Contacts of the helix formed by residues 325 - 341 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 3.5 39.9 - - + +
190C LYS* 2.7 33.4 + - - +
191C PRO 3.8 7.1 + - - -
192C ASN* 2.7 43.4 + - - +
311C SER 3.2 22.1 - - - +
312C ASP* 4.7 3.1 - - - -
323C GLY 3.6 11.8 + - - +
324C VAL* 1.3 71.6 - - - +
326C MET* 1.3 65.6 + - - +
327C LYS 3.2 4.6 + - - +
328C PHE* 3.5 5.8 + - + -
329C VAL* 3.5 9.6 + - - +
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Residues in contact with MET 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C CYS* 3.4 33.4 - - + +
225C HIS* 3.9 16.4 - - + +
227C VAL* 4.0 24.2 - - + -
285C VAL* 4.6 1.1 - - - -
286C GLY* 4.3 4.9 - - - -
309C PHE* 3.5 48.5 - - + +
310C HIS 2.9 20.6 + - - +
311C SER* 3.7 17.6 + - - +
314C MET* 4.2 3.1 - - - -
324C VAL 3.7 0.4 + - - -
325C GLN* 1.3 71.3 - - - +
327C LYS* 1.3 59.4 + - + +
329C VAL* 4.2 7.4 - - - -
330C LEU* 2.8 38.1 + - + +
603C PY0 4.0 4.9 - - - +
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Residues in contact with LYS 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LEU* 3.9 26.0 - - + -
225C HIS 5.1 2.9 - - - +
226C ASP* 2.7 47.2 + - + +
227C VAL* 3.8 12.6 - - + -
230C GLU* 2.9 29.4 + - - +
311C SER* 5.7 0.2 - - - +
325C GLN* 3.2 1.2 + - - +
326C MET* 1.3 82.2 - - - +
328C PHE* 1.3 81.7 + - + +
330C LEU* 3.7 3.1 - - - +
331C GLN* 3.1 38.0 + - - +
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Residues in contact with PHE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C SER* 5.8 2.5 - - - -
189C LEU* 3.8 33.4 - - + -
190C LYS 3.2 27.8 - - - -
191C PRO* 4.2 3.6 - - + -
192C ASN* 3.8 20.6 - - - +
197C GLU* 3.2 20.2 - - - +
325C GLN* 3.5 7.1 + - + -
326C MET 3.3 0.2 - - - -
327C LYS* 1.3 89.9 - - + +
329C VAL* 1.3 66.9 + - - +
330C LEU 3.3 0.4 - - - -
331C GLN* 3.7 22.7 - - - -
332C LYS* 3.0 38.4 + - - +
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ASN* 4.0 3.4 - - - +
197C GLU* 4.1 8.7 - - + -
200C VAL* 4.0 24.7 - - + -
201C ILE* 4.1 16.3 - - + +
204C ILE* 4.0 7.9 - - + -
309C PHE* 3.9 21.3 - - + -
314C MET* 4.2 7.0 - - + -
324C VAL* 3.6 31.2 - - + -
325C GLN 3.5 8.9 + - - +
326C MET* 3.3 9.3 + - - +
328C PHE* 1.3 77.7 - - - +
330C LEU* 1.3 57.8 + - - +
333C LEU* 2.8 33.7 + - + +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C VAL* 3.7 37.9 - - + -
230C GLU* 4.0 22.4 - - + +
231C THR* 4.8 3.1 - - - +
234C LEU* 4.5 21.1 - - + -
285C VAL* 4.6 9.6 - - + -
309C PHE* 3.6 32.8 - - + -
326C MET* 2.8 32.4 + - + +
327C LYS 3.7 4.0 - - - +
329C VAL* 1.3 74.9 - - - +
331C GLN* 1.3 61.5 + - - +
333C LEU* 3.3 7.5 + - + +
334C LEU* 3.0 34.0 + - + +
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Residues in contact with GLN 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C GLU* 2.9 32.4 + - + +
327C LYS* 3.1 35.0 + - - +
328C PHE* 3.3 25.5 + - - +
330C LEU* 1.3 78.2 - - - +
332C LYS* 1.3 64.0 + - + +
334C LEU* 3.5 19.5 + - + +
335C THR* 3.9 7.6 + - - -
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Residues in contact with LYS 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C GLU* 2.7 38.4 + - - +
201C ILE* 3.8 21.3 - - + +
328C PHE* 3.0 19.2 + - - +
331C GLN* 1.3 74.4 - - + +
333C LEU* 1.3 67.4 + - - +
334C LEU 3.1 1.8 - - - -
335C THR* 3.2 24.9 + - - -
336C ASN* 4.1 5.4 + - - +
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Residues in contact with LEU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ILE* 4.1 15.8 - - + +
