Contacts of the strand formed by residues 342 - 349 (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 ARG 342 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303Y PHE* 4.6 2.3 - - - -
304Y SER* 3.4 2.8 - - - -
305Y VAL* 2.8 56.8 + - + +
310Y ALA* 4.1 14.9 - - - +
311Y PRO* 3.2 33.1 + - - +
313Y LEU* 4.7 6.3 - - - +
332Y PHE* 3.9 44.4 - - + -
335Y PRO* 5.6 14.4 - - + -
340Y THR 4.5 5.5 + - - +
341Y VAL* 1.3 79.7 - - - +
343Y HIS* 1.3 62.1 + - - +
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Residues in contact with HIS 343 (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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303Y PHE* 3.6 9.2 - - - +
304Y SER* 2.6 28.4 + - - -
332Y PHE* 3.3 12.3 - - - +
333Y LEU* 3.0 46.4 + - + +
339Y GLU* 4.5 10.1 + - - -
341Y VAL* 3.7 33.5 - - + +
342Y ARG* 1.3 76.5 - - - +
344Y GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 344 (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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302Y PRO* 3.3 7.8 - - - +
303Y PHE* 3.1 37.8 + - - +
331Y GLU 3.2 12.3 - - - -
332Y PHE* 3.9 2.2 - - - -
333Y LEU* 4.2 10.9 - - - +
343Y HIS* 1.3 79.6 - - - +
345Y CYS* 1.3 65.7 + - - -
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Residues in contact with CYS 345 (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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296X MET* 4.9 7.0 - - - -
300Y CYS* 2.0 51.6 - - + -
301Y ILE 3.2 6.1 - - - -
302Y PRO* 5.1 0.2 - - - -
303Y PHE* 3.0 10.5 - - - -
330Y THR* 3.6 0.5 - - - -
331Y GLU* 2.8 37.5 + - + +
333Y LEU* 5.9 6.1 - - - -
344Y GLY* 1.3 77.4 - - - -
346Y LEU* 1.3 65.7 + - - +
347Y ARG* 3.3 10.5 + - + +
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Residues in contact with LEU 346 (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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300Y CYS* 3.6 1.4 - - - -
301Y ILE* 2.9 42.9 + - + -
303Y PHE* 3.8 1.2 - - - -
315Y TRP* 3.5 52.5 - - + +
322Y LEU* 4.1 7.9 - - + -
324Y GLU* 5.0 2.2 - - + -
328Y ILE* 4.1 15.5 - - + -
329Y PHE* 3.7 20.9 - - - +
330Y THR* 4.2 1.6 - - - +
345Y CYS* 1.3 70.7 - - - +
347Y ARG* 1.3 59.9 + - - +
348Y LEU* 3.6 14.7 - - + +
359Y TYR* 3.6 35.4 - - + -
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Residues in contact with ARG 347 (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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296X MET* 2.7 35.7 - - + +
298X HIS* 3.6 23.4 - - - -
347X ARG* 4.9 5.5 - - - +
298Y HIS* 3.8 13.9 + - - +
299Y TRP 3.0 15.7 - - - +
327Y PHE 3.6 1.0 - - - +
328Y ILE* 3.1 7.1 - - - +
329Y PHE* 2.6 80.5 + - + +
331Y GLU* 3.5 26.4 + - + +
345Y CYS* 3.3 12.7 + - + +
346Y LEU* 1.3 74.5 - - - +
348Y LEU* 1.3 66.1 + - - +
349Y ASN* 3.3 19.5 + - - +
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Residues in contact with LEU 348 (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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298Y HIS* 3.6 1.0 - - - -
299Y TRP* 2.8 45.4 + - + +
301Y ILE* 4.1 16.2 - - + -
327Y PHE 3.2 5.8 - - - +
328Y ILE* 3.5 31.0 - - + -
346Y LEU* 3.6 32.5 - - + +
347Y ARG* 1.3 76.5 - - - +
349Y ASN* 1.3 62.4 + - - +
350Y GLN 3.9 1.3 + - - -
351Y PRO* 3.9 24.0 - - + +
355Y ASN* 4.5 1.6 - - - +
359Y TYR* 3.9 20.2 - - + +
378Y PHE* 4.0 18.2 - - + -
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Residues in contact with ASN 349 (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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298Y HIS* 3.1 38.7 + - + -
326Y SER 4.0 7.0 + - - +
327Y PHE* 2.9 34.2 + - + +
329Y PHE* 4.0 25.3 - - - -
347Y ARG* 3.3 20.2 + - - +
348Y LEU* 1.3 70.8 - - - +
350Y GLN* 1.3 92.1 + - - +
351Y PRO 3.6 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