Contacts of the helix formed by residues 257 - 268 (chain A) in PDB entry 4YC3
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 ASP 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LYS* 4.9 7.8 + - - -
256A LEU* 1.3 74.0 - - - +
258A GLU* 1.3 60.1 + - - +
259A ASN* 4.1 7.3 - - - +
260A GLY* 2.8 34.3 + - - -
261A LEU* 3.0 29.5 + - - +
286A TYR* 3.8 16.0 - - - -
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Residues in contact with GLU 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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257A ASP* 1.3 76.2 - - - +
259A ASN* 1.3 63.1 + - - +
261A LEU* 3.7 10.1 + - + +
262A ASP* 3.1 27.4 + - - +
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Residues in contact with ASN 259 (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 ASP* 3.2 8.8 + - - +
258A GLU* 1.3 82.2 - - - +
260A GLY* 1.3 61.1 + - - +
262A ASP* 3.3 5.8 + - - +
263A LEU* 2.9 26.2 + - - +
284A HIS* 3.2 15.1 - - + -
285A PRO* 3.5 36.0 + - - +
286A TYR* 3.9 19.5 - - - +
288A ASN* 5.3 1.0 + - - -
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Residues in contact with GLY 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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194A PHE* 3.5 10.7 - - - -
256A LEU* 4.3 11.9 - - - -
257A ASP* 2.8 23.2 + - - -
259A ASN* 1.3 73.4 - - - +
261A LEU* 1.3 61.9 + - - +
263A LEU* 3.1 3.1 + - - +
264A LEU* 2.9 24.8 + - - +
286A TYR* 3.6 21.4 - - - -
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Residues in contact with LEU 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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249A LEU* 4.2 8.4 - - + +
250A ALA* 4.1 29.6 - - + +
253A VAL* 4.0 30.5 - - + +
256A LEU* 3.6 32.3 - - + +
257A ASP 3.0 17.8 + - - +
258A GLU* 3.9 8.7 - - + +
259A ASN 3.3 0.2 - - - -
260A GLY* 1.3 75.9 - - - +
262A ASP* 1.3 53.3 + - - +
264A LEU* 3.4 9.6 + - + +
265A SER* 2.8 36.3 + - - -
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Residues in contact with ASP 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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258A GLU 3.1 19.7 + - - +
259A ASN* 3.6 9.9 - - - +
260A GLY 3.2 0.2 - - - -
261A LEU* 1.3 74.4 - - - +
263A LEU* 1.3 63.7 - - - +
265A SER* 2.9 23.7 + - - -
266A LYS* 3.0 36.3 + - - +
284A HIS* 2.7 27.8 + - + +
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Residues in contact with LEU 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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109A LEU* 3.7 29.4 - - + -
194A PHE* 3.8 6.3 - - + -
259A ASN 2.9 16.9 + - - +
260A GLY* 3.5 4.9 - - - +
262A ASP* 1.3 71.9 + - - +
264A LEU* 1.3 66.9 + - - +
266A LYS* 3.0 15.1 + - - +
267A MET* 3.1 34.8 + - + +
276A ILE* 4.4 8.7 - - + -
281A ALA* 4.2 12.8 - - + -
284A HIS* 3.8 34.1 - - + +
286A TYR* 3.9 17.9 - - + -
287A PHE* 4.0 13.9 - - + -
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Residues in contact with LEU 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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191A GLY* 3.2 34.3 - - - +
194A PHE* 3.9 17.2 - - + -
195A ALA* 4.4 13.9 - - + +
203A LEU* 5.3 1.3 - - + -
249A LEU* 4.0 17.7 - - + -
253A VAL* 4.3 19.5 - - + -
256A LEU* 4.4 15.3 - - + -
260A GLY 2.9 12.8 + - - +
261A LEU* 3.4 10.5 - - + +
263A LEU* 1.3 77.4 - - - +
265A SER* 1.3 63.5 + - - +
267A MET* 3.1 15.7 + - - +
268A LEU* 3.1 32.7 + - + +
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Residues in contact with SER 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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249A LEU* 3.9 18.4 - - - +
261A LEU 2.8 18.5 + - - -
262A ASP* 2.9 22.2 + - - -
263A LEU 3.3 0.2 - - - -
264A LEU* 1.3 73.6 - - - +
266A LYS* 1.3 63.1 + - - +
268A LEU* 3.3 6.6 + - - +
269A ILE* 3.3 25.0 + - - +
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Residues in contact with LYS 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 ASP* 3.0 40.8 + - - +
263A LEU* 3.0 10.4 + - - +
265A SER* 1.3 84.4 + - - +
267A MET* 1.3 59.5 + - - +
268A LEU 3.6 0.2 + - - -
269A ILE* 3.7 20.7 + - + +
275A ARG* 3.6 7.8 - - - +
276A ILE* 3.1 55.7 + - + -
284A HIS* 4.6 7.3 + - + -
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Residues in contact with MET 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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109A LEU* 4.6 3.8 - - + -
113A LEU* 4.0 28.9 - - + -
187A ILE* 4.0 13.2 - - + +
188A TRP* 3.8 13.9 + - - -
190A ILE* 4.2 9.4 - - + -
191A GLY* 3.7 33.9 - - - -
194A PHE* 4.2 16.8 - - - -
263A LEU* 3.1 37.7 + - + +
264A LEU* 3.5 7.6 - - - +
266A LYS* 1.3 77.0 - - - +
268A LEU* 1.3 57.5 + - + +
269A ILE 3.6 0.4 - - - -
275A ARG* 3.3 22.2 - - - -
276A ILE* 3.7 15.5 - - + -
281A ALA* 4.3 6.7 - - + -
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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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188A TRP* 3.5 55.3 - - + +
191A GLY* 4.4 1.1 - - - -
192A THR* 4.4 11.9 - - + +
203A LEU* 4.1 19.7 - - + -
204A PHE* 4.6 8.3 - - + -
220A LEU* 3.7 22.1 - - + +
249A LEU* 4.8 11.9 - - + -
264A LEU* 3.1 41.4 + - + +
265A SER* 3.3 7.1 + - - +
267A MET* 1.3 82.6 - - - +
269A ILE* 1.3 64.5 + - - +
270A TYR* 3.4 3.1 + - - -
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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