Contacts of the strand formed by residues 349 - 353 (chain C) in PDB entry 2W3S
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 349 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ALA* 4.3 7.0 - - - -
346C PRO 3.6 14.3 + - - -
347C GLY* 3.2 21.4 + - - -
348C LEU* 1.3 97.8 + - - +
350C CYS* 1.3 64.6 + - - +
351C TYR* 3.6 19.3 - - + +
366C GLY 3.9 0.3 - - - +
367C CYS* 3.3 4.3 - - - +
368C LEU* 2.8 33.5 + - - +
446C TYR* 3.6 24.7 - - + -
449C GLU* 3.6 35.2 + - + +
450C LEU* 3.3 26.1 - - + +
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Residues in contact with CYS 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ALA* 3.9 20.5 - - - +
263C LEU 4.6 0.9 - - - -
266C LEU* 3.8 27.6 + - + +
297C ALA* 4.1 13.2 - - - -
348C LEU* 4.0 22.7 - - - -
349C ARG* 1.3 78.5 - - - +
351C TYR* 1.3 69.4 + - - +
352C LYS 4.1 1.0 + - - -
366C GLY 3.7 3.1 - - - -
367C CYS* 3.4 23.3 - - - -
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Residues in contact with TYR 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 4.7 0.4 - - - -
349C ARG* 3.6 20.2 - - + +
350C CYS* 1.3 78.2 - - - +
352C LYS* 1.3 59.5 - - - +
364C VAL 4.0 0.3 - - - +
365C CYS* 3.2 10.0 - - - -
366C GLY 2.8 46.8 + - - +
367C CYS* 4.6 0.4 - - - -
368C LEU* 3.8 18.8 - - + -
442C MET* 3.6 47.8 - - + -
445C ARG* 3.4 42.6 - - + +
446C TYR* 3.5 19.8 + - + -
449C GLU* 2.3 35.6 + - - -
455C VAL* 5.5 0.2 - - + -
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Residues in contact with LYS 352 (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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266C LEU* 3.9 17.8 - - + +
269C ARG* 2.7 72.1 + - + +
293C ASP* 2.9 27.0 + - - +
350C CYS 4.1 1.2 + - - -
351C TYR* 1.3 76.2 - - - +
353C LEU* 1.3 60.7 + - - +
354C SER* 4.2 10.5 - - - +
357C PHE 5.3 0.9 - - - -
360C ASP* 2.9 28.9 + - - +
362C SER* 3.2 29.9 - - - +
364C VAL 3.9 1.8 - - - -
365C CYS* 4.5 1.8 - - - -
442C MET* 4.8 0.4 - - - -
445C ARG* 5.3 1.9 + - - -
1465C FAD 3.3 3.8 + - - -
639D GLU* 3.8 10.9 - - - +
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Residues in contact with LEU 353 (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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352C LYS* 1.3 76.7 - - - +
354C SER* 1.3 62.3 + - - +
362C SER* 3.7 1.1 - - - -
363C ALA* 2.7 34.3 + - + +
364C VAL* 2.7 28.7 + - + +
434C TYR* 3.5 35.4 - - + +
438C ALA* 3.5 31.2 - - + -
442C MET* 3.8 11.4 - - + -
637D THR* 3.9 8.1 - - - -
639D GLU* 3.3 40.4 - - + +
763D PRO* 5.0 0.9 - - + -
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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