Contacts of the strand formed by residues 920 - 925 (chain K) in PDB entry 6R92
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 920 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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876K PHE* 4.0 0.7 - - - -
916K THR* 3.7 4.5 - - - -
917K LYS* 3.1 36.5 + - + +
918K GLY* 5.4 0.9 - - - -
919K ASP* 1.3 88.5 - - + +
921K ILE* 1.3 65.5 + - - +
932K LEU* 4.4 18.6 - - + -
933K LEU 3.6 11.7 - - - +
934K ALA* 4.2 17.9 - - + -
945K ILE* 5.0 7.9 - - + -
959K ILE* 5.5 2.7 - - + -
962K ASP* 4.5 27.6 - - + +
965K PHE* 6.4 0.7 - - + -
979K LYS* 5.4 10.5 - - - -
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Residues in contact with ILE 921 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876K PHE* 3.8 24.7 - - + -
881K LEU* 3.6 32.8 - - + -
888K VAL* 5.3 0.4 - - + -
914K LEU* 4.4 3.1 - - + -
915K LYS 3.9 6.7 - - - +
916K THR* 4.6 1.3 - - + -
919K ASP 4.4 0.4 - - - +
920K PHE* 1.3 79.6 - - - +
922K LEU* 1.3 65.1 + - - +
923K VAL* 3.6 24.0 + - + -
931K LEU 3.5 2.8 - - - +
932K LEU* 3.5 6.4 - - - +
933K LEU* 2.9 46.5 + - + +
935K TYR* 4.7 4.5 - - + +
942K PHE* 3.4 38.4 - - + -
959K ILE* 5.2 0.2 - - - -
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Residues in contact with LEU 922 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914K LEU* 3.7 4.7 - - - +
915K LYS* 3.1 30.2 + - + +
921K ILE* 1.3 72.6 - - - +
923K VAL* 1.3 65.2 + - - +
924K GLY 4.1 0.3 + - - -
930K VAL* 4.0 24.2 - - + -
931K LEU 3.3 16.6 - - - +
932K LEU* 4.8 5.4 - - + +
957K VAL* 4.5 12.2 - - + +
958K GLU* 3.5 33.4 - - - +
959K ILE* 3.6 29.2 - - + +
965K PHE* 3.9 32.3 - - + -
966K LEU 4.5 3.4 - - - +
992K LEU* 5.5 0.9 - - + -
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Residues in contact with VAL 923 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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888K VAL* 4.3 6.3 - - + -
908K ASN* 4.1 13.2 - - - +
911K ALA* 3.9 24.5 - - + -
913K TYR 3.6 2.5 - - - +
914K LEU* 3.7 17.7 - - + -
921K ILE* 3.6 21.5 - - + +
922K LEU* 1.3 79.0 - - - +
924K GLY* 1.3 66.6 + - - +
925K ASP* 4.0 2.6 + - + +
928K ARG 5.1 0.3 - - - +
929K SER 3.4 1.0 - - - +
930K VAL* 3.3 5.7 - - - +
931K LEU* 2.9 46.7 + - + +
933K LEU* 4.0 21.3 - - + -
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Residues in contact with GLY 924 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911K ALA* 3.6 2.3 - - - -
912K LEU* 2.9 8.5 + - - -
913K TYR* 2.6 57.4 + - - +
922K LEU 4.1 0.6 + - - -
923K VAL* 1.3 74.4 - - - +
925K ASP* 1.3 60.3 + - - -
929K SER 3.2 7.6 - - - -
954K MET* 5.1 0.4 - - - -
957K VAL* 4.2 14.7 - - - +
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Residues in contact with ASP 925 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908K ASN* 3.7 9.9 - - - +
909K ILE* 3.1 20.6 + - - +
910K MET 2.6 34.9 + - - +
911K ALA* 3.6 2.3 + - - +
912K LEU* 4.7 3.4 - - - -
913K TYR* 4.5 1.4 - - - -
923K VAL* 4.0 2.4 + - + +
924K GLY* 1.3 74.7 - - - -
926K LEU* 1.3 69.6 + - - +
927K MET 2.8 10.7 + - - -
928K ARG* 2.8 52.4 + - + +
929K SER* 2.9 7.7 + - - +
954K MET* 3.7 21.1 - - - +
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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