Contacts of the strand formed by residues 865 - 877 (chain A) in PDB entry 4UHX
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 ILE 865 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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857A ALA* 4.7 4.9 - - + -
858A GLY 3.6 5.6 - - - +
859A PHE* 4.0 10.8 - - + -
863A GLY 3.7 5.8 - - - +
864A ARG* 1.3 67.9 - - - +
866A LEU* 1.3 59.5 + - - +
867A ALA 3.4 27.1 - - - +
868A LEU* 3.9 9.9 - - + -
900A PHE* 3.8 35.8 - - + -
901A PRO* 3.5 19.4 - - - +
935A CYS* 5.4 3.6 - - - -
936A ILE* 4.7 11.0 - - + -
939A VAL* 4.3 19.3 - - + -
950A VAL* 4.1 10.8 - - + -
954A ASN* 3.0 44.6 + - - +
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Residues in contact with LEU 866 (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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731A ALA* 3.6 3.0 - - + +
734A VAL 5.1 1.8 - - - +
735A VAL* 4.3 12.1 - - + -
858A GLY 3.3 3.4 + - - -
860A MET* 3.5 43.3 - - + -
864A ARG* 3.2 28.1 + - + +
865A ILE* 1.3 74.3 - - - +
867A ALA* 1.3 57.4 - - - +
901A PRO* 4.2 22.4 - - + -
902A ASN* 2.7 43.8 + - - +
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Residues in contact with ALA 867 (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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728A VAL* 4.1 8.3 - - + +
731A ALA* 3.5 25.1 - - + +
732A PHE* 4.0 26.0 - - + +
735A VAL* 4.8 0.4 - - + -
857A ALA* 3.5 0.5 - - - -
858A GLY* 2.8 38.1 + - - +
865A ILE* 3.4 7.2 - - - +
866A LEU* 1.3 79.5 - - - +
868A LEU* 1.3 61.4 + - - +
902A ASN 3.5 5.8 - - - -
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Residues in contact with LEU 868 (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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728A VAL* 3.7 6.5 - - - +
855A TYR* 4.2 13.2 - - + -
856A LYS 3.6 9.6 - - - +
857A ALA* 4.0 6.5 - - + -
865A ILE* 3.9 8.1 - - + -
867A ALA* 1.3 75.1 - - - +
869A ASP* 1.3 62.9 + - - +
870A MET* 4.2 18.6 - - + +
894A MET* 4.8 2.5 - - + -
900A PHE* 3.5 40.2 - - + -
902A ASN 3.1 8.0 + - - +
903A LEU* 3.4 27.5 - - + +
904A ARG 3.0 23.2 + - - -
932A THR* 5.3 2.0 - - + -
935A CYS* 3.8 28.7 - - + -
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Residues in contact with ASP 869 (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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728A VAL* 4.5 4.5 - - + -
732A PHE* 4.3 18.2 - - + -
855A TYR* 3.5 2.6 - - - -
856A LYS* 2.9 61.9 + - + +
868A LEU* 1.3 73.9 - - - +
870A MET* 1.3 62.5 + - - +
871A GLU* 5.3 5.4 - - - +
904A ARG* 2.9 60.4 + - - +
906A ARG* 5.2 1.4 + - - +
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Residues in contact with MET 870 (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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854A LYS 3.7 11.7 - - - +
855A TYR* 3.7 29.6 - - + +
868A LEU* 3.9 21.7 - - + -
869A ASP* 1.3 73.6 - - - +
871A GLU* 1.3 72.1 + - - +
872A HIS* 3.4 27.4 - - + +
894A MET* 4.1 7.0 - - - -
903A LEU* 4.9 0.7 - - + -
904A ARG 2.8 11.3 + - - +
905A CYS* 3.8 19.5 - - - -
906A ARG* 3.0 24.5 + - - +
931A ILE* 3.3 33.4 - - + +
932A THR* 4.3 11.9 - - + -
935A CYS* 4.8 1.3 - - + -
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Residues in contact with GLU 871 (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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852A LEU 3.9 0.3 - - - +
853A GLY* 3.4 4.3 - - - -
854A LYS* 2.7 54.8 + - + +
856A LYS* 4.6 17.6 + - - -
