Contacts of the strand formed by residues 357 - 365 (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 GLY 357 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317X PHE* 3.5 8.1 - - - -
318X ASN* 3.6 7.2 - - - -
355X ASN 3.3 3.0 + - - -
356X ASN* 1.3 75.3 - - - +
358X ASN* 1.3 61.6 + - - -
359X TYR* 3.6 7.2 - - - -
375X MET* 3.5 11.2 - - - +
376X ALA 2.8 34.8 + - - +
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Residues in contact with ASN 358 (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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316X LEU 3.7 0.5 - - - +
317X PHE* 3.5 4.5 - - - -
318X ASN* 2.7 50.2 + - - +
319X GLY 4.7 1.7 + - - +
357X GLY* 1.3 73.9 - - - -
359X TYR* 1.3 59.6 + - - +
360X THR* 4.0 9.3 + - - -
373X SER* 3.7 23.5 + - - -
374X ILE 3.1 16.8 + - - +
375X MET* 3.2 26.6 - - - +
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Residues in contact with TYR 359 (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* 3.6 24.9 - - + -
315X TRP* 4.6 8.3 - + + -
316X LEU 3.5 5.2 - - - +
317X PHE* 3.2 33.0 - + - -
322X LEU* 4.1 17.3 - - + +
328X ILE* 5.4 2.0 - - + +
346X LEU* 3.8 22.7 - - + -
348X LEU* 3.9 8.9 - - + +
355X ASN* 2.6 38.6 + - - +
357X GLY 3.6 11.4 - - - -
358X ASN* 1.3 76.1 - - - +
360X THR* 1.3 63.7 + - - +
373X SER* 3.3 3.6 - - - -
374X ILE* 2.8 41.7 + - + +
376X ALA* 4.4 9.4 - - + -
378X PHE* 3.8 16.5 - + - -
290Y LEU* 3.7 5.0 - - - +
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Residues in contact with THR 360 (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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315X TRP* 3.2 10.7 - - - -
316X LEU* 2.8 52.6 + - + +
319X GLY 5.7 1.4 + - - -
358X ASN* 4.0 8.0 + - - -
359X TYR* 1.3 75.3 - - - +
361X LEU* 1.3 70.9 + - - +
362X LEU* 3.8 20.8 - - + +
371X SER* 4.4 4.7 - - - +
372X ALA 3.4 16.2 - - - +
373X SER* 3.3 20.1 + - - +
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Residues in contact with LEU 361 (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* 3.7 38.8 - - + -
305X VAL* 4.2 2.9 - - + -
313X LEU* 3.8 27.4 - - + -
314X ARG 3.3 15.9 - - - +
315X TRP* 3.8 30.1 - - + -
360X THR* 1.3 77.3 - - - +
362X LEU* 1.3 65.8 + - - +
371X SER* 3.3 5.4 - - - -
372X ALA 3.1 26.6 + - - +
288Y VAL* 3.5 31.1 - - + +
290Y LEU* 4.0 10.5 - - + +
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Residues in contact with LEU 362 (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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312X SER 3.5 0.9 - - - +
313X LEU* 3.3 6.1 - - - -
314X ARG* 2.8 73.7 + - + +
316X LEU* 3.5 38.1 - - + -
360X THR* 3.8 11.4 - - + +
361X LEU* 1.3 81.1 - - - +
363X ALA* 1.3 60.8 + - - +
370X ALA 3.5 3.6 - - - +
371X SER* 3.4 28.3 - - - -
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Residues in contact with ALA 363 (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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305X VAL* 4.4 2.2 - - + -
311X PRO* 4.1 12.6 - - + -
312X SER 3.2 9.4 - - - +
313X LEU* 4.1 15.0 - - + -
314X ARG* 6.4 0.2 - - - -
361X LEU 4.2 0.2 - - - -
362X LEU* 1.3 76.2 - - - +
364X ALA* 1.3 64.8 + - - +
369X GLN* 3.4 1.9 - - - +
370X ALA 2.9 32.9 + - - +
286Y ALA* 4.2 9.6 - - + -
287Y SER 4.7 2.7 - - - +
288Y VAL* 4.1 21.0 - - + +
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Residues in contact with ALA 364 (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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311X PRO* 3.3 4.7 - - - +
312X SER* 3.1 38.3 + - - +
314X ARG* 5.6 7.9 - - - +
363X ALA* 1.3 78.4 - - - +
365X ASN* 1.3 62.5 + - - +
368X GLY 3.6 6.1 - - - -
369X GLN* 4.0 21.1 - - + +
286Y ALA* 4.0 0.9 - - - -
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Residues in contact with ASN 365 (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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307X GLY 4.0 1.2 - - - -
308X GLN 3.4 12.7 + - - +
309X PRO 3.1 27.8 + - - +
310X ALA 4.6 0.9 - - - +
311X PRO* 3.9 9.9 - - + -
364X ALA* 1.3 76.1 - - - +
366X PRO* 1.4 74.7 - - + +
367X PHE* 3.0 13.8 + - - -
368X GLY 3.1 24.8 + - - +
284Y PHE 2.9 25.1 + - - -
286Y ALA* 3.3 17.0 + - - +
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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