.4 - - + -
962A TYR* 3.9 22.2 - - + +
966A ASN* 4.0 17.0 - - - +
968A ASP 4.5 2.3 + - - +
969A ALA* 3.5 23.1 - - + -
970A MET* 2.8 26.3 + - - +
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Residues in contact with VAL 896 (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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886A LEU* 3.9 33.9 - - + +
889A LEU* 4.2 12.8 - - + -
890A ILE* 3.8 22.7 - - + -
894A LYS 4.1 4.3 - - - +
895A LEU* 1.3 80.8 - - - +
897A ARG* 1.3 57.3 + - - +
942A LYS 2.7 14.8 + - - +
943A PHE* 3.6 21.2 - - + -
944A LEU* 2.8 32.6 + - - +
970A MET* 3.4 16.6 - - + +
972A LEU* 4.0 13.5 - - + -
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Residues in contact with ARG 897 (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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618A ARG* 4.4 6.1 - - - +
622A ASP* 5.0 1.8 + - - -
665A GLY 2.9 30.3 + - - -
666A TYR* 3.4 17.4 - - - -
895A LEU* 4.0 14.6 - - + +
896A VAL* 1.3 72.1 - - - +
898A LEU* 1.3 58.8 + - - +
899A SER* 4.1 4.4 + - - -
944A LEU* 3.2 16.1 - - + +
946A TYR* 3.4 24.7 + - + -
958A PHE* 3.4 13.2 - - - -
959A GLU* 2.7 39.8 + - - +
962A TYR* 3.7 38.1 - - + -
970A MET 2.8 12.8 + - - +
971A VAL* 3.4 6.0 - - + +
972A LEU* 2.8 33.8 + - - +
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Residues in contact with LEU 898 (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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882A GLU* 4.6 1.3 - - - +
883A LEU* 5.5 0.4 - - + -
886A LEU* 4.0 19.7 - - + -
896A VAL 4.0 1.4 + - - -
897A ARG* 1.3 74.1 - - - +
899A SER* 1.4 66.6 + - - +
903A THR* 3.6 15.9 - - + -
911A ARG* 3.6 35.2 - - - +
943A PHE* 4.0 26.2 - - + -
944A LEU 2.9 7.0 + - - +
945A VAL* 3.0 11.0 - - + -
946A TYR* 2.9 23.0 + - - -
972A LEU* 3.5 31.6 - - + +
974A GLU* 5.0 3.1 - - + -
1008A LEU* 4.4 16.2 - - + -
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Residues in contact with SER 899 (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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666A TYR* 3.3 21.7 + - - -
897A ARG* 4.1 2.2 + - - -
898A LEU* 1.4 79.3 - - - +
900A GLY* 1.3 58.1 + - - +
903A THR* 3.7 8.7 - - - -
946A TYR* 3.1 30.5 - - - -
959A GLU* 3.4 25.0 + - - +
972A LEU 3.1 6.1 + - - -
973A TRP* 3.2 10.7 - - - -
974A GLU* 2.9 22.5 + - - +
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Residues in contact with GLY 900 (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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899A SER* 1.3 77.5 + - - +
901A GLN* 1.3 60.2 + - - -
902A ASP 3.3 1.9 + - - -
903A THR* 3.2 14.9 + - - -
947A ASN* 3.4 4.7 - - - -
948A SER* 2.6 35.8 + - - -
973A TRP* 4.2 7.6 - - - -
974A GLU 3.4 12.8 - - - -
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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