Contacts of the helix formed by residues 260 - 279 (chain A) in PDB entry 3C7N
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A ILE 3.0 1.4 + - - +
258A ARG 3.7 0.4 - - - -
259A GLU* 1.3 80.6 - - - +
261A PRO* 1.4 75.1 - - - +
262A LYS* 3.2 41.3 + - - +
263A ALA* 3.3 21.7 - - + +
264A TYR* 3.0 32.7 + - - +
291A VAL 4.4 3.6 + - - -
292A MET* 3.5 28.0 - - + +
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Residues in contact with PRO 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 4.2 18.8 - - + +
62A LYS* 4.4 23.1 - - - +
259A GLU 4.2 4.5 - - - +
260A ASN* 1.4 89.5 - - - +
262A LYS* 1.3 76.9 + - + +
263A ALA 3.0 0.2 + - - -
264A TYR* 3.9 3.1 - - + +
265A ASN* 3.0 28.8 + - - +
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 5.5 12.1 - - + +
61A ILE* 4.5 10.4 - - + +
260A ASN* 3.2 33.0 + - - +
261A PRO* 1.3 82.1 - - + +
263A ALA* 1.3 58.9 + - - +
265A ASN* 3.9 5.1 - - - +
266A ARG* 2.9 36.3 + - + +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.5 9.2 - - + +
260A ASN* 3.3 25.3 + - + +
261A PRO 3.0 0.8 - - - -
262A LYS* 1.3 77.9 - - - +
264A TYR* 1.3 68.7 - - - +
265A ASN 3.0 1.1 - - - -
266A ARG* 3.0 17.1 + - - +
267A ILE* 3.1 17.7 + - - +
291A VAL* 3.4 31.5 - - + +
292A MET* 4.1 8.5 - - + -
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Residues in contact with TYR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.9 23.2 - - + +
242A THR* 3.9 20.6 - - + +
243A GLU* 2.3 34.4 + - - -
246A ALA* 5.1 0.4 - - + -
257A ILE* 4.0 20.7 + - + +
258A ARG* 4.1 33.2 - - + -
260A ASN 3.0 16.8 + - - +
261A PRO* 3.9 3.6 - - + +
263A ALA* 1.3 78.4 - - - +
265A ASN* 1.3 58.2 + - - +
267A ILE* 3.2 7.0 + - - +
268A LEU* 2.9 37.6 + - + +
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Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 3.8 41.0 + - - +
58A THR* 4.8 9.9 + - + +
61A ILE* 4.0 19.4 - - + +
89A THR* 5.0 3.8 + - - -
261A PRO 3.0 19.8 + - - +
262A LYS* 3.9 5.8 - - - +
264A TYR* 1.3 78.2 - - - +
266A ARG* 1.3 57.5 + - + +
268A LEU* 3.3 20.9 - - - +
269A THR* 3.0 35.7 + - - -
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Residues in contact with ARG 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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58A THR* 3.7 19.3 - - + +
262A LYS* 2.9 25.8 + - - +
263A ALA* 3.0 5.5 + - - +
265A ASN* 1.3 74.2 - - + +
267A ILE* 1.3 64.4 + - - +
269A THR* 4.1 7.7 - - - +
270A ALA* 3.3 21.5 + - - +
288A VAL* 3.4 32.3 - - + +
289A GLU* 2.4 31.3 + - - +
290A SER 3.7 13.1 + - - -
291A VAL* 4.4 2.9 - - - +
262B ARG* 4.3 7.1 - - - +
285B ASP* 3.6 45.0 + - - +
286B SER* 3.9 13.7 - - - -
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Residues in contact with ILE 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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242A THR* 3.9 25.4 - - + +
245A PHE* 4.9 6.7 - - + -
249A PHE* 4.0 21.3 - - + -
257A ILE* 4.2 25.4 - - + -
263A ALA 3.1 12.8 + - - +
264A TYR 3.5 8.3 - - - +
266A ARG* 1.3 76.6 - - - +
268A LEU* 1.3 55.5 + - - +
270A ALA* 3.1 3.8 + - - +
271A ALA* 2.6 33.1 + - - +
286A PHE* 4.0 13.3 - - + -
288A VAL* 3.7 30.1 - - + -
291A VAL* 4.2 13.9 - - + -
297A VAL* 4.4 0.2 - - + -
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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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238A ASP* 4.1 20.2 - - + -
239A LEU* 4.1 23.3 - - + -
242A THR* 3.4 23.5 + - + +
264A TYR* 2.9 23.0 + - + +
265A ASN* 3.3 26.0 - - - +
267A ILE* 1.3 74.2 - - - +
269A THR* 1.3 58.7 + - - +
271A ALA* 2.6 23.7 + - - +
272A GLU* 3.0 13.4 + - + +
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Residues in contact with THR 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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57A GLN* 5.4 5.7 - - - +
58A THR* 5.6 1.7 + - - -
265A ASN* 3.0 20.4 + - - -
266A ARG* 4.2 7.7 - - - -
268A LEU* 1.3 80.2 - - - +
270A ALA* 1.3 59.5 + - - +
272A GLU* 3.5 8.9 - - + +
273A LYS* 3.2 45.2 + - + +
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Residues in contact with ALA 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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266A ARG 3.3 17.3 + - - +
267A ILE 3.1 2.4 + - - +
268A LEU 3.0 0.6 - - - -
269A THR* 1.3 78.0 - - - +
271A ALA* 1.3 67.1 + - - +
273A LYS* 3.4 10.7 + - + +
274A LEU* 3.1 18.7 + - - +
286A PHE* 3.3 27.1 - - + -
287A SER 5.4 1.1 - - - +
288A VAL* 3.7 16.2 - - + -
