Contacts of the helix formed by residues 263 - 279 (chain A) in PDB entry 2NUP
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 SER 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A PHE* 3.8 6.6 - - - -
170A GLY 2.9 9.8 + - - -
171A ARG 2.6 26.7 + - - -
173A VAL* 4.2 7.6 - - - -
191A GLY* 3.3 27.1 - - - -
262A ARG* 1.3 69.7 - - - +
264A SER* 1.3 63.4 + - - +
265A GLY 3.0 3.7 + - - -
266A VAL 3.2 2.6 + - - -
267A ALA* 3.0 19.9 + - - +
296A GLN* 2.7 25.0 + - - -
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Residues in contact with SER 264 (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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169A PHE* 3.4 15.7 - - - -
262A ARG* 2.9 31.4 + - - +
263A SER* 1.3 74.8 - - - +
265A GLY* 1.3 61.5 + - - +
268A LEU* 3.2 20.4 + - - +
288A MET* 3.2 18.1 - - - +
290A ILE* 5.0 7.4 - - - +
292A GLY 4.5 2.1 + - - -
293A PRO 4.4 0.5 - - - -
294A ALA* 3.6 22.2 + - - +
331A PHE* 4.4 8.6 - - - -
360A MET* 5.4 5.4 - - - -
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Residues in contact with GLY 265 (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 SER 3.0 1.4 + - - -
264A SER* 1.3 81.0 - - - +
266A VAL* 1.3 57.4 + - - +
268A LEU* 3.6 2.9 + - - +
269A SER* 3.1 19.4 + - - -
294A ALA* 4.5 3.8 - - - +
296A GLN 5.3 0.8 + - - -
298A PRO 3.3 20.4 + - - -
330A HIS* 3.0 25.9 + - - -
331A PHE* 3.8 14.6 - - - -
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Residues in contact with VAL 266 (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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173A VAL* 4.3 2.0 - - + -
190A ARG 4.0 11.0 - - - +
191A GLY* 4.0 22.9 + - - +
193A LYS 3.8 34.8 - - - +
194A ASP* 3.8 11.0 - - + +
195A LEU* 5.4 1.1 - - + +
263A SER 3.2 4.1 + - - +
265A GLY* 1.3 73.1 - - - +
267A ALA* 1.3 60.4 + - - +
269A SER* 2.8 9.9 + - - +
270A ILE* 2.8 51.4 + - + +
296A GLN 5.8 0.4 + - - -
297A GLY 5.3 0.2 - - - -
298A PRO* 3.9 21.4 + - + -
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Residues in contact with ALA 267 (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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134A VAL* 4.1 8.8 - - + +
167A ILE* 4.8 2.8 - - + +
169A PHE* 3.5 43.7 - - + -
173A VAL* 3.9 15.2 - - + +
263A SER 3.0 13.9 + - - +
264A SER 3.7 4.7 - - - +
266A VAL* 1.3 77.0 - - - +
268A LEU* 1.3 62.7 + - - +
270A ILE* 3.3 2.8 + - - +
271A ALA* 3.0 22.3 + - - +
288A MET* 4.1 4.7 - - + -
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Residues in contact with LEU 268 (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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134A VAL* 4.9 1.1 - - + -
264A SER 3.2 14.0 + - - +
265A GLY 3.8 4.3 - - - +
267A ALA* 1.3 80.8 - - - +
269A SER* 1.3 56.7 + - - +
271A ALA* 3.0 7.8 + - + +
272A VAL* 2.9 40.7 + - + +
286A ILE* 4.0 25.4 - - + -
288A MET* 3.4 28.2 - - + +
331A PHE* 3.7 30.7 - - + -
334A LEU* 3.9 9.2 - - + -
345A ILE* 4.4 15.7 - - + -
347A ILE* 5.7 2.5 - - + -
360A MET* 5.6 1.3 - - - -
363A CYS* 3.9 20.2 - - - -
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Residues in contact with SER 269 (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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194A ASP* 3.0 31.6 + - - -
195A LEU 4.7 2.6 - - - +
196A SER 4.7 1.4 - - - +
200A LEU* 4.7 0.2 - - - +
265A GLY 3.1 7.1 + - - -
266A VAL* 2.8 30.7 + - - +
268A LEU* 1.3 79.1 - - - +
270A ILE* 1.3 55.5 + - - +
272A VAL* 3.3 1.9 + - - +
273A GLY* 2.8 27.0 + - - -
334A LEU* 3.4 28.0 - - - +
337A ARG* 3.9 8.3 + - - -
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Residues in contact with ILE 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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167A ILE* 4.1 7.2 - - + -
173A VAL* 3.9 15.0 - - + -
175A VAL* 3.6 28.3 - - + -
189A PHE* 3.8 31.2 - - + -
195A LEU* 4.0 23.6 - - + +
200A LEU* 3.3 21.1 - - + +
266A VAL* 2.8 40.0 + - + +
267A ALA 3.8 4.3 - - - +
269A SER* 1.3 70.6 - - - +
271A ALA* 1.3 61.0 + - - +
274A LEU* 2.8 29.7 + - + +
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Residues in contact with ALA 271 (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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132A LEU* 3.5 14.5 - - + +
134A VAL* 3.8 27.6 - - + -
