Contacts of the strand formed by residues 857 - 864 (chain A) in PDB entry 5WRZ
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 ARG 857 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848A TYR* 3.7 10.3 - - - +
851A PHE 3.5 13.7 - - - +
852A LYS 3.3 26.7 + - - -
853A GLN* 4.5 5.2 + - - +
854A LEU 2.8 27.6 + - - +
856A ASN* 1.3 77.6 - - - +
858A ARG* 1.3 60.1 + - - +
923A GLU* 3.1 30.7 + - + +
924A VAL 3.3 4.9 - - - +
925A ALA* 4.1 10.8 - - - -
965A ASP 5.3 1.2 + - - -
966A GLY* 3.3 27.2 + - - +
967A VAL* 3.9 12.2 - - + +
968A ASP* 3.5 26.7 + - - +
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Residues in contact with ARG 858 (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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856A ASN* 3.9 21.6 + - - +
857A ARG* 1.3 75.8 + - - +
859A LEU* 1.3 60.5 + - - +
860A LEU* 3.6 20.4 + - + -
922A GLY 3.3 2.1 - - - +
924A VAL* 2.9 34.1 + - - +
926A LEU* 3.8 27.5 - - + +
929A MET* 3.7 22.6 - - - +
949A LYS* 4.3 10.3 - - - +
961A ASN* 5.7 4.1 + - - -
967A VAL* 3.7 5.3 - - - +
968A ASP* 3.5 24.9 + - + +
970A PRO* 4.3 20.2 - - + +
989A TYR* 3.2 31.9 + - - -
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Residues in contact with LEU 859 (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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813A ILE* 5.8 0.2 - - + -
814A ILE* 5.5 2.0 - - + -
817A TYR* 2.8 29.5 + - + -
858A ARG* 1.3 72.4 - - - +
860A LEU* 1.3 53.1 + - - +
921A LEU* 4.1 30.5 - - + -
922A GLY 3.4 20.0 - - - +
923A GLU* 3.9 7.9 - - + +
964A LEU* 4.3 19.1 - - + -
967A VAL* 3.6 11.3 - - + +
968A ASP 3.0 15.0 + - - +
969A VAL* 4.1 29.2 - - + -
970A PRO* 3.5 7.3 - - - +
1000A LYS* 4.4 18.6 - - + -
1001A TYR* 4.7 5.8 - - + -
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Residues in contact with LEU 860 (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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817A TYR* 3.8 5.2 - - - +
858A ARG* 4.0 21.5 - - + +
859A LEU* 1.3 81.9 - - - +
861A TRP* 1.3 62.3 + - - +
862A HIS 4.1 0.3 + - - -
897A PHE* 3.8 19.8 - - + -
898A ALA 3.6 6.1 - - - +
899A ASP* 3.8 28.7 - - + -
921A LEU* 3.3 9.2 - - - -
922A GLY* 2.9 33.0 + - - +
924A VAL* 4.2 17.7 - - + -
926A LEU* 4.4 4.7 - - + -
970A PRO* 4.3 7.2 - - + -
989A TYR* 3.7 40.2 - - + -
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Residues in contact with TRP 861 (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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814A ILE 4.8 1.1 - - - -
817A TYR* 3.4 46.6 - + + -
818A VAL* 3.5 33.7 - - + -
860A LEU* 1.3 72.3 - - - +
862A HIS* 1.3 59.1 + - - +
897A PHE* 3.2 11.1 - - - +
898A ALA 2.8 48.1 + - - +
899A ASP 3.9 2.0 - - - -
900A MET 3.8 2.0 - - - -
901A VAL* 3.5 40.4 - - + +
904A SER* 3.1 22.2 + - - +
919A ILE* 3.6 30.7 - - + -
920A LEU 3.4 16.8 - - - -
921A LEU* 3.4 39.0 - - + -
1003A LEU* 3.9 7.2 - - + -
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Residues in contact with HIS 862 (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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860A LEU 4.1 0.2 + - - -
861A TRP* 1.3 73.2 - - - +
863A GLY* 1.3 70.8 + - - +
864A SER* 4.1 12.8 + - - -
869A PHE* 4.7 0.7 - - - -
872A ILE* 4.9 0.6 - - - +
877A LEU* 3.6 40.2 - - + +
895A ILE* 4.6 6.0 - - + +
896A TYR* 2.8 26.2 + - + -
897A PHE* 3.9 15.3 - - + -
919A ILE* 3.7 4.2 - - - -
920A LEU* 2.8 50.6 + - + +
1101A 7U3 3.4 25.8 + + - -
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Residues in contact with GLY 863 (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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862A HIS* 1.3 78.2 + - - +
864A SER* 1.3 63.7 + - - -
904A SER* 3.4 20.9 - - - -
907A TYR* 3.5 8.2 - - - +
908A CYS* 4.4 2.7 - - - -
918A LEU 4.3 4.0 - - - -
919A ILE* 3.9 11.7 - - - -
1101A 7U3 2.8 32.9 + - - -
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Residues in contact with SER 864 (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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767A ASN* 4.9 0.2 + - - -
862A HIS* 4.2 7.8 + - - -
863A GLY* 1.3 77.0 - - - -
865A ARG* 1.3 64.4 + - - +
866A THR* 3.6 1.0 + - - -
868A ASN* 2.7 30.8 + - - +
869A PHE* 3.5 24.4 - - - -
872A ILE* 3.9 15.7 - - - +
907A TYR* 3.4 12.9 + - - -
908A CYS* 3.6 7.6 - - - +
918A LEU 3.5 13.0 + - - +
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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