Contacts of the strand formed by residues 299 - 305 (chain X) in PDB entry 1WWA
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 TRP 299 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297X HIS* 3.6 21.4 + - - +
298X HIS* 1.3 76.1 - - - +
300X CYS* 1.3 61.5 + - - +
346X LEU 4.6 0.2 - - - -
347X ARG* 3.4 0.5 - - - -
348X LEU* 2.8 36.9 + - + +
351X PRO* 3.7 13.8 - - + +
377X ALA 3.9 21.3 - - - -
378X PHE* 3.6 46.8 + + + +
293Y ALA* 3.5 29.4 - - + -
294Y VAL 3.3 25.1 - - - -
295Y GLU* 3.6 41.6 + - + -
296Y MET* 3.0 12.3 - - - +
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Residues in contact with CYS 300 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299X TRP* 1.3 76.6 - - - +
301X ILE* 1.3 61.4 + - - +
302X PRO* 3.1 26.5 - - - +
345X CYS* 2.0 48.9 - - + -
346X LEU 3.5 4.7 - - - -
293Y ALA* 4.6 0.2 - - - -
294Y VAL* 2.7 43.7 + - + +
296Y MET* 3.7 19.5 - - + -
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Residues in contact with ILE 301 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300X CYS* 1.3 74.6 - - - +
302X PRO* 1.3 74.0 - - + +
303X PHE* 3.7 3.8 + - - -
315X TRP* 4.3 9.2 - - + -
345X CYS* 3.3 1.6 - - - -
346X LEU* 2.9 48.3 + - + +
348X LEU* 4.2 10.1 - - + -
359X TYR* 3.6 44.0 - - + -
374X ILE* 4.4 10.1 - - + -
376X ALA* 5.0 1.1 - - + -
378X PHE* 4.8 5.4 - - + -
290Y LEU* 4.1 19.3 - - + -
291Y HIS 4.2 7.0 - - - +
293Y ALA* 4.2 17.7 - - + +
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Residues in contact with PRO 302 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300X CYS* 3.1 23.3 - - - +
301X ILE* 1.3 85.2 - - - +
303X PHE* 1.3 60.6 + - - +
344X GLY 3.5 10.3 - - - +
290Y LEU* 3.6 4.0 - - - +
291Y HIS* 2.9 53.6 + - + +
292Y THR 3.1 25.1 - - - +
294Y VAL* 4.5 9.4 - - + -
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Residues in contact with PHE 303 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301X ILE 4.1 1.6 - - - -
302X PRO* 1.3 75.2 - - - +
304X SER* 1.3 71.4 + - - +
305X VAL* 4.2 4.3 - - + -
313X LEU* 4.2 9.9 - - + -
315X TRP* 3.8 18.8 - + + -
330X THR* 3.7 20.6 - - + -
331X GLU 4.3 0.4 - - - -
332X PHE* 3.7 31.9 - + - -
342X ARG 4.2 3.8 - - - -
343X HIS* 3.4 5.8 + - - +
344X GLY* 2.9 58.5 + - - +
345X CYS 3.2 31.0 - - - -
361X LEU* 3.7 15.9 - - + -
289Y GLN 3.1 11.2 - - - +
290Y LEU* 3.6 15.9 - - + -
291Y HIS* 3.8 2.9 - - - -
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Residues in contact with SER 304 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303X PHE* 1.3 73.5 - - - +
305X VAL* 1.3 67.5 + - - +
341X VAL* 4.2 8.1 - - - -
342X ARG 3.3 5.6 - - - -
343X HIS* 2.8 33.4 + - - -
288Y VAL* 3.4 2.1 - - - +
289Y GLN* 3.0 47.3 + - - +
291Y HIS* 3.5 15.0 + - - -
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Residues in contact with VAL 305 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303X PHE* 4.2 15.9 - - + -
304X SER* 1.3 72.9 - - - +
306X ASP* 1.3 60.9 + - - +
311X PRO* 3.5 30.6 - - + +
313X LEU* 3.7 27.1 - - + -
332X PHE* 5.6 0.2 - - + -
340X THR 4.2 1.6 - - - +
341X VAL* 3.5 3.1 - - - +
342X ARG* 2.9 50.4 + - + +
361X LEU* 4.2 0.9 - - + -
363X ALA* 4.4 1.6 - - + -
287Y SER 3.4 4.3 - - - +
288Y VAL* 3.2 31.9 - - + -
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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