Contacts of the strand formed by residues 742 - 748 (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 ASN 742 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B THR 5.1 0.8 - - - +
737B GLU* 3.6 14.2 - - - +
738B VAL* 4.5 0.2 - - - -
741B MET* 1.3 75.7 - - - +
743B ILE* 1.3 60.9 + - - +
744B PHE* 4.4 2.6 - - + -
758B THR* 5.0 0.9 - - - +
759B PRO* 6.4 0.2 - - + -
765B ILE* 4.0 10.2 - - + +
766B LEU 3.0 16.7 + - - +
768B GLY* 3.2 34.8 - - - +
771B ARG* 3.5 28.8 - - + +
810B GLY* 3.0 6.8 - - - -
811B SER* 2.8 44.0 + - - +
900B ILP 3.5 12.3 - - - -
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Residues in contact with ILE 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B LEU* 5.2 3.8 - - + -
726B LEU* 3.4 28.9 - - + -
735B LEU* 3.7 26.2 - - + +
736B THR 3.4 28.6 + - - +
737B GLU* 4.1 2.4 - - - +
738B VAL* 4.2 13.0 - - + -
741B MET 3.9 0.2 + - - -
742B ASN* 1.3 75.5 - - - +
744B PHE* 1.3 68.2 + - - +
745B VAL* 5.0 3.1 - - + -
758B THR* 2.6 26.7 + - - -
759B PRO* 3.2 20.3 - - + +
791B ILE* 5.5 1.8 - - + -
808B VAL* 4.5 15.3 - - + -
809B PHE 3.5 8.7 - - - +
810B GLY* 4.4 0.7 - - - -
820B VAL* 6.1 0.2 - - + -
823B ILE* 6.0 0.7 - - + -
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Residues in contact with PHE 744 (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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742B ASN* 4.5 1.8 - - + -
743B ILE* 1.3 79.4 - - - +
745B VAL* 1.3 67.5 + - - +
746B TYR 4.3 0.2 - - - -
756B LEU* 3.8 27.4 - - + -
757B VAL 3.5 3.8 - - - -
758B THR* 3.7 18.8 - - - -
771B ARG* 3.6 39.0 - - + -
774B LEU* 4.0 11.4 - - + -
775B LEU* 3.6 25.6 - - + -
808B VAL* 3.4 6.4 - - - +
809B PHE* 2.8 68.9 + + + +
811B SER* 3.3 31.0 - - - -
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Residues in contact with VAL 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B LEU* 5.1 3.6 - - + -
743B ILE* 5.0 8.3 - - + -
744B PHE* 1.3 79.7 - - - +
746B TYR* 1.3 61.7 + - - +
747B TRP* 3.5 40.7 + - + -
755B GLU 3.6 1.7 - - - +
756B LEU* 3.4 4.6 - - - -
757B VAL* 2.8 50.6 + - + +
791B ILE* 3.9 24.7 - - + -
796B LEU* 4.8 9.6 - - + -
805B VAL* 4.8 3.6 - - + -
807B GLU 3.7 6.3 - - - +
808B VAL* 4.4 20.4 - - + -
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Residues in contact with TYR 746 (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* 1.3 71.3 - - - +
747B TRP* 1.3 62.4 + - - +
754B LEU* 3.6 38.2 - - + +
755B GLU 3.4 16.2 - - - -
756B LEU* 4.3 7.0 - - + +
784B PHE* 4.0 23.6 - + - -
805B VAL* 4.2 1.2 - - - +
806B ARG* 3.0 61.9 + - + +
807B GLU* 2.8 48.6 + - + +
809B PHE* 4.8 2.2 - - + -
840B GLU* 5.6 2.2 + - - -
841B LEU* 3.7 36.9 - - + +
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Residues in contact with TRP 747 (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* 3.5 20.2 - - + -
746B TYR* 1.3 78.6 - - - +
748B THR* 1.3 65.9 + - - +
749B HIS* 3.9 22.0 - + - +
750B GLU* 5.7 0.7 - - - -
754B LEU* 3.7 6.9 - - - +
755B GLU* 2.9 60.1 + - + +
757B VAL* 3.8 21.0 - - + +
789B ARG* 4.6 5.6 - - - -
791B ILE* 4.3 19.7 - - + -
795B GLN* 4.1 27.1 - - + -
796B LEU* 4.3 12.6 - - + -
799B ALA* 3.7 27.6 - - + -
804B ARG* 3.1 18.6 - - - +
805B VAL* 3.7 11.9 - - + -
806B ARG* 4.1 5.2 - - - +
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Residues in contact with THR 748 (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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747B TRP* 1.3 72.9 - - - +
749B HIS* 1.3 71.9 + - - +
752B GLY* 3.3 37.0 - - - +
753B VAL 3.7 4.5 - - - +
754B LEU* 4.3 11.2 - - + +
804B ARG* 2.8 50.5 + - + +
806B ARG* 5.5 3.6 + - - +
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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