Contacts of the strand formed by residues 925 - 930 (chain A) in PDB entry 6NFJ
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 925 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A PHE* 5.1 1.3 - - + -
522A PRO* 5.1 0.3 - - - +
525A PHE* 3.8 25.1 - - + -
873A LEU* 4.3 20.2 - - + -
885A ILE* 3.5 28.5 - - + +
887A ILE* 3.8 21.8 - - + -
914A VAL* 4.2 16.4 - - + +
918A TYR* 3.8 36.5 - - + +
923A VAL* 2.7 24.2 + - + +
924A ARG* 1.3 72.9 - - - +
926A LYS* 1.3 67.2 + - - +
927A GLY 3.7 16.2 - - - +
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Residues in contact with LYS 926 (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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522A PRO* 5.6 9.2 - - + -
524A ASP* 4.1 24.8 - - + +
525A PHE* 3.7 12.8 - - - -
526A SER* 2.8 28.1 + - - -
884A ASP* 4.8 12.3 - - + +
885A ILE 2.9 6.6 + - - +
886A TYR* 3.7 28.5 - - + +
918A TYR* 5.8 4.0 - - - -
924A ARG* 4.4 22.8 - - - +
925A ILE* 1.3 82.1 - - - +
927A GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 927 (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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525A PHE* 3.7 7.5 - - - -
526A SER* 3.2 17.3 - - - -
885A ILE 3.9 3.8 + - - -
886A TYR* 3.9 13.1 - - - -
887A ILE* 3.0 29.0 + - - +
925A ILE* 3.7 7.8 - - - +
926A LYS* 1.3 80.4 - - - +
928A TYR* 1.3 61.4 + - - +
929A TYR* 4.6 1.8 - - - -
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Residues in contact with TYR 928 (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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525A PHE* 3.8 20.4 - - + -
526A SER 2.9 6.9 + - - +
527A TRP* 3.9 4.7 - + + -
528A GLY 2.7 33.3 + - - +
869A VAL* 6.5 0.2 - - + -
887A ILE* 3.4 19.5 - - + -
890A SER* 3.3 35.3 + - - -
906A TYR* 4.7 2.9 - - - -
907A LEU* 4.0 22.7 + - + +
910A TYR* 4.4 17.4 - + + +
911A LEU* 3.6 35.8 - - + +
914A VAL* 4.8 16.8 - - + -
927A GLY* 1.3 73.2 - - - +
929A TYR* 1.3 57.7 + - - +
930A ALA* 4.3 10.3 - - - -
958A TYR* 3.5 21.9 + + - -
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Residues in contact with TYR 929 (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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526A SER* 4.9 3.6 - - - -
528A GLY* 3.2 10.5 - - - -
529A VAL 3.2 21.8 - - - -
530A THR* 3.2 14.4 - - - +
596A HIS* 3.2 42.5 - + + +
597A TYR 4.2 0.7 - - - -
598A ARG* 3.6 20.9 - - + -
638A MET* 3.2 29.9 - - + +
886A TYR* 4.1 23.4 - + - -
887A ILE 2.7 26.8 + - - +
888A THR* 3.3 21.3 - - + +
889A ALA* 3.4 2.8 - - - -
890A SER* 2.9 26.7 + - - +
928A TYR* 1.3 85.2 - - - +
930A ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 930 (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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528A GLY 3.0 9.5 + - - +
529A VAL* 4.4 9.2 - - + -
530A THR* 3.1 25.8 + - - -
890A SER 3.4 10.1 - - - +
907A LEU* 5.0 1.3 - - + -
928A TYR* 4.3 5.3 - - + -
929A TYR* 1.3 71.4 - - - +
931A PHE* 1.3 66.8 + - - +
932A LYS 3.6 0.7 - - - -
944A PHE* 3.6 32.8 - - + -
958A TYR* 4.1 22.5 + - + +
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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