Contacts of the strand formed by residues 298 - 305 (chain Y) 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 HIS 298 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295X GLU* 3.5 4.3 + - - +
296X MET* 2.9 34.3 + - + +
298X HIS* 3.0 41.3 + - + +
347X ARG* 4.1 13.9 - - - -
296Y MET* 3.5 41.3 + - + +
297Y HIS* 1.3 78.3 - - - +
299Y TRP* 1.3 62.0 + - - +
347Y ARG* 3.8 10.8 + - - +
348Y LEU 3.6 2.9 - - - -
349Y ASN* 3.1 42.9 + - + +
350Y GLN* 4.4 7.6 + - - -
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Residues in contact with TRP 299 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293X ALA* 4.4 13.2 - - + -
294X VAL* 3.6 22.7 - - - -
295X GLU* 3.6 41.5 + - + +
296X MET* 3.9 1.6 - - - -
297Y HIS* 3.8 7.9 + - - +
298Y HIS* 1.3 78.7 - - - +
300Y CYS* 1.3 62.1 + - - +
346Y LEU 4.5 0.4 - - - -
347Y ARG* 3.0 23.4 - - - -
348Y LEU* 2.8 30.3 + - + +
351Y PRO* 3.5 28.5 - - + +
377Y ALA 3.8 19.3 - - - -
378Y PHE* 3.5 50.4 + + + +
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Residues in contact with CYS 300 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293X ALA* 3.5 1.8 - - - -
294X VAL* 2.9 42.0 + - + +
296X MET* 3.8 18.8 - - + -
299Y TRP* 1.3 77.6 - - - +
301Y ILE* 1.3 61.4 + - - +
302Y PRO* 3.3 24.7 - - - +
345Y CYS* 2.0 46.4 - - + -
346Y LEU 3.6 4.3 - - - -
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Residues in contact with ILE 301 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290X LEU* 4.3 16.2 - - + -
291X HIS 4.2 9.9 - - - +
293X ALA* 4.0 15.7 - - + +
300Y CYS* 1.3 74.6 - - - +
302Y PRO* 1.3 72.2 - - + +
303Y PHE* 3.6 3.1 + - - -
315Y TRP* 4.4 8.1 - - + -
345Y CYS* 3.2 2.1 - - - -
346Y LEU* 2.9 52.8 + - + +
348Y LEU* 4.1 12.1 - - + -
359Y TYR* 3.7 39.0 - - + -
374Y ILE* 4.4 8.7 - - + -
376Y ALA* 4.5 8.3 - - + -
378Y PHE* 4.6 2.5 - - + -
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Residues in contact with PRO 302 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290X LEU* 3.5 5.0 - - - +
291X HIS* 2.9 52.2 + - + +
292X THR 3.4 24.0 - - - +
294X VAL* 4.6 7.4 - - + -
300Y CYS* 3.3 21.7 - - - +
301Y ILE* 1.3 84.6 - - - +
303Y PHE* 1.3 60.7 + - - +
344Y GLY 3.3 11.0 - - - +
345Y CYS* 5.1 0.2 - - - -
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Residues in contact with PHE 303 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289X GLN 3.0 7.6 - - - +
290X LEU* 3.2 27.4 - - + -
291X HIS* 4.8 3.4 - - - -
301Y ILE 3.7 6.5 - - - -
302Y PRO* 1.3 71.8 - - - +
304Y SER* 1.3 70.5 + - - +
305Y VAL* 4.3 7.0 - - + -
313Y LEU* 4.5 9.0 - - + -
315Y TRP* 3.7 17.7 - + + -
330Y THR* 3.8 24.5 - - + -
331Y GLU 4.3 0.4 - - - -
332Y PHE* 4.0 23.6 - + - -
342Y ARG 4.6 3.1 - - - -
343Y HIS* 3.6 3.9 + - - +
344Y GLY* 3.1 46.7 + - - +
345Y CYS 3.0 31.0 - - - -
346Y LEU 3.8 0.2 - - - -
361Y LEU* 3.6 15.5 - - + -
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Residues in contact with SER 304 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288X VAL* 3.4 2.3 - - - +
289X GLN* 2.9 49.5 + - - +
291X HIS* 4.8 7.1 + - - -
303Y PHE* 1.3 74.1 + - - +
305Y VAL* 1.3 67.9 + - - +
306Y ASP 4.3 0.2 - - - -
341Y VAL* 4.5 6.3 - - - -
342Y ARG 3.4 7.2 - - - -
343Y HIS* 2.6 34.9 + - - -
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Residues in contact with VAL 305 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287X SER 3.5 4.5 - - - +
288X VAL* 3.6 20.2 - - + -
303Y PHE* 4.3 13.7 - - + -
304Y SER* 1.3 81.4 - - - +
306Y ASP* 1.3 61.4 - - - +
311Y PRO* 3.4 34.7 - - + +
313Y LEU* 3.6 24.9 - - + -
332Y PHE* 5.9 0.2 - - + -
340Y THR 4.0 2.1 - - - +
341Y VAL* 3.5 3.7 - - - +
342Y ARG* 2.8 55.5 + - + +
361Y LEU* 4.4 0.4 - - + -
363Y ALA* 4.5 1.6 - - + -
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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