Contacts of the helix formed by residues 879 - 893 (chain A) in PDB entry 4RIB
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 879 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A ILE* 3.4 31.2 + - - -
850A ILE 3.7 13.7 + - - -
852A MET* 3.9 22.7 + - + +
855A ILE* 3.7 28.6 - - + +
858A VAL* 4.3 5.5 - - - +
867A PRO* 3.9 10.7 - - - +
869A ASP* 3.0 37.0 + - - -
875A PHE* 3.1 43.3 + - - +
876A PHE 2.9 3.5 + - - -
877A THR 3.0 0.4 + - - -
878A SER* 1.3 87.6 - - - +
880A ARG* 1.3 71.4 + - - +
881A PRO* 3.1 8.5 - - - -
882A ALA* 3.3 4.3 + - - +
883A LEU* 3.2 32.5 + - + +
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Residues in contact with ARG 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 PHE* 2.8 38.2 + - + +
877A THR* 3.6 30.7 + - - +
879A ARG* 1.3 75.7 - - - +
881A PRO* 1.3 75.6 - - + +
883A LEU* 4.7 0.9 - - - -
884A GLU* 2.9 49.7 + - + +
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Residues in contact with PRO 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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877A THR 5.1 1.6 - - - +
878A SER 5.5 0.4 - - - -
879A ARG* 3.3 7.0 - - - +
880A ARG* 1.3 100.7 - - + +
882A ALA* 1.3 63.7 + - - +
883A LEU 3.1 0.5 + - - -
884A GLU* 3.8 4.0 - - + +
885A ALA* 3.2 19.3 + - - +
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Residues in contact with ALA 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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849A ILE* 3.3 20.1 - - + +
852A MET* 3.4 32.5 - - + -
879A ARG* 3.3 6.6 + - - +
881A PRO* 1.3 79.1 - - + +
883A LEU* 1.3 56.5 + - - +
885A ALA* 3.4 8.1 - - - +
886A ARG* 3.2 18.5 + - - +
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Residues in contact with LEU 883 (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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846A LEU* 3.5 32.8 - - + -
849A ILE* 3.7 20.4 - - + -
875A PHE* 4.3 13.2 - - + +
876A PHE* 3.5 46.0 - - + +
879A ARG* 3.2 33.7 + - + +
880A ARG 3.9 1.6 - - - +
881A PRO 3.1 1.2 - - - -
882A ALA* 1.3 74.3 - - - +
884A GLU* 1.3 68.8 + - - +
885A ALA 2.9 1.1 - - - -
886A ARG* 2.9 2.9 + - - +
887A LEU* 2.8 33.4 + - + +
948A ALA* 4.5 11.0 - - + -
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Residues in contact with GLU 884 (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 PHE* 4.1 8.7 - - + -
880A ARG* 2.9 53.9 + - + +
881A PRO* 3.8 4.0 - - + +
883A LEU* 1.3 71.8 - - - +
885A ALA* 1.3 64.2 + - - +
887A LEU* 4.2 3.9 - - - +
888A GLN* 3.3 20.8 + - - +
945A ARG* 3.2 35.3 + - - +
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Residues in contact with ALA 885 (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 3.2 11.1 + - - +
882A ALA* 3.4 14.6 - - - +
883A LEU 2.9 0.6 + - - -
884A GLU* 1.3 82.0 - - - +
886A ARG* 1.3 64.8 + - - +
888A GLN* 3.0 13.1 + - - +
889A LEU* 3.1 14.5 + - - +
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Residues in contact with ARG 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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845A LEU 3.3 23.0 + - - +
846A LEU* 4.1 8.9 - - + +
848A ASP* 3.0 42.0 + - - -
849A ILE* 3.6 38.5 - - + +
882A ALA 3.2 2.1 + - - +
883A LEU* 2.9 7.0 + - - +
885A ALA* 1.3 76.5 - - - +
887A LEU* 1.3 60.7 + - - +
889A LEU* 3.5 22.9 + - - +
890A ILE* 3.2 40.7 + - + +
901A TRP* 5.7 5.2 - - - -
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Residues in contact with LEU 887 (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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846A LEU* 4.8 16.4 - - + -
876A PHE* 4.3 16.4 - - + -
883A LEU* 2.8 25.7 + - + +
884A GLU 4.2 1.3 - - - +
886A ARG* 1.3 70.9 - - + +
888A GLN* 1.3 64.5 + - - +
890A ILE* 3.3 4.9 + - + +
891A HIS* 3.0 10.2 + - - +
941A SER* 2.6 33.5 + - - +
944A CYS* 3.7 31.0 - - + -
945A ARG* 3.4 60.3 - - + +
948A ALA* 5.6 1.8 - - + -
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Residues in contact with GLN 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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884A GLU 3.3 12.4 + - - +
885A ALA* 3.0 11.8 + - - +
887A LEU* 1.3 77.3 - - - +
889A LEU* 1.3 57.9 + - - +
891A HIS* 2.9 33.4 + - - +
892A ASP* 3.2 38.3 + - - +
945A ARG* 5.3 1.2 - - - +
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Residues in contact with LEU 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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885A ALA 3.1 11.9 + - - +
886A ARG* 3.8 24.9 - - - +
887A LEU 3.4 0.2 - - - -
888A GLN* 1.3 79.4 - - - +
890A ILE* 1.3 56.7 + - - +
892A ASP* 4.1 6.1 - - - +
893A ALA* 3.3 15.6 + - - +
901A TRP* 3.2 38.9 - - + +
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Residues in contact with ILE 890 (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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845A LEU* 4.1 28.5 - - + +
846A LEU* 4.4 7.6 - - + -
886A ARG* 3.2 36.3 + - + +
887A LEU* 3.7 9.0 - - + +
888A GLN 3.1 0.6 - - - -
889A LEU* 1.3 72.6 - - - +
891A HIS* 1.3 65.1 + - - +
892A ASP 2.9 5.9 + - - -
893A ALA* 3.1 9.5 + - - +
898A LEU* 4.3 7.9 - - + -
901A TRP* 3.8 24.5 - - + -
937A GLY* 3.0 25.8 - - - +
940A LEU* 4.1 10.5 - - + -
941A SER* 3.6 26.0 - - - +
944A CYS* 5.0 6.1 - - - -
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Residues in contact with HIS 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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887A LEU 3.0 6.5 + - - +
888A GLN* 2.9 24.2 + - - +
890A ILE* 1.3 76.3 - - - +
892A ASP* 1.3 74.5 + - - +
937A GLY* 3.8 3.6 - - - -
938A PRO* 3.3 58.1 - - + +
941A SER* 3.5 19.9 - - - +
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Residues in contact with ASP 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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888A GLN* 3.2 31.9 + - - +
889A LEU* 4.5 5.0 - - - +
890A ILE 3.0 0.6 - - - -
891A HIS* 1.3 98.5 + - - +
893A ALA* 1.3 66.5 + - - +
894A PRO* 3.5 4.7 - - - +
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Residues in contact with ALA 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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889A LEU 3.3 19.2 + - - +
890A ILE 3.1 11.4 + - - +
891A HIS 5.2 0.2 - - - +
892A ASP* 1.3 79.7 - - - +
894A PRO* 1.3 69.5 - - - +
895A GLU 3.9 0.5 + - - -
897A SER* 3.8 8.7 - - - -
898A LEU* 3.8 13.8 - - + +
901A TRP* 3.5 26.5 - - + -
937A GLY* 4.7 8.8 + - - -
938A PRO* 5.7 0.9 - - - +
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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