Contacts of the strand formed by residues 754 - 763 (chain A) in PDB entry 2X5Y
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 PHE 754 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747A PHE* 4.4 10.5 - - + -
748A LYS* 3.8 19.2 + - - +
751A MET* 3.7 39.1 - - + +
752A LYS 3.0 8.0 + - - +
753A ASN* 1.4 98.4 - - + +
755A LYS* 1.3 60.7 + - - +
825A ILE* 4.4 9.6 - - + -
828A HIS* 3.5 35.2 - + - -
893A TYR* 3.8 21.5 - + + -
894A THR 3.2 17.5 - - - +
895A GLU* 3.9 19.5 - - + -
896A ASP* 3.6 9.8 - - - +
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Residues in contact with LYS 755 (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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748A LYS* 4.7 7.2 - - - +
754A PHE* 1.3 75.0 - - - +
756A ILE* 1.3 66.0 + - - +
757A GLU* 3.4 17.4 + - - +
893A TYR* 3.2 5.6 - - - +
894A THR* 2.8 61.6 + - - +
895A GLU 3.0 16.6 + - - -
896A ASP* 3.6 25.7 + - + +
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Residues in contact with ILE 756 (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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740A TYR* 3.3 25.7 + - - +
744A SER* 3.6 38.1 - - - +
747A PHE* 3.7 36.6 - - + -
748A LYS* 4.4 11.4 - - - +
755A LYS* 1.3 77.0 - - - +
757A GLU* 1.3 65.4 - - - +
758A LYS 3.7 9.9 - - - +
759A ILE* 3.7 26.9 - - + -
891A ILE* 4.1 9.6 - - + -
892A GLU 3.6 7.4 - - - +
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Residues in contact with GLU 757 (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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732A GLU* 5.5 0.7 - - - +
740A TYR* 5.3 1.1 - - - -
755A LYS* 3.4 17.5 + - - -
756A ILE* 1.3 76.8 - - - +
758A LYS* 1.3 64.7 + - + +
892A GLU* 2.7 25.8 + - + +
893A TYR* 4.2 4.5 - - - +
894A THR* 2.7 45.1 + - + +
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Residues in contact with LYS 758 (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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732A GLU* 3.2 43.7 + - + +
740A TYR* 4.7 3.8 - - - -
756A ILE* 3.6 2.8 - - - +
757A GLU* 1.3 82.7 + - - +
759A ILE* 1.3 69.8 + - - +
760A LYS* 3.5 34.3 - - + +
890A VAL 3.9 0.8 - - - +
891A ILE* 3.5 2.9 - - - -
892A GLU* 2.9 46.3 + - + +
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Residues in contact with ILE 759 (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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732A GLU* 3.6 4.5 - - - +
733A ILE* 2.9 47.4 + - + +
740A TYR* 3.6 51.9 - - + +
743A VAL* 3.8 28.5 - - + -
744A SER 4.1 5.4 - - - +
756A ILE* 3.7 16.6 - - + -
758A LYS* 1.3 79.0 - - - +
760A LYS* 1.3 69.7 + - - +
889A TYR* 4.2 13.5 - - + -
890A VAL 3.5 7.2 - - - +
891A ILE* 4.3 7.6 - - + -
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Residues in contact with LYS 760 (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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730A LEU* 3.8 39.4 + - + +
731A SER 3.3 8.2 - - - +
732A GLU* 3.9 24.5 + - - +
758A LYS* 3.5 32.4 - - + +
759A ILE* 1.3 82.0 - - - +
761A LYS* 1.3 60.8 + - - +
762A ILE* 4.0 0.5 + - - +
889A TYR* 3.2 7.1 - - - +
890A VAL* 2.9 41.7 + - + +
892A GLU* 6.4 1.6 - - + -
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Residues in contact with LYS 761 (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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729A LYS 3.6 1.9 - - - +
730A LEU* 3.3 5.4 - - - -
731A SER* 2.8 42.7 + - - +
733A ILE* 4.0 14.9 - - + +
739A GLU* 2.8 41.1 + - - +
760A LYS* 1.3 73.0 - - - +
762A ILE* 1.3 66.6 + - - +
763A GLU* 5.5 0.6 - - + +
888A GLN* 3.5 31.6 - - - +
889A TYR* 3.9 5.4 - - + -
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Residues in contact with ILE 762 (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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728A TYR* 4.7 2.2 - - + -
729A LYS 3.6 5.8 - - - +
730A LEU* 3.6 20.6 - - + -
761A LYS* 1.3 75.7 - - - +
763A GLU* 1.3 69.7 + - - +
764A ASN* 4.7 4.5 - - + +
767A LEU* 6.4 0.2 - - + -
798A CYS* 3.7 30.5 - - + +
841A PHE* 3.6 31.2 - - + -
886A TYR* 3.4 10.1 + - + -
887A PRO* 3.5 35.0 - - + +
888A GLN* 2.9 29.1 + - - +
889A TYR* 3.8 7.0 - - - +
890A VAL* 3.8 8.7 - - + -
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Residues in contact with GLU 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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728A TYR* 3.1 5.4 - - - +
729A LYS* 2.9 70.3 + - + +
761A LYS* 6.2 0.4 - - + -
762A ILE* 1.3 73.4 - - - +
764A ASN* 1.3 62.6 + - - +
765A SER* 4.9 8.7 - - - +
768A LEU* 6.3 2.5 - - + -
886A TYR* 3.4 4.7 - - - +
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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