Contacts of the helix formed by residues 882 - 887 (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 ASN 882 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678B PHE* 3.6 9.0 - - - -
687B GLY 3.1 22.0 - - - +
688B THR* 4.4 2.9 - - - -
881B VAL* 1.4 78.5 - - - +
883B ILE* 1.3 63.1 + - + +
884B GLN* 2.9 29.7 + - - +
885B GLU* 2.8 26.0 + - - +
886B TRP* 3.1 24.3 + - - +
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Residues in contact with ILE 883 (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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517B ILE* 3.4 39.7 - - + +
675B PHE* 3.7 26.2 - - + -
678B PHE* 3.4 34.6 - - + -
687B GLY* 4.2 4.2 + - - +
882B ASN* 1.3 79.3 + - + +
884B GLN* 1.3 69.0 + - + +
885B GLU 3.3 0.2 - - - -
887B LEU* 3.2 44.1 + - + +
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Residues in contact with GLN 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ILE* 3.4 22.5 - - + +
641B PRO* 3.3 37.7 - - - +
643B GLN* 3.0 33.6 + - - +
644B LEU* 3.6 12.4 - - - +
882B ASN* 2.9 13.4 + - - +
883B ILE* 1.3 82.9 - - + +
885B GLU* 1.3 60.3 + - + +
887B LEU 4.4 0.7 - - - -
888B GLN* 3.3 26.1 + - - +
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Residues in contact with GLU 885 (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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8B LEU* 3.0 35.0 - - + +
12B ARG* 2.9 44.9 + - - +
881B VAL* 3.3 11.3 - - + -
882B ASN* 2.8 44.8 + - - +
884B GLN* 1.3 80.2 - - + +
886B TRP* 1.3 62.8 + - - +
887B LEU 3.3 1.6 - - - -
888B GLN* 2.8 19.2 + - - +
889B LEU* 2.8 17.4 + - - +
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Residues in contact with TRP 886 (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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674B LEU* 3.0 36.1 + - + +
677B ILE* 3.8 26.5 - - + -
678B PHE* 3.2 31.2 - + + +
689B ILE* 3.8 20.9 - - + -
691B LEU* 4.0 17.7 - - + -
696B TRP* 3.6 31.2 - + - -
699B PHE* 4.3 22.4 - - + -
881B VAL* 3.8 13.0 - - + +
882B ASN 3.1 15.8 + - - +
883B ILE* 4.1 1.1 - - + +
885B GLU* 1.3 78.3 - - - +
887B LEU* 1.3 61.6 + - + +
889B LEU* 3.6 5.8 + - + +
890B THR* 2.5 49.8 + - + +
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Residues in contact with LEU 887 (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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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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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