Contacts of the strand formed by residues 882 - 887 (chain A) in PDB entry 2QFD
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 PHE 882 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A VAL 3.2 1.2 - - - +
878A LYS* 2.9 8.1 - - - +
879A TYR* 2.7 51.2 + + + +
880A LYS* 3.5 6.7 - - + -
881A THR* 1.3 96.6 - - - +
883A GLU* 1.3 63.2 + - - +
884A ILE* 3.7 20.1 + - + -
918A PHE* 3.8 27.6 - + + -
920A PRO* 4.1 33.9 - - + -
923A MET* 3.9 31.2 - - + -
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Residues in contact with GLU 883 (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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839A LYS* 5.9 0.7 + - - -
859A ARG* 3.0 47.1 + - - -
876A HIS* 3.3 22.4 + - + -
877A VAL 3.2 10.5 - - - +
878A LYS* 3.6 18.2 - - + +
881A THR 5.6 1.3 - - - +
882A PHE* 1.3 72.2 - - - +
884A ILE* 1.3 63.2 + - - +
885A PRO* 4.7 0.3 - - - +
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Residues in contact with ILE 884 (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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826A ILE* 3.2 34.8 - - + -
832A THR* 3.6 17.0 - - + +
834A LEU* 6.4 1.3 - - + -
876A HIS* 3.3 7.4 + - - -
877A VAL* 2.8 56.3 + - + +
879A TYR* 3.9 16.6 - - + -
882A PHE* 3.7 18.8 - - + +
883A GLU* 1.3 80.6 - - - +
885A PRO* 1.3 72.2 - - + +
886A VAL* 4.7 1.6 - - + -
918A PHE* 4.6 12.8 - - + -
923A MET 5.2 5.4 - - - +
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Residues in contact with PRO 885 (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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832A THR* 2.5 40.8 + - - +
833A VAL 3.9 16.8 - - - +
838A PHE* 3.8 31.4 - - + -
839A LYS* 6.5 0.4 - - - -
842A PHE* 4.1 9.9 - - + -
862A ILE* 4.2 10.3 - - + -
875A ILE 3.5 6.3 - - - +
876A HIS* 3.9 18.8 - - + +
883A GLU 4.7 0.7 - - - +
884A ILE* 1.3 89.9 - - + +
886A VAL* 1.3 61.9 + - - +
887A ILE* 4.2 1.3 - - + -
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Residues in contact with VAL 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A ILE* 5.0 2.5 - - + -
830A HIS* 4.3 33.2 - - + -
831A TYR 3.1 15.7 - - - +
832A THR* 4.5 6.5 - - - -
856A PHE* 4.9 5.4 - - + -
874A GLY* 3.3 3.3 - - - -
875A ILE* 2.9 53.7 + - + +
877A VAL* 4.3 22.0 - - + -
884A ILE* 4.7 5.6 - - + -
885A PRO* 1.3 79.8 - - - +
887A ILE* 1.3 65.1 + - - +
888A LYS* 5.4 0.3 - - - +
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Residues in contact with ILE 887 (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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808A LEU* 4.6 10.3 - - + -
818A CYS* 4.7 2.2 - - - -
823A VAL* 4.9 2.9 - - + -
831A TYR* 2.9 24.7 + - - +
833A VAL* 3.4 29.8 - - + -
838A PHE* 4.1 24.7 - - + -
862A ILE* 4.1 13.5 - - + -
873A TRP* 3.2 11.2 - - + +
885A PRO* 5.0 0.9 - - + -
886A VAL* 1.3 84.6 - - - +
888A LYS* 1.3 61.8 + - - +
892A PHE* 3.8 20.9 - - + -
908A TRP* 3.2 41.1 + - + -
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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