167A ILE* 3.8 14.1 - - + -
267A ALA 3.0 12.8 + - - +
268A LEU* 3.0 11.8 + - - +
270A ILE* 1.3 78.8 - - - +
272A VAL* 1.3 61.2 + - - +
274A LEU* 3.4 3.1 + - - +
275A LEU* 3.3 19.8 + - - +
286A ILE* 4.1 14.4 - - + -
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Residues in contact with VAL 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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268A LEU* 2.9 25.7 + - + +
269A SER 3.6 6.7 - - - +
271A ALA* 1.3 77.5 - - - +
273A GLY* 1.3 57.8 + - - +
275A LEU* 3.4 2.3 + - - +
276A GLU* 2.8 37.8 + - + +
286A ILE* 3.9 22.9 - - + -
334A LEU* 4.0 17.5 - - + +
337A ARG* 4.0 22.0 - - + +
338A ALA* 4.2 26.0 - - + +
341A THR* 5.8 0.4 - - - +
343A HIS* 5.0 3.3 + - - +
345A ILE* 4.5 13.2 - - + -
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Residues in contact with GLY 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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196A SER 4.0 0.7 - - - -
197A ALA* 3.8 15.4 - - - +
200A LEU* 3.7 11.2 - - - -
269A SER 2.8 19.9 + - - -
270A ILE 3.8 0.9 - - - -
272A VAL* 1.3 70.3 - - - +
274A LEU* 1.3 66.9 + - - +
276A GLU* 3.1 3.3 + - - +
277A CYS* 3.0 27.1 + - - +
337A ARG* 3.8 15.0 - - - +
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Residues in contact with LEU 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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132A LEU* 3.9 30.5 - - + -
167A ILE* 4.2 12.6 - - + -
175A VAL* 4.2 12.1 - - + -
200A LEU* 3.5 7.4 - - + +
204A LEU* 4.2 23.6 - - + -
229A PHE* 4.4 24.2 - - + +
230A LEU* 5.0 7.0 - - + -
270A ILE* 2.8 19.8 + - + +
271A ALA 3.4 4.7 - - - +
272A VAL 3.3 0.2 - - - -
273A GLY* 1.3 77.3 - - - +
275A LEU* 1.3 60.0 + - + +
277A CYS* 3.4 7.3 + - - -
278A THR* 2.6 49.4 + - + +
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Residues in contact with LEU 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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130A ILE* 3.8 16.6 - - + -
132A LEU* 3.6 29.2 - - + -
230A LEU* 3.8 28.5 - - + -
271A ALA 3.3 6.4 + - - +
272A VAL* 4.1 1.8 - - - +
274A LEU* 1.3 80.6 - - + +
276A GLU* 1.3 60.7 + - - +
278A THR* 3.0 8.5 + - - +
279A PHE* 2.8 35.4 + - + +
284A ALA* 3.6 27.8 - - + -
285A ARG 5.0 0.9 - - - +
286A ILE* 3.8 26.7 - - + -
343A HIS* 3.3 20.4 - - + +
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Residues in contact with GLU 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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197A ALA* 3.8 18.6 - - + +
272A VAL* 2.8 21.9 + - + +
273A GLY* 3.1 6.0 + - - +
275A LEU* 1.3 76.5 - - - +
277A CYS* 1.3 56.6 + - - +
280A PRO* 3.6 19.1 - - + +
337A ARG* 3.5 33.6 + - - +
341A THR* 3.6 34.4 + - + +
343A HIS* 4.1 1.1 - - - +
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Residues in contact with CYS 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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197A ALA* 3.9 14.8 - - + +
200A LEU* 5.3 2.0 - - - -
201A GLN* 3.8 47.8 - - - +
204A LEU* 6.6 0.2 - - - -
273A GLY 3.0 13.2 + - - +
274A LEU* 3.4 18.6 - - - -
276A GLU* 1.3 77.9 - - - +
278A THR* 1.3 68.6 + - - +
280A PRO* 4.5 3.4 - - - -
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Residues in contact with THR 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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227A ASN* 3.0 37.4 + - - +
229A PHE* 6.1 0.7 - - + -
230A LEU* 3.7 5.1 - - + +
274A LEU* 2.6 37.7 + - + +
275A LEU* 3.0 14.2 - - - -
277A CYS* 1.3 91.2 - - - +
279A PHE* 1.3 78.3 + - - +
280A PRO* 3.6 6.0 - - - +
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Residues in contact with PHE 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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127A MET* 4.8 15.3 - - - -
128A PRO* 5.7 0.7 - - + -
130A ILE* 3.4 26.7 - - + -
163A LEU* 3.6 26.2 - - + -
225A PRO* 4.1 24.0 - - + -
226A SER* 4.1 13.2 - - - -
227A ASN* 3.1 30.5 - - - -
230A LEU* 3.3 18.6 - - + -
275A LEU* 2.8 14.1 + - + +
278A THR* 1.3 87.9 + - - +
280A PRO* 1.3 63.6 - - - +
282A THR* 4.3 11.3 + - - +
343A HIS* 2.8 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
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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