Contacts of the helix formed by residues 871 - 882 (chain A) in PDB entry 1HKC
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 PHE 871 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A VAL* 4.0 24.5 - - + -
745A ILE* 4.5 3.1 - - + -
750A LEU* 5.4 0.9 - - + -
827A SER* 4.0 9.9 - - - -
830A ALA* 3.6 13.0 - - + -
831A ALA* 3.2 43.2 - - + +
834A CYS* 3.8 18.2 - - + -
864A LEU* 4.0 26.0 - - + +
865A TYR* 4.1 17.5 - + - -
868A HIS* 3.0 32.7 + + + +
869A PRO 3.9 0.8 - - - -
870A HIS* 1.3 75.6 - - - +
872A SER* 1.3 70.4 + - - +
874A ILE* 5.1 0.4 - - - -
875A MET* 2.9 43.1 + - + +
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Residues in contact with SER 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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865A TYR* 3.3 55.6 + - - -
868A HIS 5.0 3.1 + - - -
869A PRO 5.7 1.2 + - - -
870A HIS 5.3 0.2 - - - -
871A PHE* 1.3 79.0 - - - +
873A ARG* 1.3 61.6 + - - +
875A MET* 4.0 2.0 - - - -
876A HIS* 2.8 42.7 + - - -
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Residues in contact with ARG 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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793A ASP* 5.3 1.6 + - - -
869A PRO 3.9 9.7 + - - +
870A HIS* 3.1 57.2 + - - +
871A PHE 3.2 0.8 - - - -
872A SER* 1.3 80.2 + - - +
874A ILE* 1.3 72.6 + - - +
876A HIS* 3.0 10.6 + - - +
877A GLN* 2.8 52.5 + - + +
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Residues in contact with ILE 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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827A SER* 5.2 2.5 - - - +
828A ARG* 4.1 41.7 - - + +
831A ALA* 3.9 16.8 - - + -
832A GLN* 3.9 25.6 - - + +
868A HIS* 6.2 0.2 - - + -
870A HIS* 3.1 33.0 + - + +
871A PHE* 5.1 0.4 - - - -
873A ARG* 1.3 93.7 - - - +
875A MET* 1.3 57.2 + - - +
877A GLN* 3.4 17.8 + - - +
878A THR* 2.7 35.9 + - - +
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Residues in contact with MET 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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676A LEU* 3.5 28.3 - - + -
831A ALA* 3.6 26.4 - - + +
834A CYS* 4.2 10.8 - - + -
835A GLY* 4.2 3.9 - - - +
838A MET* 4.9 3.6 - - - -
865A TYR* 3.5 35.0 - - + -
871A PHE* 2.9 32.3 + - + +
872A SER* 3.4 7.2 - - - +
874A ILE* 1.3 79.0 - - - +
876A HIS* 1.3 63.8 + - + +
878A THR* 3.1 3.9 + - - -
879A VAL* 3.1 31.2 + - - +
890A PHE* 3.7 30.3 - - + -
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Residues in contact with HIS 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A TYR* 2.9 32.7 + - - -
872A SER* 2.8 33.1 + - - -
873A ARG* 3.4 7.7 - - - +
875A MET* 1.3 79.5 - - - +
877A GLN* 1.3 69.5 + - + +
878A THR 3.0 0.9 + - - -
879A VAL* 3.1 12.5 + - - +
880A LYS* 3.2 11.9 + - - +
890A PHE* 3.2 49.9 - + + -
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Residues in contact with GLN 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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873A ARG* 2.8 50.8 + - + +
874A ILE* 3.7 18.3 - - + +
876A HIS* 1.3 72.9 - - + +
878A THR* 1.3 62.7 + - - +
880A LYS* 3.1 23.3 - - - +
881A GLU* 3.2 20.7 + - - +
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Residues in contact with THR 878 (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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484A LEU* 4.1 14.6 - - + -
832A GLN* 3.8 40.5 + - - +
835A GLY* 4.1 5.8 - - - -
874A ILE* 2.7 19.6 + - - +
875A MET 3.3 8.7 - - - -
876A HIS 3.0 0.2 - - - -
877A GLN* 1.3 72.8 - - - +
879A VAL* 1.3 65.5 + - - +
880A LYS 3.0 2.5 + - - -
881A GLU* 3.2 10.4 + - + +
882A LEU* 3.2 44.7 + - + +
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Residues in contact with VAL 879 (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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835A GLY* 3.8 26.0 - - - +
838A MET* 4.1 9.2 - - + -
839A ALA* 4.2 20.0 - - - +
842A VAL* 4.6 5.8 - - + -
875A MET* 3.1 16.8 + - - +
876A HIS 3.1 5.3 + - - +
878A THR* 1.3 75.5 - - - +
880A LYS* 1.3 57.3 + - - +
883A SER* 3.0 29.0 + - - +
888A VAL* 3.7 31.9 - - + -
890A PHE* 3.9 24.9 - - + -
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Residues in contact with LYS 880 (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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876A HIS 3.2 9.8 + - - +
877A GLN* 3.1 15.3 - - - +
878A THR 3.0 0.4 - - - -
879A VAL* 1.3 79.8 - - - +
881A GLU* 1.3 65.0 + - + +
883A SER 3.4 18.8 - - - +
884A PRO* 3.5 10.0 - - + +
886A CYS 5.7 2.9 - - - +
888A VAL* 6.1 2.0 - - - -
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Residues in contact with GLU 881 (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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481A LYS* 3.9 44.5 + - - +
484A LEU* 5.8 3.8 - - - +
485A LEU* 5.4 0.2 - - - +
877A GLN* 3.2 21.2 + - - +
878A THR* 3.2 12.2 + - - +
880A LYS* 1.3 82.0 - - + +
882A LEU* 1.3 67.0 + - + +
884A PRO* 3.9 11.8 - - - +
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Residues in contact with LEU 882 (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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481A LYS* 4.2 14.6 - - + +
484A LEU* 3.8 27.4 - - + +
485A LEU* 3.4 33.7 - - + +
488A LYS* 2.6 31.2 + - + -
836A ALA* 3.4 37.5 - - + +
839A ALA* 3.9 13.0 - - + -
878A THR* 3.2 31.7 + - + +
881A GLU* 1.3 79.1 - - + +
883A SER* 1.3 54.6 + - - +
884A PRO* 3.6 6.2 - - - +
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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