Contacts of the helix formed by residues 257 - 278 (chain A) in PDB entry 1ECX
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 GLU 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.0 27.5 + - - -
253A ILE* 2.9 20.6 + - + +
254A ALA 3.7 2.7 - - - -
256A GLU* 1.3 87.2 - - + +
258A LEU* 1.3 64.8 + - - +
259A SER* 3.3 2.9 + - - -
260A GLU* 3.5 8.9 + - + +
261A ALA* 3.0 23.0 + - + +
355A LYS* 2.6 40.4 + - - +
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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
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183A GLY* 3.5 19.1 - - - +
184A LYS 3.4 34.3 - - - +
185A ILE* 3.8 2.0 - - - +
186A PRO* 3.4 43.3 - - + -
254A ALA 3.1 11.9 + - - +
255A VAL* 3.1 26.9 + - + +
256A GLU 3.4 0.4 - - - -
257A GLU* 1.3 77.2 - - - +
259A SER* 1.3 66.4 + - - +
261A ALA* 4.4 3.1 - - - -
262A ALA* 2.9 33.4 + - + +
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Residues in contact with SER 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLU 5.2 1.5 + - - -
257A GLU 3.3 1.2 - - - -
258A LEU* 1.3 83.5 - - - +
260A GLU* 1.3 64.1 + - - +
262A ALA* 4.0 2.9 - - - +
263A LYS* 3.2 46.3 + - - +
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Residues in contact with GLU 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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257A GLU* 3.5 11.2 + - + +
258A LEU 3.5 0.4 - - - -
259A SER* 1.3 78.1 + - - +
261A ALA* 1.3 63.7 + - - +
263A LYS* 3.3 9.1 + - - +
264A HIS* 3.0 26.3 + - + +
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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
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183A GLY 4.4 5.4 - - - +
254A ALA 5.6 0.9 - - - +
257A GLU* 3.0 21.8 + - + +
258A LEU* 3.7 4.9 - - - +
260A GLU* 1.3 77.1 - - - +
262A ALA* 1.3 56.6 + - - +
264A HIS* 3.3 6.4 + - - +
265A MET* 2.9 45.1 + - + +
355A LYS* 4.0 32.5 - - + +
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Residues in contact with ALA 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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184A LYS 3.9 21.5 - - - +
258A LEU* 2.9 24.5 + - + +
259A SER* 4.0 3.1 - - - +
261A ALA* 1.3 70.7 - - - +
263A LYS* 1.3 67.4 + - + +
265A MET* 4.0 10.3 - - - +
266A GLU* 2.9 26.2 + - - +
292A PRO* 3.9 12.8 - - + +
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Residues in contact with LYS 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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259A SER* 3.2 33.7 + - - +
260A GLU* 3.7 7.0 - - - +
262A ALA* 1.3 75.7 - - + +
264A HIS* 1.3 63.5 + - - +
266A GLU* 3.2 8.4 + - - +
267A LYS* 3.0 23.3 + - - +
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Residues in contact with HIS 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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260A GLU* 3.0 21.4 + - + +
261A ALA* 3.5 6.3 + - - +
263A LYS* 1.3 78.3 - - - +
265A MET* 1.3 64.5 + - - +
267A LYS* 3.3 18.0 + - + +
268A LEU* 3.1 45.2 + - + +
355A LYS* 3.8 21.5 + - - -
357A ASN 2.9 30.5 + - - -
358A THR* 4.7 3.8 - - - -
359A GLU 5.2 1.0 + - - -
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Residues in contact with MET 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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183A GLY 3.6 23.8 - - - +
184A LYS* 4.5 13.5 - - + -
261A ALA* 2.9 35.0 + - + +
262A ALA* 4.0 8.7 - - - +
264A HIS* 1.3 75.0 - - - +
266A GLU* 1.3 59.7 + - - +
268A LEU* 3.4 1.2 + - + -
269A ARG* 2.9 25.5 + - - +
292A PRO* 3.3 21.5 - - + +
293A ASN* 3.7 10.5 - - + -
353A LEU* 3.6 39.7 - - + +
354A CYS* 3.6 28.0 - - - +
355A LYS* 3.7 4.7 - - - +
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Residues in contact with GLU 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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262A ALA 2.9 19.1 + - - +
263A LYS* 3.5 7.4 - - - +
265A MET* 1.3 76.6 - - - +
267A LYS* 1.3 62.6 + - - +
269A ARG* 3.2 37.4 + - - +
270A SER* 3.0 23.0 + - - -
287A LEU 5.5 0.5 - - - +
290A SER 5.4 1.4 - - - +
292A PRO* 3.6 20.2 + - + +
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Residues in contact with LYS 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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263A LYS 3.0 12.6 + - - +
264A HIS* 3.5 20.7 + - + +
266A GLU* 1.3 73.2 - - - +
268A LEU* 1.3 78.4 + - - +
270A SER* 2.9 28.2 + - - +
271A LYS* 3.1 9.2 + - - +
359A GLU* 3.5 32.0 + - - +
