Contacts of the helix formed by residues 325 - 341 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D LEU* 3.4 35.5 - - + +
190D LYS* 2.8 31.0 + - - +
191D PRO 4.4 0.2 - - - -
192D ASN* 2.8 42.9 + - - +
311D SER 3.2 24.0 - - - +
312D ASP* 4.3 5.6 - - - -
323D GLY* 3.7 11.2 + - - +
324D VAL* 1.3 71.4 - - - +
326D MET* 1.3 65.2 + - - +
327D LYS 3.2 3.1 + - - +
328D PHE* 3.4 7.6 + - + -
329D VAL* 3.3 10.8 + - - +
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Residues in contact with MET 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D CYS* 3.5 30.3 - - + +
222D CYS 4.7 0.2 - - - +
225D HIS* 3.8 16.2 - - + +
227D VAL* 3.9 26.9 - - + -
285D VAL* 4.4 4.5 - - - -
286D GLY* 4.5 0.4 - - - -
309D PHE* 3.6 40.2 - - + +
310D HIS* 3.1 27.5 + - - +
311D SER* 3.6 19.7 + - - +
314D MET* 4.2 2.9 - - - -
324D VAL 3.8 0.8 + - - -
325D GLN* 1.3 70.2 - - - +
327D LYS* 1.3 68.9 + - + +
329D VAL* 3.8 9.0 - - - -
330D LEU* 2.8 30.0 + - + +
603D PY0 4.2 3.1 - - - +
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Residues in contact with LYS 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D LEU* 4.3 21.8 - - + -
225D HIS 5.0 3.4 - - - +
226D ASP* 3.0 44.6 + - + +
227D VAL* 3.9 14.4 - - + -
229D ALA* 5.8 1.4 - - - +
230D GLU* 2.8 30.5 + - - +
311D SER* 5.5 0.4 + - - +
325D GLN* 3.2 1.4 + - - +
326D MET* 1.3 83.3 - - + +
328D PHE* 1.3 80.8 + - + +
330D LEU* 3.8 2.6 - - - +
331D GLN* 3.1 38.8 + - - +
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Residues in contact with PHE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D LEU* 3.7 38.1 - - + -
190D LYS 3.4 28.0 - - - -
191D PRO* 3.9 13.5 - - + -
192D ASN* 3.6 13.7 - - - +
197D GLU* 3.4 18.6 - - - +
325D GLN* 3.4 9.9 + - + -
326D MET 3.2 0.4 - - - -
327D LYS* 1.3 92.5 - - + +
329D VAL* 1.3 66.2 + - - +
331D GLN* 3.6 21.9 - - - +
332D LYS* 2.9 36.2 + - - +
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Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ASN* 4.1 3.6 - - - +
197D GLU* 4.1 7.5 + - + -
200D VAL* 3.8 22.2 - - + -
201D ILE* 4.1 16.7 - - + +
204D ILE* 4.0 15.7 - - + -
309D PHE* 4.1 10.1 - - + -
314D MET* 4.1 8.5 - - + -
324D VAL* 3.5 28.0 - - + -
325D GLN 3.3 17.4 + - - +
326D MET* 3.8 9.0 - - - +
328D PHE* 1.3 76.9 - - - +
330D LEU* 1.3 56.8 + - - +
332D LYS* 3.8 1.2 - - - +
333D LEU* 2.9 33.0 + - + +
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Residues in contact with LEU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D VAL* 3.9 35.0 - - + -
230D GLU* 3.9 17.9 - - + +
231D THR* 4.5 3.4 - - + -
234D LEU* 4.2 28.7 - - + -
285D VAL* 4.4 11.2 - - + -
309D PHE* 3.6 35.9 - - + -
326D MET* 2.8 28.6 + - + +
327D LYS 3.8 3.1 - - - +
329D VAL* 1.3 69.7 - - - +
331D GLN* 1.3 66.1 + - - +
333D LEU* 3.4 9.6 + - + +
334D LEU* 3.1 30.9 + - + +
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Residues in contact with GLN 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU* 3.1 32.5 + - + +
327D LYS* 3.1 37.7 + - - +
328D PHE* 3.2 26.3 + - - +
330D LEU* 1.3 78.7 - - - +
332D LYS* 1.3 63.7 + - + +
334D LEU* 3.4 19.4 + - + +
335D THR* 3.8 7.1 + - - -
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Residues in contact with LYS 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D PRO* 6.1 2.8 - - - +
197D GLU* 2.6 36.9 + - - +
201D ILE* 3.6 19.2 - - + +
328D PHE* 2.9 21.4 + - - +
331D GLN* 1.3 76.6 - - + +
333D LEU* 1.3 54.5 - - - +
334D LEU 3.3 0.2 - - - -
