Contacts of the strand formed by residues 351 - 356 (chain X) in PDB entry 2QW0
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 351 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334X ILE* 3.5 10.1 - - - +
335X VAL 3.1 14.1 - - - -
337X ILE* 4.1 17.3 - - - -
345X VAL* 4.4 0.9 - - - -
350X GLU* 1.3 76.3 - - - +
352X GLU* 1.3 61.2 + - - -
386X VAL* 3.2 6.4 - - - +
387X ALA 2.8 32.5 + - - +
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Residues in contact with GLU 352 (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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334X ILE* 3.2 4.2 - - - -
335X VAL* 2.7 40.6 + - + +
337X ILE* 3.9 15.6 - - + +
338X GLY 5.0 3.6 + - - -
351X GLY* 1.3 71.6 - - - -
353X LEU* 1.3 74.6 + - - +
354X ILE* 3.4 3.9 + - + -
382X ARG* 2.8 51.9 + - - +
384X SER* 2.9 33.8 + - - +
385X ASP 3.4 11.2 - - - +
401X VAL* 4.5 7.2 - - + -
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Residues in contact with LEU 353 (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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304X TYR* 3.5 38.6 - - + +
313X LEU* 4.0 8.5 - - + -
332X VAL* 4.1 20.2 - - + -
333X ARG 3.5 17.0 - - - +
334X ILE* 4.5 10.8 - - + +
351X GLY 3.8 1.6 + - - -
352X GLU* 1.3 73.2 - - - +
354X ILE* 1.3 66.0 + - - +
355X VAL* 4.5 4.3 - - + -
383X THR* 2.4 42.7 + - + +
385X ASP* 2.9 15.9 + - + +
387X ALA* 4.3 10.7 - - + +
395X VAL* 4.5 11.0 - - + -
397X ILE* 3.7 19.5 - - + -
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Residues in contact with ILE 354 (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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332X VAL* 3.5 3.6 - - - +
333X ARG* 3.0 50.3 + - + +
335X VAL* 3.9 30.7 - - + -
341X VAL* 3.8 33.0 - - + +
352X GLU* 3.4 4.5 + - - +
353X LEU* 1.3 78.6 - - - +
355X VAL* 1.3 64.1 + - - +
380X TRP* 3.7 27.1 - - + -
381X TYR 3.3 9.0 - - - +
382X ARG* 4.0 31.4 - - + +
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Residues in contact with VAL 355 (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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306X THR* 5.7 0.4 - - + +
309X ALA* 3.9 23.3 - - + -
312X SER* 3.3 36.6 - - - +
330X SER* 6.2 0.4 - - - -
331X GLU 3.3 9.4 - - - +
332X VAL* 3.9 10.8 - - + -
353X LEU* 4.5 7.2 - - + -
354X ILE* 1.3 78.6 - - - +
356X ALA* 1.3 62.2 + - - +
380X TRP* 3.5 5.4 - - - -
381X TYR* 2.6 54.9 + - + +
383X THR* 4.2 16.6 - - + -
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Residues in contact with ALA 356 (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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309X ALA* 5.0 3.8 - - - +
329X PHE 6.0 0.9 - - - +
331X GLU* 2.8 45.4 + - + +
355X VAL* 1.3 82.7 - - - +
357X ALA* 1.3 60.5 + - - +
358X SER* 3.4 15.4 + - - +
379X GLY 3.8 4.5 - - - +
380X TRP* 3.4 17.5 - - + -
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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