Contacts of the helix formed by residues 293 - 301 (chain C) in PDB entry 2W3S
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 ASP 293 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266C LEU* 3.5 33.0 - - + +
267C LEU* 5.4 1.1 - - + -
269C ARG 5.9 0.2 - - - -
270C PHE* 3.9 14.3 - - + -
291C ILE 3.8 8.1 - - - +
292C GLY* 1.3 73.5 - - - +
294C GLY* 1.3 64.6 + - - +
296C PRO* 3.7 8.1 - - - +
297C ALA 3.8 2.3 + - - -
352C LYS* 2.9 28.8 + - - +
362C SER* 3.0 23.9 + - - -
365C CYS* 4.0 12.3 - - - +
1465C FAD 2.5 36.5 + - - +
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Residues in contact with GLY 294 (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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263C LEU* 5.9 2.7 - - - -
267C LEU* 5.4 7.0 - - - -
270C PHE* 4.4 4.8 - - - -
281C ILE* 5.1 12.3 - - - -
284C ASN* 3.1 16.6 + - - -
285C ILE* 5.9 1.3 - - - -
293C ASP* 1.3 77.1 - - - +
295C PRO* 1.4 67.4 - - - +
297C ALA* 3.1 7.8 + - - +
298C LEU* 3.0 28.5 + - - +
1465C FAD 4.3 0.2 + - - -
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Residues in contact with PRO 295 (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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284C ASN* 3.5 13.7 - - - +
285C ILE* 4.5 15.9 - - + -
289C SER 5.3 3.8 - - - +
292C GLY* 3.7 10.3 - - - +
294C GLY* 1.4 84.4 - - - +
296C PRO* 1.4 76.4 - - + +
297C ALA 3.0 0.2 + - - -
298C LEU 3.2 0.2 + - - -
299C ILE* 2.8 31.0 + - + +
318C LEU* 4.0 11.9 - - + -
322C PHE* 3.7 38.8 - - + -
391C PRO* 3.8 13.7 - - + -
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Residues in contact with PRO 296 (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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292C GLY 3.1 28.7 - - - +
293C ASP 3.7 7.2 - - - +
295C PRO* 1.4 87.7 - - + +
297C ALA* 1.3 61.0 + - - +
299C ILE* 3.5 3.5 + - + -
300C ALA* 3.0 24.4 + - - +
365C CYS* 4.4 13.2 - - - +
367C CYS* 3.6 14.7 - - - +
383C ALA* 3.6 16.3 - - + +
384C PHE 4.1 6.1 - - - +
385C GLY* 3.7 33.7 - - - +
391C PRO* 4.3 7.4 - - + -
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Residues in contact with ALA 297 (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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263C LEU* 3.8 20.2 - - + -
266C LEU* 3.5 29.8 - - + -
293C ASP 3.8 0.8 + - - +
294C GLY 3.1 9.3 + - - +
295C PRO 3.1 1.0 - - - -
296C PRO* 1.3 80.0 - - - +
298C LEU* 1.3 64.4 + - - +
300C ALA* 3.3 4.7 + - - +
301C MET* 3.1 24.8 + - - +
348C LEU* 4.0 4.3 - - + +
350C CYS* 4.1 6.5 - - - -
367C CYS* 3.6 14.3 - - - -
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Residues in contact with LEU 298 (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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252C LEU* 5.8 4.0 - - + -
263C LEU* 4.3 26.9 - - + -
281C ILE* 5.1 11.0 - - + -
285C ILE* 4.8 5.8 - - + -
294C GLY* 3.0 18.6 + - - +
297C ALA* 1.3 75.8 - - - +
299C ILE* 1.3 64.8 + - - +
301C MET* 3.4 11.0 + - + +
302C GLY 3.0 4.2 + - - -
303C ALA* 2.8 35.1 + - + -
318C LEU* 3.5 26.9 - - + -
339C VAL* 4.2 20.0 - - + -
341C LEU* 3.7 32.8 - - + -
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Residues in contact with ILE 299 (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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295C PRO* 2.8 30.0 + - + +
296C PRO* 3.8 4.7 - - + +
298C LEU* 1.3 74.6 - - - +
300C ALA* 1.3 61.5 + - - +
302C GLY 2.8 4.3 + - - -
303C ALA 4.9 1.1 - - - +
318C LEU* 4.3 8.1 - - + -
319C GLU* 3.7 44.4 - - + +
322C PHE* 4.7 1.8 - - + -
381C ARG* 2.5 34.1 + - - +
383C ALA* 3.7 15.9 - - + -
391C PRO* 4.2 28.7 - - + +
392C LYS* 4.7 1.8 - - - +
393C ARG* 3.8 24.2 - - + +
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Residues in contact with ALA 300 (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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296C PRO 3.0 9.0 + - - +
297C ALA 3.3 0.6 + - - +
299C ILE* 1.3 77.3 - - - +
301C MET* 1.3 57.5 + - - +
348C LEU* 3.5 14.6 - - + -
367C CYS* 3.5 45.1 - - + +
368C LEU 4.3 0.2 - - - +
369C ASN* 3.4 8.9 + - + +
381C ARG* 3.1 39.6 - - - +
383C ALA* 4.4 4.3 - - + -
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Residues in contact with MET 301 (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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260C HIS* 3.5 46.2 - - + +
263C LEU* 3.9 25.4 - - + -
297C ALA 3.1 12.6 + - - +
298C LEU* 3.6 20.4 - - + +
299C ILE 3.2 0.2 - - - -
300C ALA* 1.3 75.5 - - - +
302C GLY* 1.3 58.1 + - - +
303C ALA 4.4 3.1 - - - +
341C LEU* 4.3 11.9 - - - -
342C PRO* 3.5 30.4 - - - +
345C ALA* 4.1 11.5 - - + +
348C LEU* 3.6 31.2 - - + -
369C ASN* 3.7 11.5 + - - +
381C ARG* 4.6 1.6 - - - -
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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