Contacts of the strand formed by residues 879 - 884 (chain K) in PDB entry 6R8Y
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 LYS 879 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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821K LEU* 4.0 6.7 - - - +
875K GLU* 3.6 3.8 - - - +
876K PHE* 2.5 55.3 + - + +
877K ASN* 4.0 10.3 - - + +
878K GLY* 1.3 76.6 - - - +
880K LEU* 1.3 59.0 + - - +
890K LEU* 3.4 28.3 - - + +
891K TYR 3.3 14.8 - - - +
892K GLU* 4.8 11.7 - - + +
893K TRP* 5.5 0.9 - - - +
902K GLU* 3.9 20.9 + - + -
935K TYR* 3.5 32.9 + - - -
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Residues in contact with LEU 880 (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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817K VAL* 5.2 4.0 - - + -
819K CYS* 5.0 5.4 - - - -
821K LEU* 4.2 13.1 - - + +
830K ILE* 3.9 39.5 - - + -
848K ILE* 4.0 22.2 - - + -
873K MET* 4.1 25.4 - - + -
874K VAL 3.7 18.4 - - - +
875K GLU* 4.8 1.8 - - - +
879K LYS* 1.3 71.6 - - - +
881K LEU* 1.3 63.6 + - - +
882K ALA* 4.9 0.9 - - + -
889K ARG 3.7 1.2 - - - +
890K LEU* 3.5 3.6 - - - -
891K TYR* 2.8 47.8 + - + +
899K LEU* 4.4 13.9 - - + -
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Residues in contact with LEU 881 (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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873K MET* 3.2 3.3 - - - +
874K VAL* 2.6 61.2 + - + +
876K PHE* 4.2 11.2 - - + -
879K LYS 4.0 0.8 + - - -
880K LEU* 1.3 74.4 - - - +
882K ALA* 1.3 59.2 + - - +
888K VAL* 3.6 24.0 - - + -
889K ARG 3.4 21.3 - - - +
890K LEU* 3.8 19.7 - - + +
914K LEU* 4.3 6.1 - - + -
916K THR* 4.5 0.4 - - + -
921K ILE* 3.4 44.9 - - + -
942K PHE* 4.0 10.5 - - + -
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Residues in contact with ALA 882 (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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848K ILE* 4.1 22.7 - - + -
870K VAL* 4.2 4.7 - - + -
872K SER 3.2 13.0 - - - +
873K MET* 3.7 14.1 - - + +
880K LEU* 4.9 2.2 - - + -
881K LEU* 1.3 77.2 - - - +
883K SER* 1.3 63.4 + - - +
884K ILE* 3.8 5.9 + - + -
888K VAL* 3.7 0.3 - - - -
889K ARG* 2.8 37.5 + - - +
891K TYR* 4.6 4.9 - - + -
914K LEU* 4.1 3.8 - - - -
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Residues in contact with SER 883 (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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870K VAL* 3.3 5.5 - - - +
871K TYR* 2.9 27.9 + - - -
872K SER* 2.8 20.3 + - - +
882K ALA* 1.3 71.6 - - - +
884K ILE* 1.3 60.6 + - - +
887K THR 3.4 4.3 - - - -
888K VAL* 3.7 9.9 - - - +
911K ALA* 3.3 32.0 + - - +
914K LEU* 3.0 36.0 - - - +
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Residues in contact with ILE 884 (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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848K ILE* 4.8 0.9 - - + -
866K VAL* 4.3 9.4 - - + -
867K LYS 4.6 0.9 - - - +
868K GLY* 3.9 30.7 - - - +
869K ALA 3.4 6.5 - - - -
870K VAL* 3.8 20.9 - - + -
871K TYR* 4.8 1.6 - - - -
882K ALA* 4.3 9.0 - - + +
883K SER* 1.3 80.8 - - - +
885K ASN* 1.3 69.2 + - + +
886K SER 3.5 0.9 - - - -
887K THR* 2.6 40.6 + - - +
889K ARG* 3.4 52.9 - - + +
891K TYR* 4.1 17.3 - - + +
911K ALA* 5.0 0.9 - - - +
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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