Contacts of the strand formed by residues 841 - 844 (chain B) 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 VAL 841 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839B CYS* 3.0 20.0 - - - -
840B VAL* 1.3 91.6 - - + +
842B ILE* 1.3 63.1 + - - +
904B THR 3.3 2.5 - - - -
906B PHE* 3.9 27.8 - - + -
930B VAL* 4.3 21.3 - - + +
933B CYS* 4.3 13.7 - - - +
934B TYR* 4.0 33.7 - - + -
937B ARG* 5.4 1.3 - - - +
939B CYS* 6.0 0.2 - - - -
940B PRO 5.4 0.4 + - - -
941B ILE* 3.8 18.2 - - + -
942B ILE 3.3 11.3 + - - +
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Residues in contact with ILE 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B PHE* 3.7 31.0 - - + -
831B TRP* 4.6 6.7 - - + -
834B VAL* 4.6 6.3 - - + -
839B CYS* 4.7 3.8 - - - -
841B VAL* 1.3 76.2 - - - +
843B VAL* 1.3 65.7 + - - +
859B TYR* 3.7 25.4 - - + +
890B PHE* 5.7 0.9 - - + -
903B VAL* 4.0 24.0 - - + -
904B THR 2.8 7.6 + - - +
905B GLN* 4.0 17.0 - - + -
906B PHE* 2.8 34.0 + - - +
942B ILE* 3.4 15.9 - - + +
944B HIS* 3.7 18.4 - - + -
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Residues in contact with VAL 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B VAL* 4.5 1.8 - - + -
842B ILE* 1.3 77.4 - - - +
844B MET* 1.3 54.9 - - - +
845B LEU* 3.3 31.4 - - + -
906B PHE 3.5 2.7 - - - -
926B PHE* 4.1 13.0 - - + -
930B VAL* 3.7 31.2 - - + -
941B ILE* 3.6 22.7 - - + -
942B ILE 2.7 13.1 + - - +
943B VAL* 4.0 14.1 - - + -
944B HIS* 2.7 35.2 + - - +
955B TYR* 4.4 11.7 - - + +
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Residues in contact with MET 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B ILE 4.1 0.2 - - - -
843B VAL* 1.3 72.9 - - - +
845B LEU* 1.3 60.6 + - - +
846B THR* 3.6 16.2 - - + +
847B PRO 4.4 0.9 - - - +
848B LEU* 3.7 30.3 - - + -
856B CYS* 3.8 17.9 - - - -
860B TRP* 3.9 7.0 - - + -
905B GLN* 3.4 29.4 - - + +
906B PHE 2.9 10.6 + - - +
907B HIS* 3.3 37.6 - - + +
908B PHE* 2.8 33.1 + - - +
944B HIS* 3.2 29.2 - - + +
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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