Contacts of the helix formed by residues 257 - 273 (chain A) in PDB entry 3NDM
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 ARG 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ASP* 4.3 10.9 + - - -
190A HIS* 3.2 60.0 + - + +
191A SER* 4.9 4.0 + - - +
195A ILE* 3.8 19.5 - - + +
223A MET* 3.4 30.2 - - - +
227A GLY* 4.1 5.3 + - - +
256A GLY* 1.3 65.7 - - - -
258A GLU* 1.3 61.6 + - - +
259A CYS 2.9 6.3 - - - -
260A ASP* 2.7 34.0 + - - +
261A TRP* 3.8 12.3 + - - +
325A GLY 5.7 4.7 - - - +
326A ARG 5.9 1.6 - - - +
329A VAL* 5.2 9.1 - - - +
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MET* 5.2 9.9 - - - +
244A GLU* 4.2 2.7 - - - +
255A TYR 4.5 0.2 - - - -
256A GLY* 3.7 19.4 + - - +
257A ARG* 1.3 88.0 + - - +
259A CYS* 1.3 62.7 + - - +
261A TRP* 3.1 27.6 + - + +
262A TRP 3.4 7.8 + - - -
320A ARG* 3.3 54.5 + - + +
323A ARG* 3.5 18.6 + - + -
325A GLY 5.2 1.8 - - - +
326A ARG* 4.3 25.8 - - - +
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Residues in contact with CYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ILE* 4.1 13.5 - - - -
197A ARG* 4.7 10.8 - - - -
242A SER* 3.3 21.1 + - - +
244A GLU* 3.9 12.1 - - + +
245A VAL* 4.2 9.9 - - + -
255A TYR* 4.1 19.3 - - + -
256A GLY 3.5 15.6 + - - +
257A ARG 2.8 1.6 + - - -
258A GLU* 1.3 81.3 - - + +
260A ASP* 1.3 68.1 + - - +
261A TRP 3.1 0.2 - - - -
262A TRP* 3.3 15.6 + - - +
263A SER* 3.4 9.5 + - - -
323A ARG* 3.6 9.6 - - - +
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Residues in contact with ASP 260 (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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186A LEU* 3.6 23.4 - - + +
190A HIS* 3.2 11.5 - - + +
195A ILE* 2.9 15.2 - - - +
196A HIS* 2.7 28.1 + - - +
197A ARG* 2.9 24.5 + - - -
198A ASP 4.0 0.5 + - - -
199A VAL* 3.5 19.4 - - - +
257A ARG 2.7 10.5 + - - +
259A CYS* 1.3 78.2 - - - +
261A TRP* 1.3 63.4 + - - +
263A SER* 3.5 10.4 + - - -
264A VAL* 3.2 20.6 + - - +
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Residues in contact with TRP 261 (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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183A VAL* 3.4 47.6 - - + -
186A LEU* 3.8 18.4 - - + -
187A ASP* 4.3 2.9 - - - -
190A HIS* 3.8 25.8 + + - -
257A ARG* 4.1 10.3 + - + +
258A GLU* 3.1 25.1 + - + +
260A ASP* 1.3 76.4 - - - +
262A TRP* 1.3 58.8 + - - +
263A SER 3.0 1.8 - - - -
264A VAL* 2.5 65.4 + - + +
265A GLY 3.1 3.3 + - - -
316A PHE* 3.7 25.3 - + + -
323A ARG* 4.7 1.8 - - - -
324A LEU 4.1 6.3 - - - +
325A GLY* 4.6 10.9 + - - -
329A VAL* 3.5 24.5 - - + +
332A ILE* 3.8 23.0 - - + +
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Residues in contact with TRP 262 (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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240A TYR 3.3 19.4 + - - -
241A ILE 3.9 2.4 + - - -
242A SER* 3.6 9.6 - - - -
243A PRO* 3.5 29.4 - - + -
258A GLU 3.4 3.6 + - - -
259A CYS 3.3 8.6 + - - +
261A TRP* 1.3 79.3 - - - +
263A SER* 1.3 64.4 + - - +
265A GLY* 3.1 8.7 + - - -
266A VAL* 3.0 29.2 + - + +
278A PHE* 3.9 19.3 - + - -
290A ILE* 3.8 13.6 - - + +
293A HIS* 3.3 28.9 - + + -
316A PHE* 3.5 15.3 - - - -
317A LEU* 3.4 32.5 - - + +
318A THR 3.5 7.2 - - - -
323A ARG* 2.9 54.4 - - - +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG 5.8 0.3 - - - -
198A ASP* 5.3 1.6 + - - -
199A VAL* 3.3 43.6 + - - +
240A TYR* 4.5 14.3 + - - +
241A ILE* 5.7 0.7 - - - -
242A SER 5.6 1.2 + - - -
259A CYS 3.4 12.2 + - - -
260A ASP* 3.5 6.8 + - - -
261A TRP 3.0 0.4 - - - -
262A TRP* 1.3 79.2 - - - +
264A VAL* 1.3 59.3 + - - +
266A VAL* 2.8 29.7 + - - +
267A PHE* 2.8 13.4 + - - +
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Residues in contact with VAL 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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179A THR* 4.0 22.8 - - + +
182A VAL* 4.4 12.8 - - + -
183A VAL* 4.2 9.9 - - + -
186A LEU* 4.1 9.6 - - + -
199A VAL* 5.0 3.3 - - + +
260A ASP 3.2 11.2 - - - +
261A TRP* 2.5 49.3 + - + +
263A SER* 1.3 71.6 - - - +
265A GLY* 1.3 60.3 + - - +
267A PHE* 3.1 10.3 + - + +
268A LEU* 3.0 21.1 + - - +
316A PHE* 3.3 22.7 - - + -
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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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261A TRP 3.1 9.3 + - - -
262A TRP 3.1 4.8 + - - -