869A ASP* 5.1 6.0 - - - +
870A MET* 1.3 79.0 - - - +
872A HIS* 1.3 66.1 - - - +
873A TYR* 2.8 36.2 + - + -
904A ARG* 5.8 0.2 + - - -
906A ARG* 3.3 29.4 + - + +
908A TRP* 4.1 13.6 - - + -
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Residues in contact with HIS 872 (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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851A TYR* 3.8 25.8 + + + -
852A LEU 3.7 3.1 - - - -
853A GLY* 5.0 2.2 - - - -
870A MET* 3.4 22.5 - - + +
871A GLU* 1.3 74.4 - - - +
873A TYR* 1.3 70.4 + - - +
874A SER 4.3 0.2 - - - -
887A ILE* 4.6 4.9 + - + -
890A GLY* 4.0 6.9 - - - -
891A LEU* 3.4 26.5 - - + +
894A MET* 3.8 12.7 - - + +
905A CYS* 4.1 0.4 - - - -
906A ARG 2.8 13.7 + - - +
907A GLY* 3.4 7.6 - - - -
908A TRP* 3.2 23.9 + - - -
928A ALA* 3.8 26.5 - - + -
931A ILE* 3.3 28.9 - - + +
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Residues in contact with TYR 873 (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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707A ILE* 3.6 22.2 - - + +
711A ILE* 3.9 30.6 - - + +
718A LYS* 6.2 0.2 - - - -
851A TYR* 3.2 7.8 - - - -
852A LEU* 2.8 57.9 + - + +
854A LYS* 4.3 20.9 + - + +
871A GLU* 2.8 40.6 + - + -
872A HIS* 1.3 78.0 - - - +
874A SER* 1.3 60.5 + - - +
887A ILE* 4.7 0.4 - - - -
908A TRP* 3.4 41.6 - + + +
910A CYS* 4.1 12.1 - - - -
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Residues in contact with SER 874 (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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707A ILE* 4.4 1.8 - - - -
849A HIS* 4.1 12.4 - - - -
850A PRO 3.4 5.4 - - - -
851A TYR* 3.6 25.6 - - - -
873A TYR* 1.3 71.5 - - - +
875A ASN* 1.3 57.8 + - - +
883A SER* 4.0 10.7 + - - -
886A VAL* 5.7 0.7 - - - -
887A ILE* 3.6 14.5 - - - +
908A TRP 3.3 5.7 + - - -
909A ALA* 3.4 22.9 - - - +
910A CYS* 2.8 35.4 + - - +
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Residues in contact with ASN 875 (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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705A LEU 3.3 23.2 + - - -
706A THR* 4.6 1.0 - - - +
707A ILE* 3.8 21.8 - - + +
849A HIS* 3.4 10.3 - - - -
850A PRO* 2.7 39.4 + - + +
874A SER* 1.3 70.0 - - - +
876A ALA* 1.3 58.0 + - - +
877A GLY* 3.4 2.8 + - - -
910A CYS 3.8 2.2 - - - -
912A THR* 2.6 33.8 + - - +
914A LEU* 3.9 11.9 - - - +
917A ASN* 3.1 22.4 + - - -
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Residues in contact with ALA 876 (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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849A HIS* 4.0 3.4 - - - -
874A SER 3.5 1.8 + - - +
875A ASN* 1.3 72.5 - - - +
877A GLY* 1.3 62.0 + - - +
879A SER 3.2 24.4 - - - +
880A LEU* 5.0 2.9 - - + -
883A SER* 3.3 26.5 - - - +
909A ALA* 4.6 2.9 - - + -
910A CYS 2.8 28.7 + - - +
911A ARG* 4.4 2.0 - - - +
916A SER* 3.7 0.2 - - - -
917A ASN* 3.1 25.4 + - - +
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Residues in contact with GLY 877 (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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875A ASN* 3.4 8.2 + - - -
876A ALA* 1.3 82.0 - - - +
878A ALA* 1.3 64.9 + - - -
879A SER 3.3 1.0 + - - -
910A CYS 4.1 0.2 + - - -
911A ARG* 3.5 6.6 - - - +
912A THR* 3.0 35.2 + - - +
914A LEU* 3.3 15.3 - - - -
915A PRO 3.6 10.1 - - - -
916A SER* 4.0 0.2 - - - -
917A ASN* 4.5 1.3 - - - +
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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