335D THR* 2.7 36.8 - - + +
336D ASN* 2.8 10.3 - - - +
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Residues in contact with LEU 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ILE* 4.2 13.8 - - + +
204D ILE* 3.8 32.3 - - + -
205D LEU* 3.8 34.5 - - + -
234D LEU* 4.9 5.4 - - + -
283D LEU* 6.3 0.4 - - + -
309D PHE* 4.0 27.1 - - + -
329D VAL* 2.9 23.2 + - + +
330D LEU* 3.6 12.6 - - + +
332D LYS* 1.3 71.9 - - - +
334D LEU* 1.3 57.6 + - + +
335D THR 2.8 7.9 + - - -
336D ASN* 3.0 4.1 + - - -
337D ILE* 2.8 49.8 + - + +
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU* 3.8 22.2 - - + +
233D LYS* 3.7 25.6 - - + -
234D LEU* 3.5 43.1 - - + +
237D LEU* 3.3 31.0 - - + +
330D LEU* 3.1 20.6 + - + +
331D GLN* 3.6 13.9 - - + +
332D LYS 3.3 0.8 - - - -
333D LEU* 1.3 75.4 - - - +
335D THR* 1.3 59.7 + - - +
337D ILE* 4.2 4.0 + - + -
338D ALA* 5.2 1.4 + - - +
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Residues in contact with THR 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D GLN 3.8 8.8 + - - -
332D LYS* 2.7 17.4 + - + +
333D LEU 2.8 1.0 + - - -
334D LEU* 1.3 82.0 - - - +
336D ASN* 1.3 97.9 + - - +
338D ALA* 5.5 1.4 - - - +
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Residues in contact with ASN 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 4.5 5.0 - - - +
205D LEU* 3.9 30.4 - - + +
332D LYS 2.8 11.8 - - - +
333D LEU* 3.0 3.0 + - - +
335D THR* 1.3 108.7 + - - +
337D ILE* 1.3 62.3 + - - +
338D ALA 3.3 2.9 - - - -
339D ASP* 3.3 19.6 + - - +
340D ALA* 3.3 10.0 + - - +
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Residues in contact with ILE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D ILE* 5.1 0.7 - - + -
205D LEU* 4.0 8.9 - - + +
208D VAL* 4.0 32.1 - - + -
234D LEU* 3.8 31.6 - - + -
237D LEU* 4.2 18.8 - - + -
238D THR* 4.0 15.9 - - - +
283D LEU* 5.1 4.7 - - + -
333D LEU* 2.8 39.2 + - + +
334D LEU* 4.2 12.6 - - + -
335D THR 3.8 0.6 - - - -
336D ASN* 1.3 74.7 - - - +
338D ALA* 1.3 62.5 - - - +
340D ALA* 3.0 2.7 + - + -
341D ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D LEU* 4.0 42.1 - - + +
334D LEU 5.2 1.5 + - - +
335D THR 5.9 1.6 - - - +
336D ASN 3.3 1.4 - - - -
337D ILE* 1.3 80.6 - - - +
339D ASP* 1.3 63.2 + - - +
341D ALA* 3.4 2.4 + - - +
342D LYS* 3.2 20.6 + - - +
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Residues in contact with ASP 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ASN* 3.3 11.7 + - - +
338D ALA* 1.3 77.8 - - - +
340D ALA* 1.3 65.0 + - - +
342D LYS* 3.1 47.0 + - - +
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Residues in contact with ALA 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 3.8 39.5 - - + +
208D VAL* 3.7 22.2 - - + +
209D LYS* 3.8 25.5 - - + +
336D ASN 3.3 3.1 + - - +
337D ILE* 3.0 9.4 + - - +
339D ASP* 1.3 82.9 + - - +
341D ALA* 1.3 57.2 + - - +
342D LYS* 3.8 0.3 + - - +
343D GLY 5.1 1.4 + - - -
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Residues in contact with ALA 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D VAL* 4.2 4.7 - - + -
237D LEU 4.8 2.0 - - - +
238D THR* 3.9 18.8 - - - +
240D PHE* 3.8 32.3 - - + -
337D ILE 2.9 14.6 + - - +
338D ALA 3.4 4.5 + - - +
339D ASP 3.1 0.4 - - - -
340D ALA* 1.3 76.2 - - - +
342D LYS* 1.3 64.6 + - - +
343D GLY 3.3 2.7 - - - -
344D TYR* 3.1 22.6 + - - +
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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