Contacts of the strand formed by residues 310 - 316 (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 MET 310 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180X SER 5.2 0.7 - - - +
181X ARG* 3.5 61.5 - - + +
184X PHE* 3.8 28.0 - - + -
208X VAL* 3.5 40.2 - - - +
209X VAL* 3.9 3.6 - - - +
212X PHE* 4.0 2.9 - - + -
213X ALA* 3.9 10.8 - - + -
305X GLY* 3.1 4.3 - - - -
306X THR* 2.7 41.7 + - - -
309X ALA* 1.3 76.2 - - - +
311X ASN* 1.3 68.3 + - - +
312X SER* 3.5 3.5 + - - -
360X SER* 4.6 3.1 - - - +
505X 34Z 3.6 15.9 - - + -
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Residues in contact with ASN 311 (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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184X PHE* 3.4 37.8 - - + -
188X GLN* 2.8 43.1 + - - +
303X ALA* 4.2 7.7 - - - +
304X TYR 3.0 20.7 + - - +
309X ALA 3.5 4.4 + - - +
310X MET* 1.3 82.1 - - - +
312X SER* 1.3 62.2 + - - +
313X LEU 3.0 18.5 + - - +
314X TYR* 4.8 0.4 - - - +
327X GLY 5.1 0.6 - - - +
328X PHE 5.3 0.3 - - - +
329X PHE* 5.6 2.8 - - - +
330X SER* 3.2 14.0 + - - -
360X SER* 5.5 0.2 + - - -
505X 34Z 3.6 5.7 - - + +
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Residues in contact with SER 312 (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* 3.0 23.5 + - - -
305X GLY* 5.1 0.2 - - - -
306X THR* 5.5 1.5 + - - +
309X ALA* 4.6 4.9 + - - +
310X MET 3.5 6.8 + - - -
311X ASN* 1.3 76.5 + - - +
313X LEU* 1.3 76.4 + - - +
326X PRO* 3.4 11.8 - - - +
327X GLY 4.8 0.2 - - - -
330X SER* 3.6 17.0 + - - -
332X VAL* 3.8 2.8 - - - +
355X VAL* 3.3 42.3 - - - +
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Residues in contact with LEU 313 (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* 2.9 53.7 + - + -
311X ASN* 3.0 13.4 + - - +
312X SER* 1.3 92.9 - - - +
314X TYR* 1.3 66.9 + - - +
324X MET* 3.8 17.3 - - + -
325X ALA* 3.3 12.1 - - - -
326X PRO* 3.5 28.0 - - + -
327X GLY 4.7 0.4 - - - +
332X VAL* 4.3 10.1 - - + -
353X LEU* 4.0 6.5 - - + -
395X VAL* 3.9 36.6 - - + -
397X ILE* 4.0 12.3 - - + -
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Residues in contact with TYR 314 (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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187X THR 4.8 4.5 + - - -
188X GLN* 3.5 52.6 + - + -
301X VAL* 4.1 12.6 - - + -
302X ASN 3.2 14.8 - - - +
303X ALA* 4.4 3.8 - - + -
311X ASN* 4.8 1.3 - - - +
313X LEU* 1.3 78.5 - - - +
315X MET* 1.3 72.8 + - - +
316X ARG* 3.9 22.2 + - + +
324X MET* 3.7 7.2 - - - -
325X ALA* 2.6 50.9 + - + +
326X PRO 4.1 3.6 - - - -
327X GLY* 3.7 25.0 - - - -
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Residues in contact with MET 315 (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 VAL* 3.5 5.9 - - - -
302X ASN* 3.0 28.2 + - + -
314X TYR* 1.3 85.9 - - - +
316X ARG* 1.3 94.2 + - - +
317X GLN 4.2 2.2 - - - +
318X PRO* 3.5 27.4 - - + +
319X LYS 5.2 0.9 - - - +
323X GLU 3.3 26.5 - - - +
324X MET* 3.7 9.4 - - + -
325X ALA* 4.5 4.5 - - - +
394X THR* 5.3 11.4 - - + -
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Residues in contact with ARG 316 (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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188X GLN 4.4 12.1 - - - -
189X VAL 6.0 0.4 - - - -
299X GLU* 2.7 45.5 + - - +
300X LYS 3.8 4.7 - - - -
301X VAL* 4.4 5.4 - - + -
314X TYR* 3.9 23.3 + - + +
315X MET* 1.3 91.5 - - - +
317X GLN* 1.3 67.5 + - + +
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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