204C ILE* 4.1 24.2 - - + -
205C LEU* 3.5 36.6 - - + -
234C LEU* 4.5 12.3 - - + -
283C LEU* 5.9 0.9 - - + -
309C PHE* 4.0 28.9 - - + -
329C VAL* 2.8 22.4 + - + +
330C LEU* 3.4 8.1 - - + +
332C LYS* 1.3 75.8 - - - +
334C LEU* 1.3 64.6 + - + +
336C ASN* 3.1 5.2 + - - +
337C ILE* 3.0 44.3 + - + +
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Residues in contact with LEU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLU* 3.9 36.6 - - + +
233C LYS* 3.9 18.4 - - + -
234C LEU* 3.6 41.3 - - + +
237C LEU* 3.4 29.6 - - + +
330C LEU* 3.0 27.4 + - + +
331C GLN* 3.6 11.2 - - + +
332C LYS 3.1 0.6 - - - -
333C LEU* 1.3 77.2 - - + +
335C THR* 1.3 61.2 + - - +
336C ASN 3.3 0.7 + - - -
337C ILE* 3.7 12.3 + - + +
338C ALA* 4.7 1.4 + - - +
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Residues in contact with THR 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C GLN 3.9 8.5 + - - -
332C LYS* 3.2 18.3 + - - -
334C LEU* 1.3 79.3 - - - +
336C ASN* 1.3 71.5 + - - +
338C ALA 5.5 0.2 - - - -
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Residues in contact with ASN 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ILE* 5.9 2.2 - - + +
205C LEU* 3.9 31.5 - - + +
332C LYS 4.7 3.6 + - - +
333C LEU 3.1 4.2 + - - +
335C THR* 1.3 95.1 - - - +
337C ILE* 1.3 65.9 + - - +
338C ALA* 3.3 3.8 + - - -
339C ASP* 3.4 9.4 + - - +
340C ALA* 3.4 14.7 + - - +
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Residues in contact with ILE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C LEU* 3.9 8.1 - - + -
208C VAL* 4.0 29.6 - - + -
234C LEU* 4.1 10.5 - - + -
237C LEU* 3.8 25.6 - - + -
238C THR* 3.8 19.1 - - - +
283C LEU* 5.4 2.5 - - + -
333C LEU* 3.0 45.3 + - + +
334C LEU* 3.7 26.8 + - + +
336C ASN* 1.3 77.4 - - - +
338C ALA* 1.3 66.9 + - - +
340C ALA* 3.2 2.4 + - - +
341C ALA* 2.9 22.2 + - - +
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Residues in contact with ALA 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C LEU* 3.9 40.6 - - + +
334C LEU 4.7 1.4 + - - +
335C THR 5.5 0.2 - - - -
336C ASN 3.3 1.0 - - - -
337C ILE* 1.3 81.2 - - - +
339C ASP* 1.3 57.7 + - - +
341C ALA* 3.3 3.3 + - - +
342C LYS* 3.0 44.4 + - - +
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Residues in contact with ASP 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C LYS* 5.3 4.9 - - - +
336C ASN* 3.4 9.1 + - + +
337C ILE 3.3 0.2 - - - -
338C ALA* 1.3 76.1 - - - +
340C ALA* 1.3 67.3 + - - +
342C LYS* 3.1 35.7 + - + +
343C GLY 4.6 0.9 + - - -
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C LEU* 3.9 27.1 - - + +
208C VAL* 3.7 18.9 - - + +
209C LYS* 3.5 50.0 + - + +
336C ASN 3.4 4.3 + - - +
337C ILE 3.2 8.9 + - - +
339C ASP* 1.3 80.7 + - - +
341C ALA* 1.3 57.5 + - - +
342C LYS 3.3 0.6 + - - -
343C GLY* 4.5 3.6 + - - -
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Residues in contact with ALA 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C VAL* 4.1 6.7 - - + -
237C LEU 4.5 1.8 - - - +
238C THR* 4.2 21.0 - - - +
240C PHE* 3.7 32.1 - - + -
337C ILE 2.9 15.9 + - - +
338C ALA 3.3 3.8 + - - +
340C ALA* 1.3 74.3 - - - +
342C LYS* 1.3 63.8 + - - +
343C GLY 3.1 3.8 - - - -
344C TYR* 2.9 23.0 + - - +
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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
------------------------------------------------------------
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