Contacts of the helix formed by residues 267 - 280 (chain A) in PDB entry 4EWS
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 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A PHE 3.8 0.6 + - - -
266A SER* 1.3 74.2 + - - +
268A ARG* 1.4 60.1 + - + +
270A PHE* 3.0 29.5 + - + +
271A HIS* 3.1 14.2 + - - +
331A ILE 3.7 7.6 - - - +
332A SER* 3.6 19.5 - - - -
333A CYS* 3.0 49.4 + - - +
334A GLN* 5.6 0.3 + - - -
452A ASP* 4.7 2.1 - - - +
453A GLY* 2.9 32.2 + - - +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY* 6.2 0.9 - - - -
245A LEU* 6.0 0.2 - - - +
246A PRO* 2.8 35.2 + - - +
247A LEU 4.7 1.2 + - - -
248A PRO* 3.7 35.9 - - + +
266A SER* 3.1 13.9 - - - +
267A GLU* 1.4 79.8 - - + +
269A VAL* 1.4 52.7 + - + +
271A HIS* 3.5 9.4 + - - +
272A SER* 2.8 36.3 + - - -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY* 3.6 30.7 - - - +
11A ILE* 3.8 25.1 - - + -
213A VAL* 5.8 0.7 - - + -
234A GLY 3.9 14.4 - - - +
236A PHE* 3.3 27.5 - - + -
265A PHE* 4.4 8.5 - - + -
266A SER* 3.4 12.1 - - - +
267A GLU 3.1 0.4 - - - -
268A ARG* 1.4 76.7 - - + +
270A PHE* 1.4 56.4 + - + +
272A SER* 3.3 5.0 + - - -
273A LEU* 2.8 30.5 + - - +
503A DLP 4.3 17.9 - - + -
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 3.9 22.0 - + + -
266A SER 3.6 19.5 - - - -
267A GLU* 3.0 14.9 + - + +
269A VAL* 1.4 72.9 - - + +
271A HIS* 1.3 60.1 + - - +
273A LEU* 3.5 12.4 - - + +
274A ALA 3.1 21.7 + - - -
331A ILE* 3.4 40.9 - - + +
333A CYS* 3.8 11.4 - - - -
338A VAL* 5.6 3.4 - - + -
455A LEU* 3.8 42.8 - - + -
502A 2OB 4.0 43.1 - - + -
503A DLP 4.9 7.6 - - + -
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 3.1 12.4 + - - +
268A ARG* 3.5 14.0 + - - +
270A PHE* 1.3 75.0 - - - +
272A SER* 1.3 64.1 + - - +
274A ALA* 3.2 4.9 + - - +
275A LYS* 3.1 31.7 + - + +
328A MET* 3.4 38.9 - - + +
330A LYS* 5.1 8.5 - - + +
331A ILE* 4.6 22.8 - - - +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLY 5.2 1.6 - - - -
235A HIS* 4.9 1.4 - - - -
236A PHE* 3.4 35.7 + - - +
268A ARG 2.8 21.8 + - - -
269A VAL* 3.5 6.1 - - - -
271A HIS* 1.3 76.6 + - - +
273A LEU* 1.4 58.4 + - - +
275A LYS* 3.6 19.2 + - - +
276A VAL* 3.3 26.3 + - - +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 5.2 0.4 - - + -
236A PHE* 3.6 30.7 - - + -
269A VAL 2.8 20.2 + - - +
270A PHE* 3.5 16.6 - - + +
271A HIS 3.2 0.2 - - - -
272A SER* 1.4 69.7 - - - +
274A ALA* 1.3 59.1 + - - +
276A VAL* 3.3 8.0 - - + +
277A ALA* 2.9 31.5 + - + +
331A ILE* 5.3 0.2 - - + -
429A PHE* 4.5 8.7 - - + -
502A 2OB 4.4 14.6 - - + -
503A DLP 3.8 76.5 - - + -
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Residues in contact with ALA 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 PHE 3.1 11.4 + - - +
271A HIS* 3.2 8.9 + - - +
273A LEU* 1.3 74.8 - - - +
275A LYS* 1.4 59.5 + - - +
277A ALA* 4.0 5.7 - - - +
278A PHE* 3.0 31.4 + - - +
328A MET* 3.8 2.7 - - + -
329A PRO* 3.2 40.8 - - + +
331A ILE* 3.7 15.7 - - + -
503A DLP 4.7 5.6 - - + -
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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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243A GLU* 5.8 1.0 + - - -
245A LEU* 5.2 12.3 - - - +
271A HIS* 3.1 23.2 + - + +
272A SER* 3.6 20.8 + - - +
273A LEU 3.3 0.2 - - - -
274A ALA* 1.4 76.7 - - - +
276A VAL* 1.4 61.5 + - + +
278A PHE* 3.7 1.0 - - - +
279A GLN* 3.0 46.4 + - - +
328A MET* 3.6 28.9 - - + +
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Residues in contact with VAL 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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211A ILE* 3.8 25.6 - - + +
236A PHE* 3.7 33.9 - - + +
237A ILE 4.9 0.4 - - - +
238A TYR* 3.7 31.9 - - + +
272A SER* 3.3 13.4 + - - +
273A LEU* 3.3 14.8 - - + +
275A LYS* 1.4 79.3 - - + +
277A ALA* 1.4 56.7 + - - +
279A GLN* 3.7 5.6 - - + +
280A ASP* 2.9 36.4 + - - +
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Residues in contact with ALA 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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211A ILE* 4.1 10.3 - - + -
273A LEU* 2.9 18.9 + - + +
274A ALA 4.0 2.9 - - - +
276A VAL* 1.4 76.4 - - - +
278A PHE* 1.4 62.3 + - - +
280A ASP* 3.5 3.3 + - - -
282A ARG* 3.2 29.9 + - + +
283A LEU* 4.0 11.6 + - + -
503A DLP 3.8 41.5 - - + -
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Residues in contact with PHE 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 ALA 3.0 20.8 + - - +
275A LYS 3.7 2.5 - - - +
277A ALA* 1.4 74.1 - - - +
279A GLN* 1.3 82.6 + - - +
281A GLY* 3.0 22.2 + - - -
283A LEU* 3.6 14.5 + - + +
325A CYS* 3.3 41.3 - - + -
326A LEU 3.3 19.3 - - - -
327A LYS* 3.6 17.7 - - + -
328A MET* 3.8 23.8 - - + -
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Residues in contact with GLN 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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238A TYR* 3.9 22.5 + - + -
275A LYS* 3.0 39.4 + - - +
276A VAL* 4.0 6.1 - - + +
278A PHE* 1.3 96.7 - - - +
280A ASP* 1.3 59.5 + - - +
281A GLY* 3.1 1.3 + - - -
328A MET* 5.6 1.2 - - - +
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Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 3.6 14.6 - - - +
211A ILE* 4.2 3.1 - - + -
238A TYR* 2.9 34.3 + - + -
239A LYS* 4.7 1.2 - - - -
276A VAL 2.9 21.5 + - - +
277A ALA 4.0 2.2 - - - +
278A PHE 3.3 0.6 - - - -
279A GLN* 1.3 71.8 - - - +
281A GLY* 1.3 61.1 + - - +
282A ARG* 2.8 42.7 + - - +
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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
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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