Contacts of the helix formed by residues 293 - 301 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A LEU* 5.6 0.3 - - - +
266A LEU* 3.5 31.5 - - + +
267A LEU* 5.4 2.2 - - - +
270A PHE* 4.3 11.4 - - + -
291A ILE 3.2 11.4 - - - +
292A GLY* 1.3 68.0 - - - -
294A GLY* 1.3 64.3 + - - +
296A PRO* 3.7 11.2 - - - +
297A ALA* 4.0 4.2 + - - +
352A LYS* 2.7 29.6 + - + -
361A ILE* 5.7 0.3 - - - -
362A SER* 2.6 29.9 + - - -
365A CYS* 4.0 13.8 - - - +
1465A FAD 2.8 25.0 + - - +
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Residues in contact with GLY 294 (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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263A LEU* 5.7 2.0 - - - +
267A LEU* 5.6 6.1 - - - -
270A PHE* 4.4 5.9 - - - -
281A ILE* 6.3 3.4 - - - -
284A ASN* 3.2 16.8 + - - -
285A ILE* 5.6 1.8 - - - -
292A GLY 3.2 0.8 + - - -
293A ASP* 1.3 78.8 - - - +
295A PRO* 1.4 73.7 - - - +
296A PRO 3.2 0.5 - - - -
297A ALA* 3.3 2.6 + - - +
298A LEU* 3.1 26.6 + - - +
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Residues in contact with PRO 295 (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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284A ASN* 3.1 18.6 - - - +
285A ILE* 4.3 16.1 - - + -
289A SER 5.4 4.9 - - - +
292A GLY* 3.2 16.4 - - - +
294A GLY* 1.4 79.0 - - - +
296A PRO* 1.4 68.1 - - + +
298A LEU 2.8 13.2 + - - -
299A ILE* 2.8 19.9 + - + +
318A LEU* 3.8 12.8 - - + -
322A PHE* 3.6 41.1 - - + -
391A PRO* 3.9 12.1 - - + -
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Residues in contact with PRO 296 (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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290A PRO 5.4 0.2 - - - +
292A GLY 2.8 29.4 - - - +
293A ASP* 3.7 5.2 - - - +
294A GLY 3.5 3.1 - - - -
295A PRO* 1.4 85.5 - - + +
297A ALA* 1.3 62.7 + - - +
299A ILE* 4.9 3.1 - - + -
300A ALA* 3.1 19.2 + - - +
365A CYS* 4.0 25.8 - - + +
367A CYS* 3.7 9.6 - - + -
383A ALA* 3.5 15.9 - - + +
384A PHE* 4.3 6.1 - - - +
385A GLY* 3.9 29.4 - - - +
391A PRO* 4.5 6.0 - - + -
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Residues in contact with ALA 297 (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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263A LEU* 4.1 18.2 - - + -
266A LEU* 3.7 21.3 - - + -
293A ASP 4.0 1.7 + - - +
294A GLY 3.3 7.5 + - - +
295A PRO 3.3 0.4 - - - -
296A PRO* 1.3 79.6 - - - +
298A LEU* 1.3 58.6 + - - +
300A ALA* 3.4 3.5 + - - +
301A MET* 3.0 28.0 + - + +
348A LEU* 3.9 5.1 - - + +
350A CYS* 3.8 10.5 - - - -
367A CYS* 3.3 22.1 - - - -
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Residues in contact with LEU 298 (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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252A LEU* 5.5 4.9 - - + -
263A LEU* 4.0 25.6 - - + -
281A ILE* 5.4 9.0 - - + -
285A ILE* 4.6 9.6 - - + -
294A GLY* 3.1 16.2 + - - +
295A PRO 2.8 9.0 + - - +
297A ALA* 1.3 74.0 - - - +
299A ILE* 1.3 54.4 + - - +
301A MET* 3.1 20.7 - - + +
302A GLY 2.9 21.3 + - - -
303A ALA* 3.0 16.8 + - + -
318A LEU* 3.5 24.5 - - + -
339A VAL* 4.0 18.4 - - + -
341A LEU* 3.6 34.8 - - + -
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Residues in contact with ILE 299 (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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295A PRO* 2.8 26.5 + - + +
296A PRO* 3.8 3.6 - - + +
298A LEU* 1.3 72.7 - - - +
300A ALA* 1.3 57.3 + - - +
302A GLY* 2.6 14.9 + - - +
303A ALA 4.8 1.1 - - - +
318A LEU* 3.8 9.2 - - + -
319A GLU* 3.5 50.3 - - + +
322A PHE* 4.1 16.8 - - + -
381A ARG* 2.5 38.5 + - - +
383A ALA* 3.9 15.3 - - + -
391A PRO* 4.3 17.7 - - + +
392A LYS* 5.5 0.2 - - - -
393A ARG* 4.2 12.8 - - + +
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Residues in contact with ALA 300 (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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296A PRO 3.1 6.2 + - - +
297A ALA 3.4 9.6 - - - +
299A ILE* 1.3 75.8 - - - +
301A MET* 1.3 57.9 + - - +
348A LEU* 3.5 13.5 - - + -
367A CYS* 3.4 42.0 - - + +
368A LEU 4.2 0.4 - - - +
369A ASN* 2.9 28.3 + - + +
381A ARG* 3.3 18.7 - - - +
383A ALA* 3.8 6.2 - - + +
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Residues in contact with MET 301 (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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260A HIS* 3.5 42.6 - - + +
263A LEU* 4.1 19.3 - - + -
297A ALA 3.0 7.6 + - - +
298A LEU* 3.1 31.4 + - + +
299A ILE 3.1 0.2 - - - -
300A ALA* 1.3 74.5 - - - +
302A GLY* 1.3 62.2 + - - +
303A ALA* 4.3 2.9 - - + +
341A LEU* 3.7 29.6 - - + -
342A PRO* 3.4 25.4 - - + +
345A ALA* 5.7 2.9 - - + -
348A LEU* 3.6 28.9 - - + +
369A ASN* 3.9 11.2 + - - +
381A ARG* 4.5 1.3 - - - -
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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