Contacts of the strand formed by residues 763 - 768 (chain A) in PDB entry 5HLB
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 ILE 763 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A GLN* 3.7 29.8 - - + -
668A TYR* 3.6 37.2 - - + +
669A LEU* 4.2 12.6 - - + -
759A PRO* 3.9 14.2 - - + +
760A PRO* 3.5 35.0 + - + +
761A GLU 3.3 3.1 - - - +
762A ASP* 1.3 80.2 - - - +
764A ALA* 1.3 62.5 + - - +
765A ASP* 4.7 4.5 - - - +
784A PRO* 4.1 13.2 - - + -
785A VAL 3.3 6.7 - - - +
786A TRP* 4.3 2.9 - - - -
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Residues in contact with ALA 764 (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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763A ILE* 1.3 74.5 - - - +
765A ASP* 1.3 65.0 + - - +
766A MET* 3.2 10.7 + - + +
785A VAL* 2.8 37.0 + - - +
787A THR* 4.3 12.8 - - - +
790A PRO* 3.6 32.3 - - + -
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Residues in contact with ASP 765 (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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668A TYR* 5.1 2.8 + - - -
672A TRP* 5.9 0.2 + - - -
763A ILE* 4.4 4.9 - - - +
764A ALA* 1.3 68.0 - - - +
766A MET* 1.3 62.0 + - - +
782A ILE* 3.7 23.0 - - + +
783A LEU 3.7 4.5 - - - -
784A PRO* 3.6 24.9 - - - +
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Residues in contact with MET 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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764A ALA* 3.2 12.1 + - + +
765A ASP* 1.3 75.7 - - - +
767A GLY* 1.3 61.9 + - - +
768A VAL* 4.8 1.9 - - - +
774A PHE* 3.9 25.5 - - + -
775A VAL 5.7 1.8 - - - +
781A ARG 3.7 0.5 - - - +
782A ILE* 3.4 4.3 - - - -
783A LEU* 2.9 33.6 + - - +
785A VAL* 3.6 36.6 - - + -
787A THR* 4.0 9.9 - - - -
790A PRO* 3.3 37.9 - - + +
792A SER* 3.7 15.9 - - - +
793A LEU* 3.9 17.7 - - + +
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Residues in contact with GLY 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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766A MET* 1.3 74.3 - - - +
768A VAL* 1.3 62.5 + - - +
774A PHE* 3.4 7.4 - - - +
775A VAL 2.9 31.9 + - - +
778A GLY 3.7 22.4 - - - -
779A GLY* 4.7 0.7 - - - -
781A ARG 3.3 9.2 - - - -
782A ILE* 4.5 4.9 - - - +
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Residues in contact with VAL 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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530A ASN* 3.8 22.4 - - + +
564A MET* 4.9 4.9 - - + -
766A MET 4.8 2.0 - - - +
767A GLY* 1.3 77.4 - - - +
769A ASP* 1.3 68.2 + - - +
772A GLY* 4.0 7.2 - - - -
773A ASN 3.3 14.6 - - - +
774A PHE* 3.7 24.5 - - + -
775A VAL* 4.3 0.7 - - - -
779A GLY* 4.0 5.3 - - - -
780A MET* 3.0 22.7 + - - +
781A ARG* 2.9 36.0 + - + +
783A LEU* 4.3 17.0 - - + -
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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