Contacts of the helix formed by residues 261 - 273 (chain A) in PDB entry 4C8B
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 HIS 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A ILE 3.3 1.2 + - - -
260A PRO* 1.3 83.1 - - + +
262A ARG* 1.3 66.7 + - - +
263A ALA 3.0 4.9 + - - -
264A ARG* 3.1 17.1 + - + +
265A MET* 3.0 23.5 + - + +
293A VAL* 3.6 36.5 - - + +
296A THR* 3.7 33.4 + - + -
297A PHE* 5.5 1.5 - + - -
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Residues in contact with ARG 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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250A ILE* 4.7 2.0 - - - +
251A ASN 3.0 24.2 + - - +
252A GLU 4.2 1.0 - - - +
255A LEU* 2.6 36.6 + - + +
256A PRO 3.4 11.7 + - - -
257A TYR* 4.0 35.9 - - - +
259A ILE* 3.2 34.4 + - + +
260A PRO 3.0 5.0 + - - -
261A HIS* 1.3 76.6 - - - +
263A ALA* 1.3 58.3 + - + +
265A MET* 3.2 3.4 + - - +
266A ILE* 2.8 62.5 + - + +
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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
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261A HIS 3.1 0.8 - - - -
262A ARG* 1.3 76.5 - - + +
264A ARG* 1.3 66.1 + - - +
266A ILE* 3.5 9.6 + - - +
267A SER* 3.2 26.2 + - - -
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Residues in contact with ARG 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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261A HIS* 3.1 21.7 + - + +
263A ALA* 1.3 77.0 - - - +
265A MET* 1.3 65.1 + - + +
267A SER* 3.4 7.9 + - - -
268A LEU* 3.1 25.9 + - - +
289A GLU* 5.5 14.8 - - + +
293A VAL* 5.1 6.5 - - + -
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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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122A PHE* 3.6 34.5 - - + -
125A LEU* 5.3 3.6 - - - -
219A THR* 5.1 7.6 - - - +
223A LEU* 4.0 23.8 - - + -
259A ILE* 5.3 0.2 - - + -
260A PRO 4.3 1.3 - - - +
261A HIS* 3.0 17.4 + - + +
262A ARG* 3.5 8.7 - - - +
264A ARG* 1.3 78.3 - - + +
266A ILE* 1.3 65.3 + - + +
268A LEU* 3.2 13.1 + - + +
269A ILE* 3.0 30.7 + - + +
290A LEU* 3.6 26.9 - - + -
293A VAL* 3.6 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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223A LEU* 6.6 0.2 - - + -
250A ILE* 3.8 27.8 - - + -
255A LEU* 4.0 19.1 - - + -
262A ARG* 2.8 60.1 + - + +
263A ALA* 3.9 7.4 - - - +
265A MET* 1.3 72.7 - - + +
267A SER* 1.3 58.2 + - - +
269A ILE* 3.2 8.0 + - + +
270A GLU* 2.9 51.8 + - - +
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Residues in contact with SER 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 ALA 3.2 14.9 + - - -
264A ARG* 3.4 12.1 - - - -
266A ILE* 1.3 76.1 - - - +
268A LEU* 1.3 57.5 + - - +
270A GLU* 4.0 7.7 - - - +
271A SER* 2.9 31.4 + - - -
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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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215A TYR* 5.0 9.4 - - + -
216A ALA* 4.9 0.7 - - - +
219A THR* 5.9 6.1 - - + -
264A ARG 3.1 12.6 + - - +
265A MET* 3.2 19.0 + - + +
267A SER* 1.3 76.4 - - - +
269A ILE* 1.3 58.9 + - + +
271A SER* 3.9 3.5 - - - -
272A GLY* 2.9 26.9 + - - -
281A PRO* 4.9 8.4 - - + +
286A CYS* 3.8 34.5 - - - +
289A GLU* 4.5 22.4 - - + -
290A LEU* 4.0 32.3 - - + -
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Residues in contact with ILE 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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216A ALA* 3.4 17.4 - - - +
219A THR* 3.6 30.7 - - + -
220A TRP* 4.0 16.2 - - + +
223A LEU* 4.4 11.2 - - + -
250A ILE* 4.6 4.3 - - + -
255A LEU* 4.6 13.2 - - + -
265A MET 3.0 25.7 + - - +
266A ILE* 3.2 9.4 + - - +
268A LEU* 1.3 76.8 - - - +
270A GLU* 1.3 56.7 + - - +
272A GLY 3.1 0.9 + - - -
273A TRP* 2.9 71.4 + - + -
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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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250A ILE* 4.2 18.6 - - + +
266A ILE* 2.9 38.4 + - - +
267A SER* 4.0 5.6 - - - +
269A ILE* 1.3 75.1 - - - +
271A SER* 1.3 66.1 + - - +
273A TRP* 3.7 21.3 - - - +
274A ALA* 3.3 19.6 + - - +
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Residues in contact with SER 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 SER 2.9 19.3 + - - -
268A LEU* 3.9 6.3 - - - -
270A GLU* 1.3 76.1 - - - +
272A GLY* 1.3 62.8 + - - +
274A ALA* 3.2 16.3 + - - +
279A GLU* 4.5 7.9 - - - -
280A ARG* 3.4 17.0 + - - +
281A PRO* 3.8 18.6 - - - -
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Residues in contact with GLY 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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212A ILE* 3.6 12.9 - - - +
213A TYR* 3.4 12.8 + - - -
216A ALA* 3.7 12.1 - - - -
268A LEU 2.9 15.7 + - - -
269A ILE 3.1 4.7 + - - -
271A SER* 1.3 78.3 - - - +
273A TRP* 1.3 57.0 + - - +
280A ARG* 3.3 21.3 - - - +
281A PRO* 4.0 13.0 - - - -
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Residues in contact with TRP 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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213A TYR* 3.6 25.7 - - + +
216A ALA* 3.9 5.4 - - + -
217A VAL* 4.1 23.8 - - + -
220A TRP* 3.8 26.0 - + + -
247A ARG* 2.8 60.3 + - + +
248A PRO* 3.7 39.9 - - + -
250A ILE* 3.9 16.4 - - + -
269A ILE* 2.9 43.4 + - + +
270A GLU* 3.7 21.6 - - + +
271A SER 3.2 0.4 - - - -
272A GLY* 1.3 75.8 - - - +
274A ALA* 1.3 66.2 + - - +
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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