Contacts of the helix formed by residues 257 - 273 (chain A) in PDB entry 2NPG
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 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ILE* 3.9 2.1 - - - +
249A GLU* 2.5 27.5 + - - -
253A ARG* 4.1 7.2 + - - -
255A LYS* 5.1 3.1 - - - -
256A PRO* 1.3 75.6 - - - +
258A LEU* 1.3 63.8 + - - +
259A LEU* 3.7 6.5 + - - +
260A GLY 3.0 14.0 + - - -
261A ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.9 44.4 - - + +
199A PRO* 4.6 3.8 - - + -
202A PHE* 4.2 21.8 - - + -
257A SER* 1.3 73.0 - - - +
259A LEU* 1.3 65.8 + - - +
261A ALA* 3.2 10.7 + - + +
262A CYS* 2.9 36.9 + - - -
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Residues in contact with LEU 259 (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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31A PHE* 5.6 4.3 - - + -
35A LEU* 3.9 24.9 - - + -
195A PRO* 3.9 27.6 - - + -
198A LEU* 4.2 16.9 - - + +
201A VAL* 4.1 17.9 - - + -
257A SER* 3.3 6.5 + - - +
258A LEU* 1.3 79.0 - - - +
260A GLY* 1.3 54.3 + - - +
262A CYS* 3.3 4.8 + - + +
263A SER* 2.6 47.9 + - - +
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Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A TRP* 3.3 31.1 + - - -
246A ILE* 4.1 1.1 - - - -
249A GLU* 3.4 23.8 - - - -
257A SER* 3.0 12.4 + - - -
259A LEU* 1.3 76.1 - - - +
261A ALA* 1.3 50.6 + - - +
263A SER* 3.3 1.3 + - - -
264A GLY* 2.8 30.0 + - - -
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.7 19.3 - - + +
246A ILE* 3.6 21.0 - - + +
257A SER 3.0 11.5 + - - +
258A LEU* 3.5 17.9 - - + +
260A GLY* 1.3 76.2 - - - +
262A CYS* 1.3 63.0 + - - +
264A GLY* 3.4 2.5 + - - -
265A ALA* 3.1 18.5 + - - +
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Residues in contact with CYS 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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31A PHE* 4.9 3.1 - - + -
198A LEU 5.7 0.2 - - - -
201A VAL* 4.6 10.1 - - + -
202A PHE* 3.8 35.9 - - - -
205A THR* 3.4 34.6 - - - +
258A LEU* 2.9 28.9 + - - +
259A LEU* 3.8 7.2 - - + +
261A ALA* 1.3 73.0 - - - +
263A SER* 1.3 67.1 + - - +
265A ALA* 3.2 4.7 + - - +
266A ILE* 3.1 26.2 + - - +
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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
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31A PHE* 5.7 5.1 - - - -
245A TRP* 3.4 36.5 - - - -
259A LEU* 2.6 43.3 + - - +
260A GLY 3.5 1.1 - - - -
262A CYS* 1.3 72.4 - - - +
264A GLY* 1.3 52.4 + - - +
266A ILE* 3.2 9.0 + - - +
267A ALA* 2.8 34.5 + - - +
317A VAL* 4.5 7.3 - - - +
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Residues in contact with GLY 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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241A ALA* 3.1 21.2 - - - +
242A ILE* 4.1 1.3 - - - -
245A TRP* 3.6 32.0 - - - -
260A GLY 2.8 13.1 + - - -
261A ALA 3.7 2.2 - - - -
262A CYS 3.2 0.6 - - - -
263A SER* 1.3 76.6 - - - +
265A ALA* 1.3 60.7 + - - +
267A ALA* 3.1 2.1 + - - +
268A GLY 3.0 19.8 + - - -
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Residues in contact with ALA 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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205A THR* 4.2 15.7 - - + -
209A TYR* 5.7 2.7 - - + -
238A THR* 3.7 15.1 - - + +
242A ILE* 3.5 28.1 - - + +
261A ALA 3.1 8.9 + - - +
262A CYS* 3.2 8.7 + - - +
264A GLY* 1.3 76.4 - - - +
266A ILE* 1.3 63.5 + - - +
268A GLY 3.3 0.3 + - - -
269A LEU* 3.0 32.5 + - + +
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Residues in contact with ILE 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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31A PHE* 4.1 22.2 - - + -
205A THR* 4.1 13.2 - - + -
208A LEU* 4.0 30.3 - - + -
212A TRP* 4.3 6.3 - - + -
262A CYS 3.1 17.9 + - - +
