Contacts of the strand formed by residues 384 - 389 (chain C) in PDB entry 2QY0
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 ARG 384 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C TYR* 3.6 3.1 - - - -
373C THR* 3.0 55.7 + - + +
374C THR* 3.5 19.9 + - - +
382C LYS 4.3 5.4 - - - +
383C ALA* 1.3 75.8 - - - +
385C ILE* 1.3 68.0 + - - +
386C GLN* 5.6 3.0 - - - +
409C VAL* 3.6 36.8 - - - +
410C TYR 3.5 3.4 - - - +
411C THR* 3.1 32.1 - - + +
418C TRP* 4.5 0.2 - - - -
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Residues in contact with ILE 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C PRO* 3.5 33.0 - - + -
370C PHE* 3.9 19.5 - - + -
371C ARG 3.2 8.7 - - - +
372C TYR* 3.6 31.0 - - + -
373C THR* 4.5 3.4 - - - +
384C ARG* 1.3 80.3 - - - +
386C GLN* 1.3 59.4 + - - +
387C TYR* 3.9 24.7 - - + -
409C VAL* 3.6 7.1 - - - +
410C TYR* 2.9 48.8 + - + +
418C TRP* 3.8 20.2 - - + -
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Residues in contact with GLN 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C PHE* 3.3 4.1 - - - -
371C ARG* 2.9 60.9 + - + +
373C THR* 4.6 10.2 + - - +
384C ARG* 5.6 2.2 - - - +
385C ILE* 1.3 71.7 - - - +
387C TYR* 1.3 73.9 + - - +
388C TYR* 3.9 4.3 + - - -
406C GLU* 4.6 19.6 + - - +
408C GLY 3.5 12.6 - - - +
409C VAL* 4.0 23.1 - - + +
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Residues in contact with TYR 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C PRO* 3.5 6.6 - - - +
363C ARG* 2.6 40.7 + - - -
365C LEU* 3.5 31.6 - - + -
369C ASP 3.2 20.6 - - - -
370C PHE* 3.7 17.5 - + + -
385C ILE* 3.9 17.9 - - + -
386C GLN* 1.3 86.9 + - - +
388C TYR* 1.3 62.4 + - - +
396C MET* 3.8 9.9 - - + +
408C GLY* 2.9 16.1 + - - +
410C TYR* 3.5 41.1 - + - -
418C TRP* 6.1 1.3 - - + +
427C ILE* 4.1 11.7 - - + +
428C PRO* 3.6 20.9 - - + -
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Residues in contact with TYR 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LEU* 3.8 1.4 - - - +
368C GLY* 3.2 3.1 - - - -
369C ASP* 3.0 56.0 + - + +
370C PHE 3.9 22.1 + - - -
371C ARG* 3.3 46.7 - - + +
386C GLN* 3.9 8.7 - - + -
387C TYR* 1.3 75.9 - - - +
389C CYS* 1.3 74.4 + - - +
390C HIS* 4.8 11.0 - + - -
396C MET* 3.8 7.4 - - - -
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Residues in contact with CYS 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ASN 3.8 0.7 - - - -
388C TYR* 1.3 87.8 - - - +
390C HIS* 1.3 55.2 + - - +
391C GLU* 2.8 27.3 + - + +
394C TYR 4.0 11.7 - - - +
395C LYS* 4.3 0.2 - - - -
396C MET* 3.4 49.0 - - + +
430C CYS* 2.0 50.5 - - + -
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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