Contacts of the strand formed by residues 957 - 964 (chain A) in PDB entry 1HXK
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 957 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A PRO* 3.6 13.6 - - - +
563A HIS* 4.8 4.9 + - - -
923A GLN* 5.3 1.8 + - - -
953A ALA* 4.1 8.5 - - + -
954A ARG* 2.9 19.9 + - + +
955A GLU 3.2 4.7 - - - +
956A ASP* 1.3 83.8 + - - +
958A ASP* 1.3 63.1 + - - +
979A LEU* 3.8 29.4 - - + -
980A HIS 3.5 16.6 - - - +
981A ARG* 3.9 20.9 - - + -
997A LEU* 4.0 15.9 - - + -
1030A GLU* 3.7 35.2 - - + +
1031A VAL* 4.1 12.6 - - + +
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Residues in contact with ASP 958 (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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176A ARG* 5.2 3.6 + - - -
437A ARG* 2.8 42.0 + - - -
561A LEU* 3.6 10.4 - - - +
562A PRO* 3.1 14.2 - - - +
919A HIS* 6.2 1.3 - - + +
923A GLN* 4.5 11.8 + - - +
927A ASP* 5.3 0.5 - - - +
956A ASP 5.5 0.4 - - - +
957A LEU* 1.3 76.6 - - - +
959A VAL* 1.3 71.7 + - - +
960A SER* 3.4 9.9 + - - +
979A LEU* 3.5 8.3 - - - +
980A HIS* 2.8 39.1 + - + +
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Residues in contact with VAL 959 (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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437A ARG* 3.1 19.1 + - - -
441A MET* 3.8 17.3 - - + +
562A PRO* 3.8 14.4 - - + +
627A MET* 4.0 22.7 - - + -
958A ASP* 1.3 76.3 + - - +
960A SER* 1.3 62.2 + - - +
961A VAL 3.3 22.4 + - - +
962A MET* 4.3 0.2 - - + -
977A TYR* 4.1 12.1 - - + -
978A VAL 3.5 5.4 - - - +
979A LEU* 4.1 11.7 - - + -
997A LEU* 3.7 31.0 - - + -
999A VAL* 4.2 4.9 - - + -
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Residues in contact with SER 960 (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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175A TRP* 3.4 35.1 - - - -
176A ARG* 4.5 13.8 + - - +
437A ARG* 3.5 35.2 + - - +
958A ASP* 3.4 7.3 + - - -
959A VAL* 1.3 73.4 - - - +
961A VAL* 1.3 67.5 + - - +
978A VAL* 2.9 16.7 + - - -
980A HIS* 3.4 18.4 - - - +
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Residues in contact with VAL 961 (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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175A TRP* 6.4 0.2 - - + -
176A ARG* 5.8 8.7 - - + +
179A LEU* 5.0 8.3 - - + -
180A LEU* 6.3 0.7 - - + -
437A ARG* 5.4 3.6 - - + +
440A GLU* 4.7 3.6 - - + +
441A MET* 5.6 0.2 - - - -
959A VAL* 3.2 11.0 - - - +
960A SER* 1.3 89.6 - - - +
962A MET* 1.3 71.5 + - - +
963A ARG* 3.9 38.1 - - + +
977A TYR* 3.1 6.3 - - - -
978A VAL* 2.9 51.9 + - + -
1016A PHE* 4.5 4.5 - - + -
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Residues in contact with MET 962 (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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437A ARG* 5.0 1.9 + - - +
440A GLU* 3.4 26.7 - - - +
441A MET* 3.6 33.1 + - + +
444A ALA* 3.9 25.6 - - + +
445A TRP* 3.8 38.1 - - + -
627A MET* 3.6 25.1 - - - -
959A VAL* 4.3 1.6 - - + -
961A VAL* 1.3 73.8 - - - +
963A ARG* 1.3 63.5 + - - +
975A VAL* 4.2 8.3 - - + -
976A GLY 3.4 4.3 - - - -
977A TYR* 3.5 36.8 - - + +
1003A LEU* 4.5 4.3 - - + -
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Residues in contact with ARG 963 (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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180A LEU* 3.4 26.0 - - - +
183A THR* 3.9 24.1 + - - +
440A GLU* 2.8 43.7 + - + +
444A ALA* 4.5 1.3 - - - -
462A ARG* 4.1 15.3 - - - +
961A VAL* 3.9 23.7 - - + +
962A MET* 1.3 76.8 - - - +
964A ARG* 1.3 76.8 + - - +
965A LEU* 3.3 18.4 + - + +
975A VAL* 4.2 2.7 - - - -
976A GLY 2.8 37.4 + - - +
1016A PHE* 3.5 24.1 - - + -
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Residues in contact with ARG 964 (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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440A GLU 5.0 0.6 + - - -
443A SER 5.3 0.7 - - - +
444A ALA* 2.9 47.7 + - - +
445A TRP 3.5 16.8 + - - -
446A HIS* 3.2 22.2 + - - +
447A SER* 4.2 9.8 - - - +
448A TRP* 5.6 0.4 - - - +
455A GLU* 6.0 0.7 - - - -
963A ARG* 1.3 81.6 - - - +
965A LEU* 1.3 61.3 + - - +
966A THR 3.5 18.4 - - - +
973A GLN* 3.0 46.2 - - - +
974A ARG 3.6 11.2 - - - +
975A VAL* 4.1 14.2 - - + +
1003A LEU* 3.6 18.0 - - - +
1043A HIS* 5.8 0.4 - - - -
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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