263A SER* 3.6 9.0 - - - +
265A ALA* 1.3 74.8 - - - +
267A ALA* 1.3 59.6 + - - +
269A LEU* 3.6 18.3 - - + +
270A VAL* 2.8 33.3 + - + +
317A VAL* 4.0 12.6 - - + -
318A PHE* 3.6 35.7 - - + -
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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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245A TRP* 4.0 11.2 - - + -
263A SER 2.8 17.2 + - - +
264A GLY 3.1 10.1 + - - +
266A ILE* 1.3 74.0 - - - +
268A GLY* 1.3 56.6 + - - +
271A GLY* 2.9 22.9 + - - -
291A ALA* 3.5 32.9 - - - +
292A GLY* 3.9 10.1 - - - -
317A VAL* 3.9 9.8 - - + +
321A CYS* 3.7 13.7 - - - +
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Residues in contact with GLY 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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237A ALA* 3.7 11.4 - - - +
238A THR* 4.2 6.3 - - - -
241A ALA* 3.2 22.6 - - - +
264A GLY 3.0 11.3 + - - -
265A ALA 3.9 1.8 - - - -
267A ALA* 1.3 73.1 - - - +
269A LEU* 1.3 59.6 + - - +
271A GLY 3.8 0.4 - - - -
272A VAL* 2.9 34.6 + - - +
287A ILE* 5.6 0.2 - - - +
288A GLY* 4.7 2.9 - - - -
291A ALA* 4.5 5.2 - - - -
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Residues in contact with LEU 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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205A THR 5.3 0.2 - - - +
209A TYR* 4.0 28.0 - - + -
212A TRP* 3.6 56.5 + - + -
216A ASN* 5.2 0.2 - - - +
234A THR* 3.7 17.3 - - + -
238A THR* 3.2 23.1 + - + +
265A ALA* 3.0 29.4 + - + +
266A ILE* 3.6 16.6 - - + +
268A GLY* 1.3 76.3 - - - +
270A VAL* 1.3 55.0 + - - +
272A VAL* 3.5 7.0 + - - +
273A THR* 2.7 32.5 + - - -
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Residues in contact with VAL 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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168A HIS* 3.7 16.5 + - + +
212A TRP* 3.8 7.4 - - + -
266A ILE* 2.8 25.7 + - + +
267A ALA 3.9 2.9 - - - +
269A LEU* 1.3 75.4 - - - +
271A GLY* 1.3 62.8 + - - +
273A THR* 3.1 22.9 + - - -
274A PRO* 3.4 6.8 - - - +
317A VAL* 4.9 0.7 - - + -
318A PHE* 3.5 50.7 - - + +
321A CYS* 3.6 8.1 - - + +
322A GLY* 3.5 29.1 - - - +
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Residues in contact with GLY 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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267A ALA 2.9 18.0 + - - -
268A GLY 3.8 1.1 - - - -
269A LEU 3.4 0.2 - - - -
270A VAL* 1.3 77.8 - - - +
272A VAL* 1.3 57.7 + - - +
274A PRO* 3.5 5.2 - - - +
275A ALA* 4.5 1.7 - - - +
287A ILE* 3.6 12.0 - - - +
291A ALA* 4.3 12.1 - - - -
321A CYS 3.6 18.4 + - - -
325A GLY* 3.2 24.1 - - - +
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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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216A ASN* 3.6 18.4 - - - +
233A ASN* 4.0 9.4 - - + +
234A THR* 4.1 11.9 - - + +
237A ALA* 3.4 31.6 - - + -
268A GLY 2.9 15.6 + - - +
269A LEU* 3.5 11.0 - - - +
271A GLY* 1.3 75.9 - - - +
273A THR* 1.3 62.0 + - - +
274A PRO 3.4 0.4 - - - -
275A ALA* 3.0 2.9 + - - +
276A CYS* 2.6 51.3 + - + +
279A ILE* 4.1 18.2 - - + -
284A ALA* 4.7 0.9 - - + -
287A ILE* 4.3 5.1 - - + +
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Residues in contact with THR 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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162A ALA* 3.2 47.0 + - + +
163A GLY 3.6 3.1 - - - +
164A GLY 3.6 6.1 - - - +
168A HIS* 3.1 29.8 - - + -
212A TRP* 3.1 10.9 + - - -
215A PHE* 3.7 6.3 - - + -
216A ASN* 3.8 7.9 - - - -
269A LEU 2.7 22.0 + - - -
270A VAL 3.1 11.3 + - - -
272A VAL* 1.3 79.3 - - - +
274A PRO* 1.3 65.9 - - - +
276A CYS* 3.6 9.5 - - - -
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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