Contacts of the helix formed by residues 250 - 260 (chain D) in PDB entry 2WWR
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 ASN 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224D GLY* 5.0 6.2 + - - +
226D CYS 3.0 17.8 + - - +
227D ASN* 3.9 17.8 - - + +
248D VAL 4.0 1.2 + - - -
249D VAL* 1.3 68.3 - - - +
251D GLN* 1.3 60.2 + - - +
252D ASP* 3.7 8.3 + - - +
253D ASP* 3.0 37.2 + - + +
254D LEU* 2.9 27.9 + - - +
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Residues in contact with GLN 251 (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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246D GLY 4.3 5.4 - - - +
249D VAL* 3.4 21.0 + - + +
250D ASN* 1.3 69.9 + - - +
252D ASP* 1.3 63.4 + - - +
254D LEU* 3.6 3.3 + - - +
255D TYR* 3.1 25.3 + - - +
268D LEU* 5.2 2.6 - - + +
270D VAL 5.0 0.5 - - - +
271D THR* 3.6 11.8 - - - +
272D SER* 2.6 59.0 + - - -
276D LEU* 4.3 1.8 - - - +
280D HIS* 3.9 20.8 + - + +
282D LEU* 3.5 31.3 - - + +
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Residues in contact with ASP 252 (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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250D ASN* 3.3 8.4 + - - +
251D GLN* 1.3 76.8 - - - +
253D ASP* 1.3 65.9 + - - +
255D TYR* 3.2 9.5 + - - +
256D GLN* 3.0 28.8 + - - +
280D HIS* 5.7 3.6 + - - -
281D PRO* 5.6 6.6 - - - +
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Residues in contact with ASP 253 (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 ASN* 3.4 12.1 - - - +
228D LYS* 2.6 56.0 + - + +
231D PHE* 3.9 4.1 - - + -
250D ASN* 3.0 28.6 + - + +
252D ASP* 1.3 80.7 - - - +
254D LEU* 1.3 55.9 + - - +
256D GLN* 3.4 7.9 + - - +
257D ALA* 3.0 30.3 + - - +
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Residues in contact with LEU 254 (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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231D PHE* 3.7 30.2 - - + -
240D PHE* 4.4 4.9 - - + -
249D VAL* 3.9 19.5 - - + -
250D ASN 2.9 15.8 + - - +
251D GLN 3.8 5.8 - - - +
253D ASP* 1.3 74.5 - - - +
255D TYR* 1.3 64.4 + - - +
257D ALA* 4.0 1.0 - - - +
258D LEU* 3.1 46.1 + - + +
263D ILE* 4.1 7.0 - - + -
266D ALA* 4.0 13.5 - - + -
268D LEU* 3.7 36.6 - - + -
282D LEU* 3.9 13.5 - - + -
288D CYS* 5.0 0.2 - - - -
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Residues in contact with TYR 255 (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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251D GLN 3.1 16.5 + - - +
252D ASP* 3.2 10.5 + - - +
254D LEU* 1.3 75.2 - - - +
256D GLN* 1.3 64.1 + - + +
258D LEU* 3.8 1.0 - - - +
259D ALA* 2.9 47.7 + - + +
280D HIS* 6.3 0.2 - - + -
281D PRO* 3.6 44.0 - - + -
282D LEU* 4.1 12.5 - - + +
284D THR* 4.1 6.4 + - - -
285D LEU* 3.3 39.3 - - + +
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Residues in contact with GLN 256 (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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252D ASP 3.0 16.1 + - - +
253D ASP* 3.8 7.4 - - - +
255D TYR* 1.3 84.1 - - + +
257D ALA* 1.3 58.1 + - - +
259D ALA* 4.1 2.9 - - - +
260D SER* 2.6 55.8 + - - -
262D LYS* 4.1 18.1 - - - +
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Residues in contact with ALA 257 (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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231D PHE* 3.7 25.6 - - + -
253D ASP 3.0 17.8 + - - +
254D LEU* 4.0 2.9 - - - +
256D GLN* 1.3 79.0 + - - +
258D LEU* 1.3 65.0 + - - +
260D SER* 4.0 0.2 - - - -
261D GLY 3.2 4.5 + - - -
262D LYS* 3.0 48.6 + - + -
263D ILE* 3.6 12.9 + - + -
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Residues in contact with LEU 258 (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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254D LEU* 3.1 36.3 + - + +
257D ALA* 1.3 78.3 - - - +
259D ALA* 1.3 61.1 + - - +
260D SER 3.5 0.3 + - - -
261D GLY* 4.0 4.7 + - - -
263D ILE* 3.8 17.1 - - + +
264D ALA 4.5 0.2 - - - -
265D ALA* 3.6 9.2 - - - -
266D ALA* 3.5 25.4 - - + +
282D LEU* 4.2 1.3 - - + -
285D LEU* 3.9 17.7 - - + -
287D ASN* 2.9 52.4 + - - +
288D CYS* 3.7 29.4 - - + -
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Residues in contact with ALA 259 (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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255D TYR* 2.9 35.9 + - + +
256D GLN* 4.2 3.6 - - - +
258D LEU* 1.3 77.8 - - - +
260D SER* 1.3 59.5 + - - +
261D GLY 3.6 0.2 - - - -
285D LEU* 4.1 21.3 - - + +
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Residues in contact with SER 260 (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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256D GLN* 2.6 36.0 + - - -
257D ALA 3.9 0.2 + - - -
259D ALA* 1.3 79.9 - - - +
261D GLY* 1.3 58.3 + - - +
262D LYS* 3.2 31.1 + - - +
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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