Contacts of the helix formed by residues 325 - 341 (chain A) in PDB entry 2W93
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 GLN 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 3.8 31.0 - - + +
190A LYS* 2.7 31.5 + - - +
191A PRO 4.3 1.0 + - - -
192A ASN* 2.8 44.1 + - - +
311A SER 3.1 24.1 - - - +
312A ASP* 4.1 7.2 - - - +
323A GLY 3.7 10.8 + - - +
324A VAL* 1.3 72.0 - - - +
326A MET* 1.3 65.0 + - - +
327A LYS 3.3 3.3 + - - +
328A PHE* 3.5 14.6 + - + -
329A VAL* 3.4 11.0 + - - +
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Residues in contact with MET 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A CYS* 3.3 31.2 - - + +
225A HIS* 3.8 18.8 - - + -
227A VAL* 3.9 23.6 - - + -
285A VAL* 4.3 1.3 - - - -
286A GLY* 4.2 5.4 - - - -
309A PHE* 3.5 44.2 - - + +
310A HIS 3.1 27.6 + - - +
311A SER* 3.9 14.5 + - - +
314A MET* 4.2 9.2 - - - -
324A VAL 3.8 0.6 + - - -
325A GLN* 1.3 70.6 - - - +
327A LYS* 1.3 71.0 + - + +
329A VAL* 4.2 1.6 - - - -
330A LEU* 2.8 28.6 + - + +
603A PY0 4.1 5.2 - - - +
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.1 25.4 - - + -
225A HIS* 4.2 7.6 - - + +
226A ASP* 2.9 41.4 + - + +
227A VAL* 3.9 15.9 - - + -
230A GLU* 2.4 33.4 + - - +
311A SER* 5.5 0.6 + - - +
325A GLN 3.3 1.0 - - - -
326A MET* 1.3 82.0 - - + +
328A PHE* 1.3 79.0 + - + +
330A LEU* 3.6 3.1 + - - +
331A GLN* 3.2 35.5 + - - +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 3.9 34.3 - - + -
190A LYS 3.6 22.0 - - - -
191A PRO* 4.1 8.3 - - + -
192A ASN* 3.8 22.2 - - - +
197A GLU* 3.2 20.0 - - - +
325A GLN* 3.5 14.2 + - + -
326A MET 3.2 0.4 - - - -
327A LYS* 1.3 83.3 - - + +
329A VAL* 1.3 67.9 + - - +
331A GLN* 3.5 22.2 + - - +
332A LYS* 3.3 34.7 + - + +
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 4.1 2.9 - - - +
197A GLU* 4.2 8.0 + - + -
200A VAL* 3.8 23.8 - - + -
201A ILE* 4.1 18.5 - - + +
204A ILE* 4.2 5.2 - - + -
309A PHE* 4.0 19.7 - - + -
314A MET* 4.1 11.0 - - + -
324A VAL* 3.7 26.0 - - + -
325A GLN 3.4 15.8 + - - +
326A MET* 3.2 8.6 + - - +
328A PHE* 1.3 77.3 - - - +
330A LEU* 1.3 63.2 + - - +
332A LYS* 3.5 1.2 + - - +
333A LEU* 3.0 24.5 + - + +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL* 3.7 35.4 - - + -
230A GLU* 3.9 20.9 - - + +
231A THR* 4.8 3.6 - - + -
234A LEU* 4.3 25.8 - - + -
285A VAL* 4.5 10.5 - - + -
309A PHE* 3.6 36.6 - - + -
326A MET* 2.8 28.3 + - + +
327A LYS 3.8 3.6 - - - +
329A VAL* 1.3 75.3 - - - +
331A GLN* 1.3 62.2 - - - +
333A LEU* 3.4 5.7 + - + +
334A LEU* 3.1 31.2 + - + +
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Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 3.9 19.9 + - + +
327A LYS* 3.2 22.0 - - - +
328A PHE* 3.7 31.6 - - - +
329A VAL 3.3 0.4 - - - -
330A LEU* 1.3 77.6 - - - +
332A LYS* 1.3 65.5 + - + +
334A LEU* 3.2 22.4 + - - +
335A THR* 3.4 12.9 + - - -
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Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLU* 2.6 37.2 + - - +
201A ILE* 3.7 24.4 - - + +
328A PHE* 3.3 23.8 + - + +
331A GLN* 1.3 79.6 - - + +
333A LEU* 1.3 66.5 + - - +
335A THR* 3.3 22.9 + - - +
336A ASN* 3.7 8.1 + - - +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 4.1 21.2 - - + +