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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
----------------------------------------------------------
238A ASP* 3.9 11.2 - - - +
241A ILE* 4.0 21.2 - - + +
242A THR* 3.3 25.6 - - - +
245A PHE* 5.4 0.2 - - + -
267A ILE 2.6 14.4 + - - +
268A LEU 2.6 11.0 + - - +
270A ALA* 1.3 69.7 - - - +
272A GLU* 1.3 63.7 + - - +
274A LEU* 3.1 8.6 + - - +
275A LYS* 2.9 24.8 + - - +
286A PHE* 3.7 9.6 - - + -
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Residues in contact with GLU 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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12A ASN* 4.7 9.0 + - - +
206A HIS* 5.3 1.2 - - - -
238A ASP* 2.9 40.3 + - + +
268A LEU* 3.0 9.3 + - + +
269A THR* 3.5 14.5 - - + +
271A ALA* 1.3 76.3 - - - +
273A LYS* 1.3 67.6 + - - +
275A LYS* 3.3 3.7 + - - +
276A LYS* 3.1 53.0 + - - +
668A SO4 4.9 0.9 + - - -
672A ADP 3.1 31.1 + - - +
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Residues in contact with LYS 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 THR* 3.2 34.7 + - - +
270A ALA* 3.7 11.4 - - + +
271A ALA 3.2 1.0 - - - -
272A GLU* 1.3 83.3 - - - +
274A LEU* 1.3 63.2 + - - +
276A LYS* 3.5 9.5 + - + +
277A VAL* 3.3 24.8 + - - +
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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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241A ILE* 4.1 17.5 - - + -
245A PHE* 3.9 30.3 - - + -
270A ALA 3.1 12.5 + - - +
271A ALA* 3.1 7.6 + - - +
273A LYS* 1.3 73.4 - - - +
275A LYS* 1.3 58.2 + - - +
277A VAL* 2.8 28.9 + - - +
278A LEU* 2.9 20.1 + - + +
284A ALA* 3.4 36.8 - - + +
285A PRO 3.7 16.6 - - - +
286A PHE* 4.1 11.0 - - + -
301A LEU* 4.2 16.8 - - + -
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Residues in contact with LYS 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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234A GLY* 4.0 6.2 - - - -
237A PHE* 3.9 19.6 - - + +
238A ASP* 2.7 30.7 - - - +
241A ILE* 3.9 21.3 - - + -
271A ALA 2.9 11.7 + - - +
272A GLU 3.4 12.3 - - - +
274A LEU* 1.3 74.6 - - - +
276A LYS* 1.3 66.5 + - - +
278A LEU* 3.0 19.6 + - - +
279A SER* 3.2 13.7 + - - +
306A LEU* 5.1 9.4 - - + +
344A THR* 3.0 35.4 - - - +
347A ILE* 4.6 7.6 - - + +
672A ADP 3.2 36.3 + - + -
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Residues in contact with LYS 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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272A GLU* 3.1 43.2 + - - +
273A LYS* 3.6 11.4 - - + +
275A LYS* 1.3 77.4 - - - +
277A VAL* 1.3 62.9 + - + +
279A SER* 3.2 17.3 + - - -
668A SO4 3.3 35.1 + - - -
672A ADP 3.6 46.2 + - + +
33B GLN* 3.5 15.3 + - - +
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Residues in contact with VAL 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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273A LYS 3.3 14.1 + - - +
274A LEU* 2.8 14.3 + - - +
276A LYS* 1.3 74.9 - - + +
278A LEU* 1.3 55.6 + - - +
279A SER 3.1 4.9 - - - -
280A ALA* 3.2 4.6 + - - +
281A ASN* 2.9 39.1 + - + +
283A ASN 4.9 0.7 - - - +
284A ALA* 3.7 24.9 - - + -
285A PRO* 5.7 1.6 - - + -
33B GLN* 5.5 0.2 - - - +
57B ASN* 4.3 22.2 - - + +
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Residues in contact with LEU 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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274A LEU* 2.9 36.5 + - + +
275A LYS* 3.0 8.9 + - - +
277A VAL* 1.3 72.1 - - - +
279A SER* 1.3 55.5 + - - +
280A ALA 3.1 5.8 - - - -
281A ASN 3.0 14.8 - - - +
282A THR 3.7 8.3 - - - +
283A ASN* 3.9 6.5 - - - +
284A ALA* 3.8 7.9 - - + -
301A LEU* 3.5 41.1 - - + +
303A ARG* 2.9 59.8 + - - +
306A LEU* 3.8 23.6 - - + +
348A PRO* 4.7 1.4 - - - +
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Residues in contact with SER 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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275A LYS 3.2 6.8 + - - -
276A LYS 3.3 8.7 - - - -
277A VAL 3.1 1.2 - - - -
278A LEU* 1.3 77.9 - - - +
280A ALA* 1.3 57.6 + - - +
303A ARG* 3.4 8.1 + - - -
306A LEU* 5.9 0.5 - - - +
346A ARG 3.7 10.3 - - - +
347A ILE* 3.6 13.6 - - - +
348A PRO* 3.8 19.3 - - - +
672A ADP 2.7 39.3 + - - -
33B GLN* 3.5 16.7 - - - +
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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
------------------------------------------------------------
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