Contacts of the helix formed by residues 885 - 895 (chain A) in PDB entry 6A69
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 VAL 885 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A GLU* 4.8 5.8 - - + +
158A ALA* 3.6 26.0 - - + -
159A ILE* 3.7 18.6 - - + -
162A SER* 4.3 19.2 + - - +
883A LYS* 3.3 2.3 - - + +
884A ALA* 1.3 76.0 - - + +
886A GLN* 1.3 62.0 + - - +
887A MET 3.1 1.3 - - - -
888A LEU* 2.9 23.0 + - - +
889A TRP* 3.0 10.7 + - + +
1030A PRO 4.7 6.1 - - - +
1031A PHE* 3.8 41.3 - - + -
1032A SER* 5.8 1.3 - - - +
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Residues in contact with GLN 886 (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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881A PRO 4.1 4.8 + - - -
882A LEU* 4.0 10.3 - - + +
883A LYS* 3.0 36.2 - - - +
885A VAL* 1.3 72.9 - - - +
887A MET* 1.3 59.8 + - - +
888A LEU 3.3 0.2 - - - -
889A TRP* 3.2 11.9 + - + +
890A VAL* 2.9 32.3 + - - +
972A TYR* 5.8 1.2 + - - +
976A PHE* 3.1 55.3 - - + +
1031A PHE* 4.0 8.5 + - + +
1032A SER* 2.9 32.9 + - - +
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Residues in contact with MET 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A THR* 3.3 45.8 - - + +
426A VAL* 4.9 10.5 - - + -
428A VAL* 5.5 1.7 - - + +
429A VAL* 3.6 25.5 - - + +
866A ALA* 4.9 9.9 - - - +
870A ALA* 4.9 11.0 - - + -
880A SER* 5.2 2.9 - - - +
882A LEU* 3.7 45.7 - - + +
883A LYS 3.1 15.2 + - - +
884A ALA* 4.4 1.1 - - - +
886A GLN* 1.3 77.2 - - - +
888A LEU* 1.3 57.7 + - - +
890A VAL* 3.2 9.9 + - - +
891A ASN* 2.9 24.1 + - - +
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Residues in contact with LEU 888 (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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114A LEU* 4.1 19.5 - - + -
159A ILE* 4.6 9.4 - - + +
162A SER* 4.3 22.2 - - - +
163A VAL* 4.0 26.7 - - + +
166A VAL* 5.0 15.7 - - + +
425A THR* 4.9 4.7 - - - +
428A VAL* 3.7 30.1 - - + -
884A ALA 3.7 17.3 - - - +
885A VAL* 2.9 9.8 + - - +
887A MET* 1.3 74.0 - - - +
889A TRP* 1.3 60.1 + - - +
891A ASN* 3.2 9.2 - - - +
892A LEU* 2.9 26.9 + - - +
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Residues in contact with TRP 889 (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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162A SER* 5.8 0.4 + - - -
885A VAL* 3.0 7.4 + - + +
886A GLN* 3.4 16.6 - - - +
887A MET 3.2 0.4 - - - -
888A LEU* 1.3 77.9 - - - +
890A VAL* 1.3 58.2 + - - +
892A LEU* 3.1 30.2 + - + +
893A ILE* 2.9 30.0 + - + +
897A LEU* 5.8 2.9 - - + -
976A PHE* 4.4 20.0 - + + -
980A VAL* 4.2 24.5 - - + +
1016A THR* 3.8 31.9 - - + -
1019A VAL* 3.6 31.9 - - + -
1020A GLN* 4.8 10.2 - - + +
1023A ILE* 5.9 9.4 - - + -
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Residues in contact with VAL 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A VAL* 5.1 8.7 - - + -
862A VAL* 4.0 24.5 - - + -
866A ALA* 5.3 3.4 - - + -
882A LEU* 5.3 3.1 - - + -
886A GLN 2.9 14.5 + - - +
887A MET* 3.2 12.5 + - - +
889A TRP* 1.3 73.3 - - + +
891A ASN* 1.3 64.9 + - - +
893A ILE* 3.2 13.3 - - + +
894A MET* 3.0 24.4 + - - +
976A PHE* 4.9 2.7 - - + -
979A PHE* 4.0 29.6 - - + -
980A VAL* 4.1 21.5 - - + -
983A GLN* 5.7 2.5 - - + -
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Residues in contact with ASN 891 (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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166A VAL* 4.9 11.8 - - + +
428A VAL* 3.2 32.3 + - + +
429A VAL* 4.8 3.2 - - + +
431A VAL 5.6 0.2 + - - -
433A GLU* 3.6 15.8 + - - +
887A MET 2.9 13.8 + - - +
888A LEU* 3.2 16.9 - - - +
890A VAL* 1.3 75.9 - - - +
892A LEU* 1.3 58.6 + - - +
894A MET* 3.2 19.9 + - + +
895A ASP* 3.0 50.2 + - - +
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Residues in contact with LEU 892 (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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165A CYS* 5.3 3.4 - - - -
166A VAL* 3.7 37.0 - - + +
169A VAL* 4.4 24.7 - - + -
888A LEU 2.9 15.4 + - - +
889A TRP* 3.1 31.8 + - + +
891A ASN* 1.3 77.2 - - - +
893A ILE* 1.3 59.6 + - - +
895A ASP 4.4 0.2 - - - -
896A THR* 4.5 14.8 - - + -
897A LEU* 3.2 46.8 + - + +
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Residues in contact with ILE 893 (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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858A PHE* 4.1 8.4 - - + -
862A VAL* 5.6 1.6 - - + -
889A TRP* 2.9 17.8 + - + +
890A VAL* 3.2 30.3 - - + +
891A ASN 3.2 0.4 - - - -
892A LEU* 1.3 79.1 - - - +
894A MET* 1.3 60.0 + - + +
897A LEU* 4.6 6.9 - - + -
898A ALA* 3.3 20.0 + - - +
980A VAL* 4.5 15.7 - - + +
983A GLN* 5.3 12.6 - - + -
984A LEU* 3.7 29.8 - - + +
987A GLU* 4.6 8.2 - - - +
1016A THR* 3.7 32.3 - - + +
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Residues in contact with MET 894 (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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428A VAL 4.6 0.9 - - - +
429A VAL* 3.3 49.1 - - + +
431A VAL 5.3 1.8 - - - +
432A PRO* 5.5 0.2 - - + -
855A PHE* 4.3 2.8 - - - -
858A PHE* 4.3 3.7 - - + -
859A GLN* 3.7 39.7 - - + +
862A VAL* 3.7 42.4 - - + -
863A ASN* 4.7 2.9 - - - -
890A VAL* 3.0 18.2 + - - +
891A ASN* 3.6 22.0 - - - +
893A ILE* 1.3 82.3 - - + +
895A ASP* 1.3 64.5 + - + +
898A ALA* 3.4 18.0 - - - +
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Residues in contact with ASP 895 (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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431A VAL 4.8 0.2 - - - +
432A PRO* 4.1 10.1 - - - +
433A GLU* 2.9 42.9 + - - +
434A GLY 3.9 19.7 + - - +
855A PHE* 4.6 7.0 - - - -
859A GLN* 5.1 4.1 + - - +
891A ASN* 3.0 31.0 + - - +
893A ILE 3.7 1.2 - - - -
894A MET* 1.3 84.5 - - + +
896A THR* 1.3 65.2 + - + +
898A ALA* 4.4 1.3 - - - +
899A SER* 3.5 17.0 + - - -
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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