Contacts of the helix formed by residues 882 - 892 (chain A) in PDB entry 1QXP
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 ASN 882 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A PHE* 3.4 3.6 - - - -
687A GLY 3.4 17.9 - - - +
688A THR* 4.5 7.6 - - + +
881A VAL* 1.4 71.3 - - - +
883A ILE* 1.4 57.8 + - + +
884A GLN* 3.0 16.7 - - + +
885A GLU* 2.9 53.3 + - - +
886A TRP* 2.7 35.2 + - - +
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Residues in contact with ILE 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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517A ILE* 3.4 39.7 - - + +
675A PHE* 3.6 36.6 - - + -
678A PHE* 3.0 39.2 - - + -
687A GLY 4.1 0.6 + - - -
882A ASN* 1.4 70.2 - - + +
884A GLN* 1.3 72.8 + - + +
886A TRP* 4.1 2.5 - - + -
887A LEU* 2.6 49.6 + - + +
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Residues in contact with GLN 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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517A ILE* 3.0 36.8 - - + +
641A PRO* 3.4 26.6 - - - +
643A GLN* 5.3 6.4 - - - +
644A LEU* 5.0 5.4 - - + -
882A ASN* 3.0 15.0 + - - +
883A ILE* 1.3 90.0 - - + +
885A GLU* 1.3 65.2 + - + +
886A TRP 3.0 0.5 + - - -
887A LEU* 3.0 7.0 + - - +
888A GLN* 3.1 30.8 + - - +
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Residues in contact with GLU 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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8A LEU* 3.9 26.8 - - + +
11A ASP* 6.0 0.7 - - - +
12A ARG* 3.1 43.5 + - - +
881A VAL* 2.6 40.2 - - + +
882A ASN* 2.9 33.6 + - - +
884A GLN* 1.3 74.5 - - + +
886A TRP* 1.3 58.7 + - - +
888A GLN* 3.6 12.4 - - - +
889A LEU* 3.0 36.8 + - - +
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Residues in contact with TRP 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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674A LEU* 3.1 44.2 + - + +
677A ILE* 4.1 31.2 - - + -
678A PHE* 3.5 32.9 - + + +
681A LEU* 5.4 1.3 - - + -
689A ILE* 4.8 5.6 - - + -
691A LEU* 3.9 31.0 - - + -
696A TRP* 4.1 11.7 - + - -
699A PHE* 4.7 17.0 - - + -
881A VAL* 4.1 8.3 - - + +
882A ASN 2.7 17.1 + - - +
883A ILE* 3.7 6.3 - - + +
885A GLU* 1.3 76.4 - - - +
887A LEU* 1.3 79.2 + - + +
889A LEU* 3.7 6.5 - - + +
890A THR* 2.9 51.7 + - + +
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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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517A ILE* 3.8 24.0 - - + -
640A LEU* 4.0 11.4 - - + -
644A LEU* 3.8 31.6 - - + -
671A LEU* 5.5 2.7 - - + +
674A LEU* 3.8 28.9 - - + -
675A PHE* 4.2 15.3 - - + +
883A ILE* 2.6 32.6 + - + +
884A GLN 3.0 4.0 + - - +
886A TRP* 1.3 81.6 - - + +
888A GLN* 1.3 65.1 + - - +
889A LEU 3.0 1.3 - - - -
891A MET* 2.8 42.1 + - + +
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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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4A ILE* 3.8 23.1 - - + +
8A LEU* 3.7 28.0 - - + +
643A GLN* 3.4 26.6 + - - +
644A LEU* 3.5 23.9 - - + +
647A VAL* 4.7 6.9 - - + +
884A GLN* 3.1 23.9 + - - +
885A GLU* 3.6 10.9 - - - +
887A LEU* 1.3 74.1 - - - +
889A LEU* 1.4 58.1 + - + +
891A MET* 4.3 0.2 - - - +
892A TYR* 3.0 35.5 + - - +
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Residues in contact with LEU 889 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.4 28.5 - - + -
5A ALA* 4.4 12.8 - - + -
8A LEU* 4.1 12.1 - - + -
696A TRP* 4.2 31.6 - - + -
867A ALA* 4.7 4.5 - - + -
871A LEU* 4.6 11.4 - - + -
879A ILE* 5.5 1.3 - - + -
881A VAL* 5.1 10.1 - - + -
885A GLU 3.0 23.0 + - - +
886A TRP* 3.7 9.2 - - + +
887A LEU 3.0 1.4 - - - -
888A GLN* 1.4 78.3 - - - +
890A THR* 1.3 75.4 + - + +
892A TYR 3.5 12.6 - - - +
893A SER* 3.8 3.1 + - - -
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Residues in contact with THR 890 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670A ARG* 4.1 7.0 + - - -
674A LEU* 3.0 35.0 - - + +
696A TRP* 4.7 9.0 - - + -
699A PHE 5.0 7.6 - - - +
700A SER* 6.1 1.1 - - - -
702A LEU* 6.1 2.8 - - - +
886A TRP* 2.9 55.5 + - + +
887A LEU* 3.5 2.1 + - - -
889A LEU* 1.3 80.8 - - + +
891A MET* 1.4 59.8 + - - +
893A SER* 2.5 25.5 + - - -
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Residues in contact with MET 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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640A LEU* 6.2 3.6 - - + -
644A LEU* 5.8 3.4 - - + -
647A VAL* 3.3 20.9 - - + -
648A ILE* 4.5 16.4 - - + -
651A ARG* 4.8 3.0 - - + +
652A PHE* 3.4 38.1 - - + -
667A CYS* 4.4 9.2 - - + +
670A ARG* 3.3 41.8 + - + +
671A LEU* 4.3 15.9 - - + -
674A LEU* 3.6 12.1 - - + -
887A LEU* 2.8 36.2 + - + +
890A THR* 1.4 80.9 + - - +
892A TYR* 1.2 60.3 + - - +
893A SER* 2.7 9.2 + - - +
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Residues in contact with TYR 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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3A GLY* 5.8 0.4 - - - -
4A ILE* 4.3 26.1 - - + +
647A VAL* 3.7 31.2 - - + -
650A ALA* 3.6 26.6 + - + +
651A ARG* 3.9 13.0 - - + -
774A ALA* 3.2 44.8 + - + +
775A VAL* 5.2 3.0 + - - +
777A ASP* 2.7 31.8 + - - -
780A THR* 4.8 8.3 - - + -
782A GLY* 3.9 14.9 + - - -
888A GLN 3.0 19.1 + - - +
889A LEU 3.5 6.8 - - - +
890A THR 3.1 0.4 - - - -
891A MET* 1.2 78.3 - - - +
893A SER* 1.3 64.4 + - - +
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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