264A VAL* 1.3 75.4 - - - +
266A VAL* 1.3 57.5 + - - +
268A LEU* 3.3 6.7 + - - +
269A TYR* 2.9 32.1 + - - +
313A ILE* 4.4 7.6 - - - +
316A PHE* 3.3 18.7 - - - -
317A LEU* 3.6 19.4 - - - +
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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
----------------------------------------------------------
239A ASP 3.2 25.6 - - - +
240A TYR* 3.2 27.4 - - + +
262A TRP* 3.0 44.6 - - + +
263A SER* 2.8 11.4 + - - +
265A GLY* 1.3 76.2 - - - +
267A PHE* 1.3 60.0 + - - +
269A TYR* 3.9 1.0 - - - +
270A GLU* 3.3 23.2 + - - +
276A THR* 4.9 1.1 - - + -
277A PRO* 3.9 26.0 - - + +
278A PHE* 5.7 1.3 - - + -
317A LEU* 4.6 4.3 - - + -
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Residues in contact with PHE 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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161A LEU* 3.3 24.9 - - + -
165A MET* 4.5 9.2 - - - -
178A TYR* 4.5 5.6 - - + -
179A THR* 4.7 11.7 - - + -
182A VAL* 4.2 14.4 - - + -
199A VAL* 5.5 2.2 - - + -
200A LYS* 5.2 0.4 - - - -
201A PRO* 3.9 27.4 - - + -
204A MET* 3.3 44.4 - - + -
240A TYR* 4.3 7.4 - + + -
263A SER 2.8 10.3 + - - +
264A VAL* 3.4 12.3 - - + +
266A VAL* 1.3 75.2 - - - +
268A LEU* 1.3 57.4 + - - +
269A TYR 3.1 0.7 + - - -
270A GLU* 3.2 4.7 + - - +
271A MET* 2.7 65.1 + - + +
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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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175A ALA* 4.4 6.5 - - + -
179A THR* 4.0 22.9 + - + +
264A VAL 3.0 12.2 + - - +
265A GLY* 3.7 8.5 - - - +
267A PHE* 1.3 75.8 - - - +
269A TYR* 1.3 64.6 + - - +
271A MET* 3.4 5.0 + - - +
272A LEU* 3.1 41.9 + - + +
309A ALA* 4.1 5.4 - - - +
312A LEU* 3.3 41.5 - - + -
313A ILE* 3.6 24.5 - - + -
337A PHE* 3.9 20.9 - - + -
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Residues in contact with TYR 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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265A GLY 2.9 18.3 + - - +
266A VAL 3.9 0.4 - - - +
267A PHE 3.1 0.2 - - - -
268A LEU* 1.3 77.4 - - - +
270A GLU* 1.3 55.8 + - - +
271A MET 3.0 1.0 + - - -
272A LEU* 3.7 0.6 - - - -
273A VAL* 2.7 65.8 + - + +
275A ASP 2.9 26.9 - - - -
276A THR 3.8 1.3 + - - -
277A PRO* 3.3 47.0 - - + +
297A LEU* 4.9 2.5 - - + -
298A THR* 3.8 33.0 + - - -
299A PHE* 4.4 12.3 - + - -
300A PRO* 4.1 10.0 - - - +
313A ILE* 3.6 31.4 - - + +
317A LEU* 5.5 0.2 - - + -
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Residues in contact with GLU 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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162A VAL* 4.5 13.0 - - - +
165A MET* 3.0 30.2 - - + +
201A PRO* 4.4 5.6 - - - +
240A TYR* 2.5 30.9 + - - +
266A VAL 3.3 13.1 + - - +
267A PHE* 3.2 5.9 + - + +
269A TYR* 1.3 79.1 - - - +
271A MET* 1.3 63.4 + - - +
274A GLY* 3.4 32.0 + - - +
275A ASP* 3.8 26.1 - - - +
276A THR* 4.0 13.4 - - - +
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Residues in contact with MET 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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161A LEU* 4.6 0.2 - - + -
164A LEU* 4.4 7.9 - - + -
165A MET* 3.8 27.3 - - + +
175A ALA* 3.9 37.9 - - + +
178A TYR* 3.4 33.4 - - + -
179A THR* 4.5 5.6 - - - -
267A PHE* 2.7 55.5 + - + +
268A LEU* 3.5 7.0 - - - +
270A GLU* 1.3 80.1 - - - +
272A LEU* 1.3 63.5 + - + +
273A VAL 4.8 0.7 - - - +
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Residues in contact with LEU 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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172A GLU* 4.1 23.6 - - + +
175A ALA* 3.7 26.5 - - + -
268A LEU* 3.1 36.3 + - + +
269A TYR* 3.9 1.8 - - - +
271A MET* 1.3 82.9 - - + +
273A VAL* 1.3 70.3 + - + +
305A ILE* 4.8 20.2 - - + -
309A ALA* 3.8 25.1 - - + -
313A ILE* 5.1 6.5 - - + -
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Residues in contact with VAL 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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269A TYR* 2.7 73.3 + - + +
270A GLU 3.9 1.3 - - - -
271A MET 4.8 0.4 - - - +
272A LEU* 1.3 79.2 - - + +
274A GLY* 1.3 61.4 + - - +
275A ASP* 3.9 7.6 - - + +
299A PHE* 5.8 2.7 - - + -
300A PRO* 4.3 23.3 - - + -
313A ILE* 5.7 0.9 - - + -
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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