Contacts of the helix formed by residues 876 - 888 (chain A) in PDB entry 3QER
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 876 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741A VAL* 4.2 10.1 - - + -
744A ALA* 3.7 25.4 - - + -
745A LEU* 3.7 34.1 - - + +
748A CYS* 3.8 19.7 - - - -
764A PHE* 3.5 35.0 - + - -
767A PHE* 3.5 35.4 - + + -
768A GLU* 5.5 0.7 - - - -
771A PHE* 5.3 0.2 - - + -
872A LEU* 3.0 33.5 + - + +
875A THR* 1.3 82.9 + - - +
877A ILE* 1.3 68.5 + - + +
878A LYS 3.5 1.1 - - - -
879A PRO* 3.4 1.8 - - - +
880A LEU* 3.1 29.8 + - + +
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Residues in contact with ILE 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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764A PHE* 4.1 23.3 - - + -
768A GLU* 4.3 10.5 - - - +
872A LEU* 2.9 43.2 + - + +
873A GLU* 3.7 40.2 - - + +
876A PHE* 1.3 75.7 - - + +
878A LYS* 1.3 59.5 + - - +
880A LEU* 3.2 5.2 + - - +
881A GLU* 2.8 30.9 + - + +
891A TYR* 3.7 24.5 - - + +
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Residues in contact with LYS 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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873A GLU* 2.8 40.2 + - - +
874A LYS* 4.1 20.0 - - - +
877A ILE* 1.3 76.0 - - - +
879A PRO* 1.4 67.6 - - + +
881A GLU* 3.4 10.1 + - + +
882A GLY* 3.2 16.3 + - - -
11T A 4.3 24.5 - - - +
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Residues in contact with PRO 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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707A ARG* 5.2 1.1 + - - +
731A GLU* 3.8 39.3 - - + +
745A LEU* 4.1 11.7 - - + -
874A LYS 3.5 15.5 - - - +
875A THR* 3.3 20.0 - - - +
876A PHE 3.4 11.0 - - - +
878A LYS* 1.4 92.9 - - + +
880A LEU* 1.3 61.4 + - - +
882A GLY* 3.0 12.6 + - - -
883A PHE* 3.0 23.8 + - + -
11T A 4.7 6.7 - - - +
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Residues in contact with LEU 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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745A LEU* 4.0 6.9 - - + +
748A CYS* 3.8 30.5 - - + -
752A MET* 4.7 2.9 - - - -
760A LEU* 4.3 4.7 - - + -
764A PHE* 3.5 34.5 - - + -
876A PHE* 3.1 30.7 + - + +
877A ILE 3.7 3.6 - - - +
879A PRO* 1.3 77.3 - - - +
881A GLU* 1.3 62.6 + - - +
883A PHE* 3.1 19.1 + - + +
884A THR* 3.0 37.5 + - + +
891A TYR* 3.7 22.4 - - + -
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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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877A ILE* 2.8 22.4 + - + +
878A LYS* 3.5 11.9 - - + +
880A LEU* 1.3 73.6 - - - +
882A GLY* 1.3 57.6 + - - +
884A THR* 3.7 6.3 + - - -
885A SER* 2.9 47.8 + - - +
891A TYR* 3.6 27.2 + - + +
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Residues in contact with GLY 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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703A THR* 3.8 7.3 - - - +
707A ARG* 5.9 1.8 - - - -
878A LYS 3.2 9.1 + - - -
879A PRO* 3.0 9.1 + - - -
881A GLU* 1.3 75.0 - - - +
883A PHE* 1.3 66.9 + - - +
885A SER* 3.3 6.3 + - - -
886A ALA* 3.3 24.6 + - - +
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Residues in contact with PHE 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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701A PHE* 3.7 24.6 - + + -
703A THR* 4.2 4.0 - - + -
707A ARG* 3.5 26.7 - - - -
730A LEU* 3.9 27.6 - - + -
731A GLU* 3.5 16.8 - - - -
732A THR 5.3 0.7 - - - -
745A LEU* 3.9 26.5 - - + -
749A ILE* 3.8 30.5 - - + -
752A MET* 4.0 11.0 - - + +
879A PRO* 3.0 18.9 + - + -
880A LEU* 3.1 20.2 + - + +
882A GLY* 1.3 77.6 - - - +
884A THR* 1.3 59.3 + - - +
886A ALA* 3.5 3.3 + - - +
887A ALA* 3.0 29.3 + - - +
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Residues in contact with THR 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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752A MET* 4.2 12.3 - - + -
760A LEU* 3.8 29.2 - - + -
880A LEU* 3.0 33.9 + - + +
881A GLU* 3.4 7.4 + - - -
883A PHE* 1.3 74.7 - - - +
885A SER* 1.3 62.4 + - - +
887A ALA* 3.2 1.1 + - - +
888A LYS 2.8 25.1 + - - -
889A LEU* 2.9 30.7 + - + -
891A TYR* 3.6 20.2 + - + -
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Residues in contact with SER 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 GLU* 2.9 38.7 + - - +
882A GLY* 3.3 8.7 + - - -
884A THR* 1.3 78.4 + - - +
886A ALA* 1.3 65.2 + - - +
888A LYS* 3.3 19.3 + - - +
889A LEU 4.7 2.0 - - - -
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Residues in contact with ALA 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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401A PRO* 3.8 13.8 - - + +
402A ASN* 3.1 25.7 + - - -
701A PHE* 4.8 1.8 - - + -
702A TRP 3.5 22.4 - - - +
703A THR* 3.7 17.9 - - + -
882A GLY 3.3 15.6 + - - +
883A PHE 3.6 4.0 - - - +
885A SER* 1.3 85.0 + - - +
887A ALA* 1.3 59.8 + - - +
888A LYS* 3.3 5.9 + - - +
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Residues in contact with ALA 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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402A ASN 4.3 0.4 - - - -
403A ARG* 2.8 42.8 + - - +
698A ILE* 3.7 13.2 - - + -
701A PHE* 4.0 7.9 - - + -
752A MET* 3.7 13.2 - - + -
883A PHE 3.0 18.4 + - - +
884A THR 3.2 2.2 + - - +
886A ALA* 1.3 74.7 - - - +
888A LYS* 1.3 62.9 + - - +
889A LEU* 3.3 19.3 - - + -
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Residues in contact with LYS 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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401A PRO 4.3 11.7 + - - -
402A ASN* 3.7 26.9 - - - +
403A ARG* 3.0 19.2 + - + +
757A GLU* 5.0 0.5 - - - +
884A THR 2.8 7.2 + - - -
885A SER* 3.3 13.1 + - - +
886A ALA 3.2 5.7 + - - +
887A ALA* 1.3 82.5 - - - +
889A LEU* 1.3 55.5 + - - +
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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