Contacts of the strand formed by residues 672 - 675 (chain C) in PDB entry 3JW0
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 THR 672 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665C TYR* 4.3 0.9 - - - -
666C SER* 3.0 42.1 + - - -
670C ASN* 2.9 15.8 + - - +
671C TYR* 1.3 77.4 - - - +
673C LEU* 1.3 62.5 + - - +
710C PHE* 3.4 11.7 - - + +
711C PHE 4.2 18.6 - - - +
712C ILE* 3.8 7.1 - - - +
732C VAL* 6.0 0.2 - - - -
885C THR* 5.5 0.2 - - - +
887C ARG* 3.7 28.7 - - + +
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Residues in contact with LEU 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656C PHE* 3.3 55.4 - - + +
658C PRO* 4.3 7.2 - - + -
663C PHE* 4.1 14.8 - - + -
664C GLU 3.2 16.4 - - - +
665C TYR* 4.2 21.1 - - + -
671C TYR 4.7 1.8 - - - +
672C THR* 1.3 72.5 - - - +
674C GLN* 1.3 60.6 + - - +
709C GLY* 4.2 8.5 - - - -
710C PHE 2.6 32.1 + - - +
711C PHE* 3.1 19.7 - - + +
712C ILE 3.0 26.3 + - - -
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Residues in contact with GLN 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C PHE* 3.5 9.1 - - - -
664C GLU* 3.0 53.4 + - + +
666C SER* 3.4 29.7 - - - +
673C LEU* 1.3 78.7 - - - +
675C ILE* 1.3 75.2 + - - +
677C PRO* 4.9 4.0 - - - +
711C PHE* 5.2 2.2 - - - -
712C ILE* 3.7 30.0 - - + +
715C PHE* 5.8 3.1 - - - -
732C VAL* 5.0 2.4 - - - +
795C ARG* 4.5 16.5 + - - +
796C PHE* 5.0 4.3 - - - +
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Residues in contact with ILE 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662C LEU 4.1 4.9 - - - -
663C PHE* 4.0 18.8 - - + -
674C GLN* 1.3 84.5 + - - +
676C ASN* 1.3 71.9 + - - +
677C PRO* 3.2 10.4 - - - +
690C PHE* 3.9 15.0 - - + -
715C PHE* 4.2 11.6 - - + -
800C VAL* 3.5 32.9 - - + +
803C GLN* 3.8 19.7 - - + -
804C MET* 3.6 50.9 - - + +
807C PHE* 5.8 1.1 - - + -
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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