Contacts of the strand formed by residues 762 - 770 (chain A) in PDB entry 3NKO
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 HIS 762 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A GLN 4.7 11.2 + - - -
427A HIS* 6.1 0.4 - - - -
428A LEU 5.5 0.8 + - - -
430A LYS* 3.5 36.3 - - + +
733A ILE* 2.8 40.5 + - + +
735A ASP* 5.1 2.5 - - + -
760A PRO* 3.3 8.9 - - - +
761A THR* 1.3 113.2 + - - +
763A TYR* 1.3 65.3 + - - +
790A ILE* 3.6 34.3 - - + -
791A LEU 3.0 8.3 - - - +
792A PRO* 3.5 30.2 - - + +
793A HIS* 4.0 2.0 - - - +
818A HIS* 6.0 0.4 - - - -
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Residues in contact with TYR 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A LEU* 4.3 9.4 - - + -
698A VAL* 3.4 35.3 - - + +
699A PRO* 2.6 29.9 + - - +
700A MET* 4.0 11.4 - - + -
704A PHE* 3.6 31.6 - + + -
708A TRP* 4.4 13.2 - - + -
731A GLY 3.3 15.9 - - - +
732A PRO* 3.8 9.9 - - + -
733A ILE* 5.1 0.4 - - - -
760A PRO* 3.2 28.9 - - + +
762A HIS* 1.3 77.0 - - - +
764A TYR* 1.3 61.4 + - - +
790A ILE* 4.6 1.3 - - - -
791A LEU* 2.9 35.6 + - - +
793A HIS* 4.0 18.8 - + + -
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Residues in contact with TYR 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU 2.8 24.2 + - - -
626A TRP* 3.2 18.9 - - - +
708A TRP* 4.4 4.9 - - - -
729A ILE* 3.6 26.4 - - + +
730A SER* 3.2 6.8 - - - -
731A GLY* 2.8 65.4 + - - +
732A PRO 3.8 6.3 - - - -
733A ILE* 3.8 29.8 - - + -
763A TYR* 1.3 74.5 - - - +
765A SER* 1.3 66.7 + - - +
766A ILE* 4.2 7.9 - - + -
789A PHE 3.2 12.8 - - - +
790A ILE* 4.5 0.9 - - + +
791A LEU* 6.3 0.7 - - - -
825A ILE* 3.7 27.6 - - + -
829A THR* 3.9 10.1 - - + -
831A LEU* 3.7 6.3 - - + +
833A PHE* 4.3 7.6 - + - -
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Residues in contact with SER 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A TRP* 4.7 3.8 - - - -
711A PHE* 3.3 31.5 - - - -
728A VAL* 3.4 10.7 - - - +
729A ILE 3.3 5.6 - - - -
730A SER* 2.9 18.4 + - - -
764A TYR* 1.3 77.7 - - - +
766A ILE* 1.3 65.0 + - - +
767A ILE* 3.9 7.0 - - - +
788A SER* 3.2 5.9 - - - -
789A PHE* 3.0 37.3 + - - +
791A LEU* 6.2 0.9 - - - +
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Residues in contact with ILE 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A ASN* 3.5 5.0 - - - +
728A VAL* 3.5 0.7 - - - -
729A ILE* 2.8 42.4 + - + +
764A TYR* 4.2 7.0 - - + -
765A SER* 1.3 71.8 + - - +
767A ILE* 1.3 62.7 + - - +
768A THR* 4.0 4.1 + - - +
786A VAL* 3.7 5.2 - - + -
788A SER* 3.6 15.3 - - - +
822A VAL* 3.8 12.3 - - + -
825A ILE* 3.6 30.5 - - + -
833A PHE* 3.8 46.2 - - + -
834A TYR* 3.5 26.0 - - + +
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Residues in contact with ILE 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711A PHE* 4.1 13.9 - - + -
716A VAL* 5.8 0.2 - - + -
719A TYR* 3.5 35.4 - - + -
723A ARG* 3.0 24.8 + - - +
726A VAL* 3.5 42.2 - - + -
727A ASN 3.4 3.6 - - - +
728A VAL* 4.3 9.9 - - + -
765A SER* 3.9 12.1 - - - +
766A ILE* 1.3 77.4 - - - +
768A THR* 1.3 60.0 + - - +
786A VAL* 3.4 2.1 - - - -
787A SER* 2.8 30.2 + - - +
789A PHE* 4.0 20.6 - - + -
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Residues in contact with THR 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A TYR* 3.1 38.8 + - + +
723A ARG* 3.6 1.1 - - - -
726A VAL* 3.5 1.9 - - - -
727A ASN* 2.8 37.3 + - - -
766A ILE* 4.0 5.9 + - - +
767A ILE* 1.3 74.7 - - - +
769A SER* 1.3 71.2 + - - +
777A ALA* 4.4 0.7 - - - +
784A LEU* 4.0 12.6 - - + -
785A SER 3.3 11.9 - - - +
786A VAL* 3.9 0.6 - - + +
834A TYR* 2.7 36.7 + - + +
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Residues in contact with SER 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A TYR* 4.6 1.6 - - - -
723A ARG* 2.7 44.7 + - - +
725A GLY 3.6 21.3 - - - -
726A VAL* 4.4 0.4 - - - -
768A THR* 1.3 76.5 - - - +
770A CYS* 1.3 64.0 + - - +
777A ALA* 4.2 10.3 - - - -
780A CYS* 5.5 0.2 - - - -
784A LEU* 3.5 12.8 - - - +
785A SER* 2.8 34.0 + - - +
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Residues in contact with CYS 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A ARG 4.8 2.4 + - - +
769A SER* 1.3 81.9 + - - +
771A LEU* 1.3 66.4 + - - +
772A ASP* 3.3 31.7 + - - +
773A PHE* 3.7 6.9 + - - +
775A GLN* 3.5 27.3 + - - +
776A PRO 4.4 2.7 - - - +
777A ALA* 4.4 4.8 - - - +
780A CYS* 2.0 56.8 - - + -
782A GLY 4.8 1.3 - - - -
783A PRO 4.1 0.4 - - - -
785A SER* 4.3 2.9 - - - -
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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