Contacts of the helix formed by residues 693 - 700 (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 LEU 693 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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692A ASP* 1.4 74.2 + - - +
694A ILE* 1.3 75.3 + - + +
696A TRP* 3.0 1.9 + - - +
697A LEU* 2.9 38.1 + - + +
865A PHE* 6.0 2.9 - - + -
868A PHE* 3.0 37.9 - - + -
877A GLY 3.4 5.6 + - - +
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Residues in contact with ILE 694 (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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692A ASP* 2.3 26.5 + - + +
693A LEU* 1.3 83.5 - - + +
695A SER* 1.3 62.3 + - - +
697A LEU* 3.4 18.5 - - + +
698A SER* 3.7 4.7 + - - -
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Residues in contact with SER 695 (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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681A LEU* 6.5 0.7 - - - -
690A GLN 5.6 0.4 - - - -
691A LEU* 3.4 16.1 - - - -
692A ASP* 2.5 56.8 + - - -
694A ILE* 1.3 67.5 - - - +
696A TRP* 1.4 54.6 + - - +
697A LEU 2.4 15.4 + - - -
698A SER* 2.5 23.0 + - - -
699A PHE* 3.1 13.6 + - - -
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Residues in contact with TRP 696 (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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691A LEU* 3.8 30.4 - - + +
692A ASP 2.9 10.5 + - - +
693A LEU 3.3 7.9 - - - +
695A SER* 1.4 77.6 + - - +
697A LEU* 1.2 70.6 + - + +
698A SER 3.3 0.3 + - - -
699A PHE* 4.6 1.8 - - + +
700A SER* 2.9 46.1 + - - -
864A MET* 2.9 37.3 + - + +
867A ALA* 4.3 11.5 - - + +
868A PHE* 3.4 27.0 - + + +
871A LEU* 6.1 0.4 - - + -
879A ILE* 4.5 11.2 - - + -
886A TRP* 4.1 24.5 - + - -
889A LEU* 4.2 39.3 - - + -
890A THR* 4.7 7.2 - - + -
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Residues in contact with LEU 697 (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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693A LEU* 3.1 25.6 - - + +
694A ILE* 3.4 16.4 - - + +
695A SER 2.4 4.6 + - - -
696A TRP* 1.2 86.7 - - + +
698A SER* 1.3 59.6 + - - +
700A SER* 3.1 17.0 + - - +
701A VAL* 4.0 6.2 - - - +
833A HIS* 5.7 10.3 - - + -
861A LEU* 4.9 14.9 - - + +
864A MET* 4.8 13.0 - - + +
865A PHE* 3.8 45.1 - - + -
868A PHE* 6.1 1.3 - - + -
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Residues in contact with SER 698 (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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694A ILE 3.7 4.6 + - - -
695A SER* 2.5 14.2 + - - -
697A LEU* 1.3 72.5 - - - +
699A PHE* 1.4 52.5 + - - -
700A SER 2.4 5.8 + - - -
701A VAL* 1.8 53.9 + - - +
702A LEU 3.2 8.4 + - - -
833A HIS* 6.3 1.9 - - - -
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Residues in contact with PHE 699 (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* 5.5 3.6 - - - +
677A ILE* 5.2 13.0 - - + +
681A LEU* 5.9 4.5 - - + -
691A LEU* 4.5 20.2 - - + -
695A SER* 3.1 14.1 + - - +
696A TRP* 4.5 4.7 - - + +
698A SER* 1.4 73.5 - - - +
700A SER* 1.3 54.6 - - - +
701A VAL 3.0 3.1 + - - -
702A LEU* 3.9 21.6 + - - +
886A TRP* 4.7 20.7 - - + -
890A THR* 5.0 6.6 - - - +
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Residues in contact with SER 700 (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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696A TRP* 2.9 51.9 + - - -
697A LEU 3.1 7.8 + - - +
698A SER 2.4 3.7 + - - -
699A PHE* 1.3 74.0 - - - +
701A VAL* 1.3 63.2 + - - +
702A LEU* 5.8 1.3 - - - -
860A ARG* 4.3 13.0 + - - +
864A MET* 3.6 21.4 - - - +
890A THR* 6.1 1.3 - - - -
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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