Contacts of the helix formed by residues 269 - 282 (chain A) in PDB entry 2H3W
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A ASN 4.5 0.2 + - - -
266A LEU 3.8 1.4 + - - +
267A ILE 3.1 0.6 - - - -
268A LYS* 1.3 80.5 - - - +
270A LYS* 1.3 67.5 + - - +
271A VAL* 3.1 4.8 + - - +
272A ASN* 2.8 42.9 + - - +
273A ARG* 2.9 27.5 + - - +
384A ASN* 2.7 38.7 + - + +
386A THR* 6.6 0.2 - - + -
389A ILE* 6.2 0.2 - - + -
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Residues in contact with LYS 270 (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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268A LYS 3.9 1.8 + - - -
269A ASP* 1.3 77.0 + - - +
271A VAL* 1.3 68.4 + - + +
273A ARG* 3.7 23.6 + - - +
274A GLU* 3.0 30.4 + - + +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASP* 3.1 9.3 + - - +
270A LYS* 1.3 78.9 - - + +
272A ASN* 1.3 67.1 + - - +
274A GLU* 3.1 16.4 + - - +
275A SER* 2.9 23.3 + - - +
382A ARG* 3.6 31.9 - - + +
384A ASN* 3.2 22.2 - - - +
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Residues in contact with ASN 272 (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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266A LEU* 3.0 44.6 + - + +
267A ILE* 4.8 0.2 - - - -
269A ASP* 2.8 26.9 + - - +
270A LYS 3.4 0.2 - - - -
271A VAL* 1.3 71.5 - - - +
273A ARG* 1.3 63.0 + - - +
275A SER* 3.0 3.6 + - - -
276A VAL* 2.9 28.7 + - - +
382A ARG 4.5 0.2 - - - -
383A PHE* 3.3 23.6 - - + +
384A ASN* 2.6 47.6 + - - +
389A ILE* 3.7 6.1 - - - +
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Residues in contact with ARG 273 (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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267A ILE* 2.7 61.6 + - + +
268A LYS* 3.9 7.7 + - - +
269A ASP 2.9 18.1 + - - +
270A LYS* 3.7 27.7 + - - +
272A ASN* 1.3 77.3 - - - +
274A GLU* 1.3 58.8 + - - +
276A VAL* 3.8 1.6 - - - +
277A ASN* 3.0 31.1 + - + +
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Residues in contact with GLU 274 (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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270A LYS* 3.0 23.1 + - + +
271A VAL* 3.1 18.5 + - - +
273A ARG* 1.3 77.4 - - - +
275A SER* 1.3 61.9 + - - +
277A ASN* 3.5 6.6 + - - +
278A SER* 3.1 22.2 + - - -
379A LYS* 3.5 33.5 + - - +
381A LEU* 5.0 2.0 - - + +
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Residues in contact with SER 275 (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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271A VAL* 2.9 11.1 + - - +
272A ASN 3.5 6.5 - - - -
274A GLU* 1.3 74.2 + - - +
276A VAL* 1.3 64.8 + - - +
278A SER* 3.2 5.2 + - - -
279A ILE* 3.1 28.0 + - - +
381A LEU* 3.2 35.0 - - - +
382A ARG 2.6 29.8 + - - -
383A PHE* 3.8 14.8 - - - -
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Residues in contact with VAL 276 (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 TYR* 3.7 18.4 - - + +
266A LEU* 4.0 12.6 - - + -
267A ILE* 4.1 11.7 - - + -
272A ASN 2.9 18.6 + - - +
273A ARG 3.8 3.8 - - - +
275A SER* 1.3 75.6 - - - +
277A ASN* 1.3 59.5 + - - +
279A ILE* 3.0 11.0 + - - +
280A GLN* 2.9 60.8 + - + +
322A TRP* 3.9 22.9 - - + -
383A PHE* 3.9 16.8 - - + -
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Residues in contact with ASN 277 (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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193A PHE* 5.6 2.2 - - - -
273A ARG* 3.0 21.5 + - + +
274A GLU* 3.7 7.0 - - - +
275A SER 3.3 0.2 - - - -
276A VAL* 1.3 76.0 - - - +
278A SER* 1.3 64.2 + - - +
280A GLN* 3.8 13.8 + - - +
281A LYS* 2.8 68.2 + - - +
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Residues in contact with SER 278 (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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202A HIS* 2.9 37.5 - - - -
204A THR* 4.2 1.1 - - - +
213A GLU* 2.7 31.1 + - - +
274A GLU 3.1 11.5 + - - -
275A SER 3.4 9.6 - - - -
277A ASN* 1.3 79.5 + - - +
279A ILE* 1.3 56.7 + - - +
281A LYS* 4.8 0.4 - - - -
282A SER* 2.9 13.5 + - - -
381A LEU* 3.5 24.7 - - - +
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Residues in contact with ILE 279 (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 THR* 3.7 17.3 - - + +
211A PHE* 3.6 35.9 - - + -
275A SER 3.1 13.8 + - - +
276A VAL* 3.0 9.7 + - - +
278A SER* 1.3 76.3 - - - +
280A GLN* 1.3 58.6 + - - +
282A SER* 2.6 22.0 + - - -
285A THR* 4.8 1.3 - - - +
322A TRP* 3.6 57.7 - - + +
325A LYS* 2.8 16.4 + - + -
381A LEU* 3.9 12.8 - - + -
383A PHE* 4.4 9.4 - - + -
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Residues in contact with GLN 280 (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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179A SER 3.7 4.3 + - - +
180A CYS* 3.5 34.4 - - + +
181A ARG 4.3 7.3 + - - -
182A VAL* 4.2 22.4 - - - +
183A PRO* 5.0 0.8 - - - +
191A VAL* 4.6 3.9 - - + +
193A PHE* 3.8 19.8 - - + -
263A TYR* 3.2 30.4 + - - -
276A VAL* 2.9 35.3 + - + +
277A ASN* 3.8 13.5 + - - +
279A ILE* 1.3 77.2 - - + +
281A LYS* 1.3 55.4 + - + +
322A TRP* 5.0 5.5 - - - +
324A ASP* 5.7 0.6 + - - -
325A LYS* 2.7 17.7 + - - -
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Residues in contact with LYS 281 (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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178A SER* 3.8 6.8 - - - -
193A PHE* 3.7 43.1 - - + -
198A ARG* 5.7 8.1 - - - +
200A PRO* 3.2 33.4 - - + +
202A HIS* 4.1 8.1 - - - +
277A ASN* 2.8 53.1 + - - +
278A SER* 4.0 3.1 - - - +
280A GLN* 1.3 73.7 - - + +
282A SER* 1.3 68.6 + - - +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER* 3.4 4.0 - - - -
202A HIS* 3.3 17.0 - - - -
203A ILE* 3.8 0.2 - - - -
204A THR* 3.0 48.6 + - - -
278A SER 2.9 8.6 + - - -
279A ILE 2.6 18.5 + - - -
281A LYS* 1.3 77.4 - - - +
283A ILE* 1.3 64.2 + - - +
284A PHE 3.9 2.0 + - - -
325A LYS* 2.5 32.7 + - - -
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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