Contacts of the strand formed by residues 786 - 789 (chain B) in PDB entry 5M64
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 ALA 786 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A PRO* 4.5 9.9 - - + -
628A PHE* 4.4 7.2 - - + -
781B TYR 4.2 4.0 - - - +
782B ASP* 3.3 35.8 - - + +
783B MET 4.2 5.1 + - - +
784B ASP 4.5 0.4 - - - +
785B ASP* 1.3 80.8 + - - +
787B MET* 1.3 76.9 + - - +
924B LYS 4.8 0.7 - - - +
925B GLY* 4.1 0.9 - - - -
926B VAL* 3.3 23.1 - - + +
928B SER* 4.7 0.7 - - - -
948B ILE 5.1 0.5 - - - +
949B ILE* 5.1 2.6 - - - +
950B ASN* 4.2 5.2 + - - -
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Residues in contact with MET 787 (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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782B ASP* 2.9 15.9 + - - +
786B ALA* 1.3 87.9 - - - +
788B ILE* 1.3 57.8 + - - +
917B PHE* 5.1 14.4 - - + +
923B GLN* 4.4 7.2 - - - +
924B LYS 4.8 0.9 - - - +
925B GLY* 4.1 11.4 - - - +
926B VAL 2.5 27.3 + - - +
927B CYS* 3.9 4.9 - - - +
928B SER* 2.6 31.5 + - - -
947B ILE* 3.7 38.8 - - + -
948B ILE 4.1 4.0 - - - +
949B ILE* 3.7 39.5 - - + -
1033B TYR* 3.8 17.9 - - + +
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Residues in contact with ILE 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B THR* 3.4 24.7 - - - +
781B TYR* 5.3 6.5 - - + -
782B ASP* 3.3 16.4 - - - +
787B MET* 1.3 77.3 - - - +
789B ILE* 1.3 69.9 + - - +
927B CYS* 4.7 2.2 - - - -
928B SER* 4.7 1.8 - - - +
929B ARG* 3.3 23.3 - - - +
931B TRP* 3.8 27.6 - - + -
936B MET* 5.1 10.1 - - + -
946B ASP 4.5 0.2 - - - -
947B ILE* 3.3 26.7 - - - +
948B ILE* 3.6 33.4 + - + +
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Residues in contact with ILE 789 (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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788B ILE* 1.3 79.4 - - - +
790B ASN* 1.3 74.5 + - - +
793B ALA* 4.5 2.0 - - + -
794B ASP* 5.3 3.8 - - + +
798B PHE* 3.5 56.8 - - + -
911B PRO 5.8 2.0 - - - +
917B PHE* 5.5 7.2 - - + -
927B CYS* 3.7 26.1 - - + -
929B ARG 4.4 0.6 + - - -
930B LYS* 4.2 21.3 - - + -
931B TRP 3.2 25.1 + - - +
936B MET* 5.6 0.9 - - - -
946B ASP 3.5 12.8 - - - +
947B ILE* 4.3 12.1 - - + -
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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