Contacts of the strand formed by residues 817 - 824 (chain B) in PDB entry 1KT8
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 817 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674B PHE* 4.0 5.4 - - - -
774B LEU* 4.5 5.4 - - + -
809B PHE* 3.4 35.2 - - + -
810B GLY 3.5 2.0 - - - -
815B CYS* 4.2 2.0 - - - -
816B GLN* 1.3 90.0 - - + +
818B CYS* 1.3 59.2 + - - +
819B PRO* 3.6 5.6 - - - +
842B ILE* 3.8 24.9 - - + +
845B PHE* 4.0 19.3 - - + -
846B GLN* 3.1 44.9 + - + +
849B LEU* 4.2 11.9 - - + -
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Residues in contact with CYS 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B TYR* 4.3 7.6 - - - -
674B PHE* 4.4 5.4 - - - -
682B VAL* 4.0 33.0 - - - -
741B MET* 3.7 20.4 - - + +
809B PHE* 3.2 6.3 - - - -
810B GLY 2.7 35.3 + - - +
815B CYS* 3.2 28.3 - - - -
817B VAL* 1.3 71.9 - - - +
819B PRO* 1.3 71.9 - - - +
820B VAL* 3.8 3.1 - - - +
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Residues in contact with PRO 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B PHE* 4.0 9.0 - - + -
679B VAL* 3.3 31.6 - - + -
680B THR 4.1 6.5 - - - +
681B PRO* 3.1 9.3 - - + +
682B VAL* 2.9 26.3 + - - +
808B VAL 3.9 6.3 - - - +
809B PHE* 4.1 0.4 - - - -
817B VAL 3.6 7.6 - - - +
818B CYS* 1.3 87.1 - - + +
820B VAL* 1.3 59.7 + - - +
834B THR* 4.2 2.0 - - + -
835B MET* 3.8 26.9 - - - -
839B PRO* 4.7 0.4 - - + -
842B ILE* 3.9 25.1 - - + -
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Residues in contact with VAL 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B PRO* 4.2 0.9 - - - -
682B VAL* 3.5 20.4 - - + +
684B LEU* 3.8 28.9 - - + -
738B VAL* 5.5 3.1 - - + -
741B MET* 6.2 0.7 - - + -
743B ILE* 6.1 0.7 - - + -
808B VAL* 3.1 29.6 + - + +
809B PHE* 4.0 9.9 - - - -
810B GLY* 4.5 2.0 - - - +
818B CYS 3.8 9.4 - - - +
819B PRO* 1.3 80.0 - - - +
821B HIS* 1.3 64.1 + - - +
822B ARG 3.8 16.6 - - - +
823B ILE* 4.1 9.4 - - + -
832B ILE* 3.6 7.7 - - + +
834B THR* 2.7 28.8 + - - -
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Residues in contact with HIS 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681B PRO* 3.3 39.0 - - + +
682B VAL* 3.1 28.1 + - - -
683B SER* 3.7 10.1 - - - -
723B GLU* 4.3 4.3 - - - -
820B VAL* 1.3 74.2 - - - +
822B ARG* 1.3 77.3 + - + +
831B HIS* 3.6 17.3 + + + -
832B ILE* 2.6 41.6 + - - +
835B MET* 4.8 7.9 - - + -
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Residues in contact with ARG 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682B VAL 3.7 0.4 + - - -
683B SER* 3.3 24.4 + - - -
684B LEU 2.9 23.0 + - - -
720B ARG 5.3 0.6 + - - -
721B GLY* 2.8 28.9 + - - -
722B CYS* 4.2 15.0 - - - -
820B VAL* 3.7 4.1 - - - +
821B HIS* 1.3 103.4 + - + +
823B ILE* 1.3 71.9 + - - +
824B LEU* 4.4 5.3 - - - +
829B ASN* 2.7 47.6 + - - +
830B LEU 3.3 13.2 - - - +
831B HIS* 5.2 1.8 - - - +
832B ILE* 3.9 1.3 - - - +
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Residues in contact with ILE 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684B LEU* 3.3 15.5 - - + +
686B ALA* 3.8 26.7 - - + -
726B LEU* 4.3 16.6 - - + -
735B LEU* 5.4 1.3 - - + -
743B ILE* 6.0 0.7 - - + -
793B MET* 4.7 2.9 - - + -
796B LEU* 4.0 24.5 - - + -
808B VAL* 5.1 8.3 - - + -
820B VAL* 4.1 13.0 - - + -
822B ARG* 1.3 83.5 - - - +
824B LEU* 1.3 60.9 + - - +
825B TYR* 4.5 1.6 - - + +
830B LEU* 2.7 58.3 + - + +
832B ILE* 4.0 17.9 - - + -
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Residues in contact with LEU 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684B LEU 2.9 8.5 + - - -
685B LEU* 3.7 12.9 - - + +
686B ALA 2.9 28.0 + - - +
720B ARG* 3.7 49.4 - - + +
722B CYS* 3.8 21.5 - - - -
822B ARG* 4.3 2.6 - - - +
823B ILE* 1.3 70.5 - - - +
825B TYR* 1.3 58.2 + - - +
826B LYS 4.5 0.2 + - - -
827B ASP* 3.1 32.5 - - - +
828B ARG 3.0 18.2 - - - +
829B ASN* 3.7 22.7 - - - +
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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