Contacts of the strand formed by residues 739 - 744 (chain A) in PDB entry 3OSE
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 LEU 739 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A MET* 4.2 0.4 - - - +
735A LYS* 3.0 42.6 + - + -
736A GLU* 3.2 46.0 + - + +
737A ARG 3.6 0.2 - - - -
738A PHE* 1.3 80.8 - - - +
740A LEU* 1.3 70.9 + - - +
756A GLU* 4.4 14.1 - - + +
757A MET 3.5 15.0 - - - +
758A GLU* 3.8 21.5 - - + -
771A ARG* 3.8 16.8 - - - +
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Residues in contact with LEU 740 (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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718A MET* 3.8 17.3 - - + -
721A ILE* 3.7 30.3 - - + -
722A ARG* 4.2 10.1 - - + -
725A LEU* 3.7 15.7 - - + -
732A TYR* 4.1 14.4 - - + -
733A GLU 3.4 9.4 - - - +
734A GLN* 3.4 41.1 - - - +
739A LEU* 1.3 79.9 - - - +
741A PHE* 1.3 59.2 + - - +
742A CYS* 3.8 13.0 + - - -
756A GLU* 3.4 6.4 - - - +
757A MET* 2.9 39.7 + - + +
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Residues in contact with PHE 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A TYR* 3.2 1.8 - - - -
733A GLU* 2.8 60.5 + - + +
735A LYS* 3.9 30.0 - - + +
740A LEU* 1.3 69.9 - - - +
742A CYS* 1.3 60.1 + - - +
743A VAL* 3.7 17.2 - - + +
754A GLN* 3.5 42.6 - - + -
755A TRP 3.8 3.4 - - - -
756A GLU* 4.8 6.3 - - + +
775A ILE* 3.8 33.9 - - + -
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Residues in contact with CYS 742 (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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725A LEU* 3.9 28.7 - - + -
731A ASP 3.3 7.4 - - - +
732A TYR* 4.3 1.8 - - - -
740A LEU* 3.9 14.6 - - - -
741A PHE* 1.3 74.5 - - - +
743A VAL* 1.3 66.2 + - - +
754A GLN* 3.2 6.9 - - - +
755A TRP* 2.7 61.8 + - + +
757A MET* 3.9 26.5 - - - -
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Residues in contact with VAL 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A ASN 4.4 0.2 - - - +
730A CYS* 3.3 4.2 - - - -
731A ASP* 2.9 47.9 + - + +
733A GLU* 4.6 6.5 - - + +
741A PHE* 3.7 28.5 - - + +
742A CYS* 1.3 81.8 - - - +
744A HIS* 1.3 63.9 + - - +
745A GLY 5.4 0.9 - - - +
752A LEU* 3.7 26.7 - - + -
753A VAL 3.3 7.2 - - - +
754A GLN* 4.2 12.1 - - + +
755A TRP* 4.0 2.2 - - - -
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Residues in contact with HIS 744 (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 ASN 3.2 27.5 + - - -
729A ASN* 3.4 16.5 + - - +
730A CYS* 3.6 11.4 - - - -
743A VAL* 1.3 75.6 - - - +
745A GLY* 1.3 76.8 + - - +
751A SER* 3.3 6.1 + - - +
752A LEU* 3.4 6.4 - - - +
753A VAL* 2.9 33.9 + - + +
755A TRP* 3.8 18.1 - - + -
785A ILE* 3.8 29.8 - - + +
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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