Contacts of the helix formed by residues 887 - 892 (chain B) 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 LEU 887 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517B ILE* 4.0 14.1 - - + -
640B LEU* 4.3 8.5 - - + -
644B LEU* 3.5 22.8 - - + +
671B LEU* 4.4 11.9 - - + +
674B LEU* 3.7 32.8 - - + -
675B PHE* 4.1 16.6 - - + +
883B ILE* 3.2 42.5 + - + +
884B GLN 4.4 0.4 - - - +
885B GLU 3.3 0.4 - - - -
886B TRP* 1.3 78.6 - - + +
888B GLN* 1.3 57.9 + - - +
889B LEU 3.3 0.2 - - - -
890B THR* 3.8 0.4 - - - -
891B MET* 3.0 34.2 + - + +
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Residues in contact with GLN 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.2 30.8 - - + +
8B LEU* 3.4 36.5 - - + +
643B GLN* 3.7 35.1 + - - +
644B LEU* 4.3 15.9 - - + -
647B VAL* 4.5 14.8 - - + +
780B THR* 5.0 4.6 - - - +
884B GLN* 3.3 22.6 + - - +
885B GLU* 2.8 14.8 + - - +
887B LEU* 1.3 71.9 - - - +
889B LEU* 1.4 57.8 - - - +
890B THR 3.1 6.3 + - - -
892B TYR* 3.1 20.6 + - - +
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Residues in contact with LEU 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.0 28.2 - - + +
5B ALA* 3.7 27.4 - - + -
8B LEU* 4.6 5.2 - - + -
696B TRP* 4.0 37.8 - - + -
700B SER 4.7 6.1 - - - +
860B ARG* 5.8 0.2 + - - -
864B MET* 4.9 10.8 - - + +
867B ALA* 4.5 3.1 - - + -
871B LEU* 3.9 15.7 - - + -
879B ILE* 5.7 0.4 - - + -
881B VAL* 3.6 30.5 - - + -
885B GLU* 2.8 20.5 + - + +
886B TRP* 3.6 6.9 + - + +
887B LEU 3.3 0.2 - - - -
888B GLN* 1.4 77.5 - - - +
890B THR* 1.3 64.6 + - + +
892B TYR 4.6 1.3 - - - -
893B SER* 5.3 6.5 + - - -
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Residues in contact with THR 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B ARG* 2.7 15.7 + - - -
670B ARG* 3.3 10.9 + - - -
674B LEU* 2.9 40.6 - - + +
696B TRP* 5.1 3.1 - - + -
699B PHE 5.1 4.7 - - - +
700B SER* 4.9 11.4 - - - +
860B ARG* 5.5 1.2 + - - +
886B TRP* 2.5 47.8 + - + +
887B LEU* 3.9 1.9 - - - -
888B GLN 3.1 0.6 - - - -
889B LEU* 1.3 86.0 - - + +
891B MET* 1.3 67.5 + - - +
892B TYR 3.5 0.7 - - - -
893B SER* 4.3 2.9 - - - +
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Residues in contact with MET 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644B LEU* 4.5 8.5 - - + -
647B VAL* 4.2 16.4 - - + +
648B ILE* 4.0 14.6 - - + -
651B ARG* 2.9 54.2 + - - +
652B PHE* 3.2 34.5 - - + -
667B CYS* 3.7 16.4 - - - -
670B ARG* 3.9 15.7 - - - -
671B LEU* 4.4 22.4 - - + -
674B LEU* 4.4 6.7 - - + -
887B LEU* 3.0 25.8 + - + +
890B THR* 1.3 81.8 - - - +
892B TYR* 1.4 58.7 + - - +
893B SER 3.1 0.9 + - - -
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Residues in contact with TYR 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.7 31.6 - - + +
647B VAL* 3.6 26.2 - - + -
650B ALA* 4.4 19.7 - - + -
651B ARG* 4.5 6.3 - - + -
774B ALA* 4.0 20.9 - - + -
775B VAL* 3.9 12.6 + - - -
777B ASP* 2.9 39.6 - - + +
780B THR* 3.4 25.1 - - + -
781B THR 3.2 3.3 + - - -
782B GLY* 2.9 32.1 + - - -
888B GLN 3.1 18.4 + - - +
890B THR 3.5 1.8 - - - +
891B MET* 1.4 80.6 - - - +
893B SER* 1.3 67.3 + - - +
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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