Contacts of the strand formed by residues 805 - 811 (chain B) in PDB entry 1KTA
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 805 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745B VAL* 4.7 3.4 - - + -
746B TYR 4.1 6.7 - - - +
747B TRP* 3.7 10.3 - - + -
796B LEU* 4.0 9.4 - - + -
799B ALA* 3.6 26.4 + - + -
800B LEU* 3.6 36.8 - - + +
803B GLY* 3.5 5.3 - - - +
804B ARG* 1.3 77.3 - - - +
806B ARG* 1.3 64.1 + - - +
807B GLU 4.1 4.9 - - - +
808B VAL* 4.0 27.1 - - + -
832B ILE* 4.7 2.2 - - + -
833B PRO* 3.4 22.4 - - + +
837B ASN* 3.9 3.5 + - - -
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Residues in contact with ARG 806 (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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746B TYR* 2.8 50.7 + - + +
747B TRP* 4.8 1.6 - - - +
748B THR* 5.3 3.8 - - - -
754B LEU* 3.9 35.0 - - - +
803B GLY 6.1 0.2 - - - +
804B ARG 3.6 7.8 + - - +
805B VAL* 1.3 78.4 - - - +
807B GLU* 1.3 68.7 + - + +
833B PRO 3.5 0.7 - - - +
834B THR* 3.4 10.1 - - - -
837B ASN* 2.9 43.7 + - - +
840B GLU* 3.5 27.1 + - - +
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Residues in contact with GLU 807 (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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745B VAL* 4.3 0.2 - - - +
746B TYR* 2.8 52.5 + - + +
805B VAL* 3.9 1.5 - - - +
806B ARG* 1.3 88.2 + - + +
808B VAL* 1.3 66.6 + - - +
809B PHE* 4.4 4.9 - - + -
834B THR* 3.7 27.4 - - + +
837B ASN* 4.0 7.3 - - + +
839B PRO* 3.4 4.5 - - - +
840B GLU* 3.3 13.5 + - - +
841B LEU* 2.8 31.3 + - - +
842B ILE* 2.9 38.9 + - + +
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Residues in contact with VAL 808 (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* 5.7 0.7 - - + -
735B LEU* 6.1 0.4 - - + -
743B ILE* 4.4 19.7 - - + -
744B PHE 3.3 12.1 - - - +
745B VAL* 4.3 16.2 - - + -
796B LEU* 5.2 8.5 - - + -
805B VAL* 4.0 12.8 - - + -
807B GLU* 1.3 79.6 - - - +
809B PHE* 1.3 68.2 + - - +
819B PRO* 3.8 1.4 - - - +
820B VAL* 3.0 40.9 + - + -
823B ILE* 5.2 6.7 - - + -
832B ILE* 3.5 31.0 - - + -
834B THR* 3.2 9.9 + - - +
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Residues in contact with PHE 809 (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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743B ILE* 3.5 4.6 - - - +
744B PHE* 2.8 64.1 + + + +
746B TYR* 4.8 0.9 - - + -
756B LEU* 3.7 21.8 - - + -
774B LEU* 3.8 20.0 - - + -
807B GLU* 4.4 10.3 - - + -
808B VAL* 1.3 85.1 - - - +
810B GLY* 1.3 65.2 + - - +
817B VAL* 3.4 17.7 - - + -
818B CYS 3.1 22.4 - - - +
820B VAL* 4.1 5.8 - - - -
841B LEU* 4.6 8.5 - - + -
842B ILE* 3.6 26.7 - - + -
845B PHE* 3.9 14.8 - + - -
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Residues in contact with GLY 810 (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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738B VAL* 4.0 12.6 - - - -
741B MET* 3.9 20.4 - - - +
742B ASN 3.0 11.2 - - - -
809B PHE* 1.3 79.0 - - - +
811B SER* 1.3 59.5 + - - -
817B VAL* 3.5 3.3 - - - -
818B CYS* 2.8 34.2 + - - +
820B VAL* 4.4 3.4 - - - +
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Residues in contact with SER 811 (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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741B MET* 3.3 7.5 - - - +
742B ASN* 2.8 35.1 + - - +
744B PHE* 3.3 30.7 - - - -
770B VAL* 3.9 7.6 - - - -
771B ARG* 3.6 10.0 + - - +
774B LEU* 3.9 14.4 - - - -
810B GLY* 1.3 74.2 - - - -
812B GLY* 1.3 58.3 - - - +
815B CYS 4.1 0.2 - - - -
816B GLN 3.1 13.9 - - - -
900B PMP 3.8 4.4 - - - +
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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