204A ILE* 3.8 30.5 - - + -
205A LEU* 3.8 28.7 - - + -
234A LEU* 4.8 14.6 - - + -
283A LEU* 6.2 0.9 - - + -
309A PHE* 3.7 35.4 - - + -
329A VAL* 3.0 19.9 + - + +
330A LEU* 3.5 7.2 - - + +
332A LYS* 1.3 76.6 - - - +
334A LEU* 1.3 51.6 + - + +
336A ASN* 3.0 7.1 + - - +
337A ILE* 2.7 45.3 + - + +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 3.5 37.9 - - + +
233A LYS* 3.7 25.8 - - + +
234A LEU* 3.4 42.2 - - + +
237A LEU* 3.7 23.6 - - + +
330A LEU* 3.1 17.6 + - + +
331A GLN* 3.4 9.2 - - - +
332A LYS 3.2 0.6 - - - -
333A LEU* 1.3 76.2 - - + +
335A THR* 1.3 62.7 + - - +
336A ASN 3.0 6.6 + - - -
337A ILE* 3.6 12.8 + - + -
338A ALA 4.9 0.3 + - - -
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Residues in contact with THR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A GLN 3.4 8.8 + - - -
332A LYS* 3.3 16.6 + - - +
334A LEU* 1.3 76.0 - - - +
336A ASN* 1.3 67.8 + - - +
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Residues in contact with ASN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 6.0 3.6 - - + -
205A LEU* 4.7 21.4 - - + +
332A LYS 3.7 5.5 + - - +
333A LEU* 3.0 7.4 + - - +
334A LEU 3.0 0.8 - - - -
335A THR* 1.3 101.1 - - - +
337A ILE* 1.3 63.6 + - - +
338A ALA* 3.1 4.9 + - - +
339A ASP* 3.5 16.8 + - - +
340A ALA* 4.5 0.9 + - - +
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 5.1 1.1 - - + -
205A LEU* 4.2 18.6 - - + -
208A VAL* 4.1 30.5 - - + -
234A LEU* 4.4 18.2 - - + -
237A LEU* 3.6 32.5 - - + -
238A THR* 4.8 15.9 - - - +
240A PHE* 6.1 0.2 - - + -
283A LEU* 5.5 3.6 - - + -
333A LEU* 2.7 33.8 + - + +
334A LEU* 3.6 16.3 + - + -
336A ASN* 1.3 72.6 - - - +
338A ALA* 1.3 66.4 + - - +
340A ALA* 3.1 13.9 + - - +
341A ALA* 3.8 4.5 + - - +
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LEU* 4.1 37.0 - - + +
334A LEU 4.9 0.8 + - - +
336A ASN 3.1 2.1 + - - +
337A ILE* 1.3 81.8 - - - +
339A ASP* 1.3 63.7 + - - +
340A ALA 3.3 0.2 + - - -
341A ALA* 3.4 8.7 + - - +
342A LYS* 3.2 31.8 + - - +
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Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LYS* 4.3 16.3 + - - +
336A ASN 3.5 10.4 + - - +
337A ILE 3.2 0.6 + - - -
338A ALA* 1.3 79.4 - - - +
340A ALA* 1.3 58.6 + - - +
341A ALA 3.1 5.6 + - - -
342A LYS* 3.4 26.5 + - - +
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 3.7 42.2 - - + +
208A VAL* 3.3 10.6 - - + +
209A LYS* 3.2 46.1 - - + +
336A ASN 4.5 0.4 + - - -
337A ILE* 3.1 11.7 + - + +
339A ASP* 1.3 78.8 - - - +
341A ALA* 1.3 57.4 + - - +
342A LYS 3.7 0.4 - - - -
343A GLY 5.2 0.9 + - - -
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Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A VAL* 3.8 8.3 - - + -
237A LEU 5.0 1.1 - - - +
238A THR* 3.4 35.8 - - - +
240A PHE* 3.8 15.0 - - + -
337A ILE 3.8 5.1 + - - +
338A ALA 3.4 6.5 + - - +
339A ASP 3.1 1.0 - - - -
340A ALA* 1.3 79.6 - - - +
342A LYS* 1.3 58.7 + - - +
343A GLY 3.2 3.4 - - - -
344A TYR* 3.0 30.5 + - - +
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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
------------------------------------------------------------
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