Contacts of the strand formed by residues 386 - 389 (chain C) in PDB entry 4GQS
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 386 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLU* 3.0 28.0 + - - +
73C ARG 4.0 4.9 + - - -
74C MET* 3.1 12.5 - - + +
75C VAL 2.8 26.2 + - - -
98C GLY* 4.1 2.3 - - - -
99C HIS* 3.4 27.6 + - + +
367C PRO* 4.5 6.3 - - + -
368C HIS 3.3 13.2 - - - +
369C ALA* 4.3 0.7 - - - +
384C GLY 3.3 4.6 + - - -
385C THR* 1.3 75.7 - - - +
387C ILE* 1.3 62.6 + - - +
388C LEU* 3.5 22.7 - - + -
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Residues in contact with ILE 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C VAL* 3.3 15.3 - - + +
77C LEU* 3.6 37.0 - - + -
87C LEU* 6.0 0.2 - - + -
94C PHE* 3.8 21.8 - - + -
366C LEU 4.7 0.5 - - - +
367C PRO* 4.3 0.2 - - - +
368C HIS* 2.7 47.3 + - + +
369C ALA* 3.5 2.9 - - - -
370C VAL* 3.2 33.0 - - + +
381C ILE* 4.6 2.0 - - + -
385C THR* 2.8 33.9 - - + +
386C THR* 1.3 73.3 - - - +
388C LEU* 1.3 67.9 + - - +
389C THR* 4.1 9.9 + - + -
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C VAL* 6.1 2.2 - - + -
54C LEU* 4.8 14.6 - - + -
69C PHE* 4.5 12.6 - - + -
74C MET* 3.3 41.5 - - + -
75C VAL 3.0 11.3 + - - +
76C VAL* 3.5 19.0 - - + +
77C LEU 2.8 29.7 + - - +
364C THR* 5.2 15.9 - - + +
366C LEU 5.9 0.4 - - - -
367C PRO* 5.3 10.8 - - + -
386C THR* 3.5 16.8 - - + -
387C ILE* 1.3 78.8 - - - +
389C THR* 1.3 62.2 + - - +
390C SER 4.0 0.2 - - - -
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Residues in contact with THR 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 6.4 0.2 - - - -
77C LEU* 3.7 27.6 - - + -
83C VAL* 4.8 10.1 - - + -
87C LEU* 3.9 34.9 - - + +
364C THR* 3.5 23.2 + - - -
365C SER* 3.9 10.4 + - - -
366C LEU 5.4 1.2 + - - -
368C HIS* 5.0 8.1 - - + -
387C ILE* 4.1 9.3 + - + +
388C LEU* 1.3 73.9 - - - +
390C SER* 1.3 61.2 + - - +
391C LEU* 3.0 25.6 + - - +
429C SER* 4.9 0.3 + - - -
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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