Contacts of the helix formed by residues 260 - 271 (chain A) in PDB entry 1YWV
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLU* 2.7 35.7 + - - -
258A ARG* 3.7 21.3 - - - +
259A VAL* 1.3 77.4 - - - +
261A SER* 1.3 61.0 + - - +
262A GLU* 3.7 5.8 + - - +
263A CYS* 3.2 14.7 + - - +
264A GLN* 2.9 26.2 + - - +
289A TRP* 3.8 5.2 - - - -
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Residues in contact with SER 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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258A ARG* 5.1 4.6 + - - +
259A VAL 3.7 0.8 + - - -
260A SER* 1.3 74.6 - - - +
262A GLU* 1.3 60.5 + - - +
264A GLN* 3.5 10.6 + - - +
265A HIS* 3.0 28.4 + - - +
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Residues in contact with GLU 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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260A SER* 3.2 6.9 - - - +
261A SER* 1.3 79.9 - - - +
263A CYS* 1.3 62.7 + - - +
265A HIS* 3.2 6.6 + - - +
266A LEU* 3.0 18.2 + - - +
287A HIS* 3.2 15.2 + - - +
288A PRO* 3.5 38.3 - - - +
289A TRP* 3.8 17.0 + - + +
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Residues in contact with CYS 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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141A GLU* 3.8 2.0 - - - +
232A LEU* 4.3 7.9 - - - -
236A VAL* 4.1 13.2 - - - -
259A VAL* 3.5 21.1 - - + -
260A SER* 3.2 19.5 + - - +
262A GLU* 1.3 72.1 - - - +
264A GLN* 1.3 66.6 + - - +
266A LEU* 3.2 4.5 + - - +
267A ILE* 2.9 41.0 + - - +
289A TRP* 3.5 41.8 - - - +
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Residues in contact with GLN 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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255A PHE* 3.5 48.2 - - + +
257A GLN 5.4 0.2 + - - -
259A VAL* 3.4 25.8 + - + +
260A SER 2.9 19.2 + - - +
261A SER* 3.7 8.8 - - - +
263A CYS* 1.3 75.4 - - - +
265A HIS* 1.3 57.8 + - - +
267A ILE* 3.3 1.4 + - - +
268A ARG* 2.9 53.7 + - - +
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Residues in contact with HIS 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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261A SER 3.0 15.9 + - - +
262A GLU* 3.5 10.1 - - - +
263A CYS 3.2 0.2 - - - -
264A GLN* 1.3 73.4 - - - +
266A LEU* 1.3 65.4 + - - +
268A ARG* 3.4 7.6 + - - +
269A TRP* 3.0 41.5 + + + +
287A HIS* 3.1 28.9 - + + -
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Residues in contact with LEU 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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148A PHE* 4.3 7.6 - - + -
232A LEU* 3.9 16.2 - - + -
262A GLU 3.0 7.9 + - - +
263A CYS* 3.7 8.1 - - - +
265A HIS* 1.3 75.9 - - - +
267A ILE* 1.3 62.7 + - - +
269A TRP* 3.2 13.1 + - + +
270A CYS* 3.0 36.4 + - - -
284A ILE* 4.2 17.5 - - + -
287A HIS* 3.7 38.1 - - + +
289A TRP* 3.7 27.1 - - + -
290A MET* 3.9 18.6 - - + -
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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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229A GLY* 4.2 7.6 - - - +
232A LEU* 3.7 26.0 - - + -
233A TYR* 3.8 26.7 - - + +
236A VAL* 3.9 14.1 - - + -
253A VAL* 4.5 3.1 - - + -
255A PHE* 3.6 35.9 - - + -
263A CYS* 2.9 25.8 + - - +
264A GLN 3.6 3.6 - - - +
266A LEU* 1.3 75.3 - - - +
268A ARG* 1.3 58.0 + - - +
270A CYS* 3.2 7.6 + - - +
271A LEU* 3.0 49.0 + - + +
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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
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251A GLY 5.6 0.2 + - - -
252A GLN* 5.3 5.1 - - - +
253A VAL* 3.0 54.4 + - + +
254A PHE* 5.1 0.2 - - - +
255A PHE* 3.5 27.3 - - + +
264A GLN* 2.9 34.0 + - - +
265A HIS* 3.8 7.2 - - - +
267A ILE* 1.3 76.7 - - - +
269A TRP* 1.3 62.0 + - - +
271A LEU* 3.4 8.0 + - - +
272A ALA* 3.3 18.4 + - - +
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Residues in contact with TRP 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 HIS* 3.0 32.6 + + + +
266A LEU* 3.5 8.5 - - + +
267A ILE 3.2 0.2 - - - -
268A ARG* 1.3 76.0 - - - +
270A CYS* 1.3 63.6 + - - +
271A LEU 3.1 0.2 - - - -
272A ALA* 3.2 18.3 + - + +
277A ASP 3.0 28.2 + - - -
278A ARG* 3.6 1.2 - - - -
279A PRO* 3.3 41.0 - - + +
283A GLU* 3.7 50.7 - - + -
287A HIS* 4.1 22.7 - - + -
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Residues in contact with CYS 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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148A PHE* 5.0 5.4 - - - -
225A VAL* 3.7 10.8 - - - +
226A TRP* 3.6 11.6 + - - -
228A LEU 5.0 2.0 - - - -
229A GLY* 3.5 27.8 - - - -
232A LEU* 5.9 0.9 - - - -
266A LEU* 3.0 28.8 + - - -
267A ILE* 3.6 4.9 - - - +
269A TRP* 1.3 76.5 - - - +
271A LEU* 1.3 57.2 + - - +
272A ALA 3.3 0.4 - - - -
278A ARG* 3.3 23.9 - - - -
279A PRO* 3.8 15.0 - - - +
284A ILE* 4.0 27.6 - - - -
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Residues in contact with LEU 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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226A TRP* 3.2 59.9 - - + +
229A GLY* 3.9 9.0 - - - +
230A ILE* 3.7 20.9 - - + +
233A TYR* 5.2 0.2 - - + -
241A PRO* 4.3 7.6 - - + -
242A PHE* 4.1 15.7 - - + -
251A GLY 4.6 9.0 - - - +
253A VAL* 4.0 23.3 - - + -
267A ILE* 3.0 35.6 + - + +
268A ARG 3.5 7.1 - - - +
269A TRP 3.1 0.6 - - - -
270A CYS* 1.3 76.3 - - - +
272A ALA* 1.3 64.8 + - - +
273A LEU* 3.4 3.6 + - - +
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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