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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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264A HIS* 3.1 46.3 + - + +
265A MET* 3.8 4.9 - - - +
267A LYS* 1.3 86.4 - - - +
269A ARG* 1.3 62.7 + - - +
271A LYS* 3.4 7.6 + - + +
272A LEU* 3.1 26.6 + - - +
353A LEU* 3.8 14.4 - - + -
354A CYS 5.3 0.9 - - - +
357A ASN* 3.6 27.6 - - + +
358A THR 4.0 2.2 - - - +
359A GLU* 3.4 31.2 - - + +
362A VAL* 3.4 26.9 - - + +
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Residues in contact with ARG 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 MET 2.9 18.7 + - - +
266A GLU* 3.2 33.3 + - - +
267A LYS 3.1 0.2 - - - -
268A LEU* 1.3 74.3 - - - +
270A SER* 1.3 60.5 + - - +
272A LEU* 3.1 12.8 + - + +
273A VAL* 2.9 42.5 + - + +
285A THR* 3.7 7.7 - - - +
287A LEU* 3.6 31.5 + - - +
290A SER* 2.8 32.3 + - - -
291A LEU 3.1 12.8 + - - -
292A PRO* 3.6 12.0 + - - +
293A ASN 4.5 1.1 - - - -
294A THR 2.7 43.2 + - - +
295A LEU* 4.1 13.7 - - + +
353A LEU* 4.2 5.5 - - + +
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Residues in contact with SER 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 GLU* 3.0 12.1 + - - -
267A LYS* 2.9 22.1 + - - +
269A ARG* 1.3 75.6 - - - +
271A LYS* 1.3 59.0 + - - +
273A VAL* 3.2 8.3 + - - +
274A SER* 2.9 32.2 + - - -
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Residues in contact with LYS 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 LYS* 3.1 8.8 + - - +
268A LEU* 3.6 12.1 - - + +
269A ARG 3.2 0.2 - - - -
270A SER* 1.3 82.2 + - - +
272A LEU* 1.3 57.9 + - - +
274A SER* 3.5 6.9 - - - -
275A GLY 3.1 22.2 + - - -
359A GLU* 2.6 44.2 + - + +
362A VAL* 4.2 13.2 - - + -
363A ASP* 2.8 33.9 + - - +
366A LEU* 3.9 11.8 - - + +
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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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5A PHE* 4.6 5.8 - - + -
268A LEU 3.1 19.4 + - - +
269A ARG* 3.1 16.2 + - + +
271A LYS* 1.3 75.4 - - - +
273A VAL* 1.3 56.8 + - - +
274A SER 3.2 0.2 + - - -
275A GLY 3.2 1.2 + - - -
276A LEU* 2.8 41.7 + - + +
295A LEU* 3.9 12.6 - - + -
351A ILE* 4.3 24.9 - - + -
353A LEU* 4.4 15.9 - - + -
362A VAL* 3.6 25.1 - - + -
365A PHE* 3.7 36.3 - - + -
366A LEU* 4.3 7.4 - - + +
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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 ARG* 2.9 27.2 + - + +
270A SER* 3.7 8.3 - - - +
272A LEU* 1.3 75.3 - - - +
274A SER* 1.3 66.2 + - - +
276A LEU* 4.1 3.3 - - - +
277A MET* 3.0 50.8 + - + +
283A ILE* 4.1 12.8 - - + -
287A LEU* 4.0 29.8 - - + -
295A LEU* 3.5 31.6 - - + -
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Residues in contact with SER 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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270A SER 2.9 17.4 + - - -
271A LYS* 3.5 8.7 - - - -
273A VAL* 1.3 81.0 - - - +
275A GLY* 1.3 57.0 + - - -
277A MET* 3.3 12.5 + - - +
278A ASN* 2.6 37.4 + - - +
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Residues in contact with GLY 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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271A LYS 3.1 9.7 + - - -
272A LEU 3.7 1.3 - - - -
274A SER* 1.3 78.9 - - - +
276A LEU* 1.3 62.2 + - - +
278A ASN* 3.2 18.8 + - - +
279A LEU* 3.2 21.1 - - - +
366A LEU* 3.7 22.9 - - - -
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Residues in contact with LEU 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 LEU* 2.8 26.5 + - + +
273A VAL* 4.1 3.6 - - - +
275A GLY* 1.3 70.5 - - - +
277A MET* 1.3 65.7 + - - +
279A LEU* 3.0 18.6 + - + +
280A GLY 3.4 0.2 + - - -
281A ALA* 3.0 29.4 + - + +
283A ILE* 4.8 2.5 - - + -
295A LEU* 4.3 8.1 - - + -
297A VAL* 3.7 31.2 - - + -
299A PHE* 4.6 6.5 - - + -
351A ILE* 3.8 22.4 - - + -
365A PHE* 3.9 18.2 - - + -
366A LEU* 3.7 19.1 - - + -
369A ILE* 4.4 17.7 - - + -
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Residues in contact with MET 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 VAL* 3.0 38.7 + - + +
274A SER* 3.8 9.2 - - - +
276A LEU* 1.3 70.5 - - - +
278A ASN* 1.3 60.1 + - - +
279A LEU 2.9 10.8 + - - -
280A GLY* 3.0 14.0 + - - -
281A ALA 4.1 12.6 - - - +
283A ILE* 3.7 32.1 - - + -
287A LEU* 6.0 1.8 - - - -
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Residues in contact with ASN 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 SER* 2.6 35.7 + - - +
275A GLY* 3.4 13.2 - - - +
276A LEU 3.1 0.4 - - - -
277A MET* 1.3 78.4 - - - +
279A LEU* 1.3 66.9 + - + +
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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