Contacts of the strand formed by residues 941 - 944 (chain A) in PDB entry 2QEP
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 ILE 941 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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815A ALA 3.1 11.6 + - - +
816A TYR* 3.2 24.5 - - + +
817A ILE 2.9 21.0 + - - -
841A VAL* 3.6 15.0 - - + +
843A VAL* 3.8 19.7 - - + -
930A VAL* 4.4 9.0 - - + -
931A ASN* 4.3 13.9 - - - +
934A TYR* 3.6 48.0 - - + -
939A CYS 3.7 0.4 + - - -
940A PRO* 1.3 71.3 - - - +
942A ILE* 1.3 61.2 + - - +
943A VAL* 3.5 21.9 + - + -
955A TYR* 5.6 2.7 - - + -
959A ASP* 5.3 2.0 - - - +
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Residues in contact with ILE 942 (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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817A ILE* 3.4 22.0 - - + +
819A THR* 4.2 13.0 - - + -
830A PHE* 4.1 22.9 - - + -
833A MET* 4.0 28.3 - - + -
834A VAL* 3.7 26.9 - - + -
837A SER* 4.1 4.5 - - - +
839A CYS* 3.3 27.6 - - + -
841A VAL 3.2 8.7 + - - -
842A ILE* 3.3 13.4 - - + +
843A VAL 2.8 24.3 + - - -
940A PRO 3.7 1.3 + - - +
941A ILE* 1.3 72.0 - - - +
943A VAL* 1.3 61.4 + - - +
944A HIS* 5.1 0.7 - - - +
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Residues in contact with VAL 943 (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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816A TYR* 4.1 17.9 - - + -
817A ILE 2.9 11.3 + - - +
818A ALA* 3.3 7.2 - - - -
819A THR 3.1 22.5 + - - -
843A VAL* 3.4 17.5 - - + +
845A LEU* 4.3 13.2 - - + -
941A ILE* 3.8 23.8 - - + +
942A ILE* 1.3 73.0 - - - +
944A HIS* 1.3 64.2 + - - +
952A SER* 3.6 36.2 + - - +
955A TYR* 4.2 14.4 - - + -
956A VAL* 4.5 7.9 - - + -
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Residues in contact with HIS 944 (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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819A THR* 3.2 26.2 - - + +
820A GLN 3.6 8.5 - - - +
821A GLY* 4.0 3.8 - - - -
822A PRO* 4.4 1.8 - - + -
830A PHE* 4.5 6.4 - + - -
842A ILE* 3.9 10.0 - - + +
843A VAL 2.9 12.2 + - - +
844A MET* 3.1 38.8 - - + +
845A LEU* 3.0 25.6 + - - +
846A THR* 4.7 0.2 - - + -
856A CYS* 3.7 13.0 - - - -
859A TYR* 3.1 38.6 - + - -
942A ILE* 5.3 0.4 - - + +
943A VAL* 1.3 74.3 - - - +
945A CYS* 1.3 74.7 + - - +
952A SER* 3.2 8.4 + - - -
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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