Contacts of the helix formed by residues 258 - 273 (chain A) in PDB entry 2CRX
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 THR 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ILE* 3.9 17.2 - - + +
175A ALA* 3.5 41.5 - - + +
178A ALA* 4.9 4.0 - - + -
255A GLN* 6.1 0.2 - - - +
256A LEU 3.7 0.4 + - - -
257A SER* 1.3 72.7 - - - +
259A ARG* 1.3 59.8 + - - +
261A LEU* 3.0 15.2 + - - +
262A GLU* 2.9 31.3 + - - +
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Residues in contact with ARG 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 SER* 3.2 7.3 - - - +
258A THR* 1.3 84.0 + - - +
260A ALA* 1.3 56.3 + - - +
262A GLU* 3.1 30.2 + - - +
263A GLY* 2.8 24.9 + - - +
266A GLU* 3.3 32.3 + - - -
7D T 4.4 10.5 + - + +
8D T 3.6 32.5 - - + +
9D C 4.0 13.9 - - - +
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Residues in contact with ALA 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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256A LEU* 3.9 17.5 - - + -
257A SER* 3.0 24.9 + - - +
258A THR 3.1 0.4 - - - -
259A ARG* 1.3 72.8 - - - +
261A LEU* 1.3 68.3 + - - +
263A GLY* 2.9 12.3 + - - +
264A ILE* 3.1 16.9 + - - +
6D C 4.3 17.2 - - - +
7D T 3.5 19.9 - - + +
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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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163A PHE* 3.3 41.3 - - + -
174A ILE* 3.2 41.1 - - + +
178A ALA* 3.6 22.9 - - + +
239A PHE* 5.0 8.1 - - + -
256A LEU* 4.0 26.2 - - + -
257A SER 3.5 11.4 - - - +
258A THR* 3.0 8.0 + - - +
260A ALA* 1.3 76.2 - - - +
262A GLU* 1.3 62.4 + - - +
264A ILE* 3.2 23.3 + - + +
265A PHE* 3.4 13.5 + - - -
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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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174A ILE* 3.8 20.4 - - + +
258A THR* 2.9 12.1 + - - +
259A ARG* 3.2 44.4 + - - +
261A LEU* 1.3 77.1 - - - +
263A GLY* 1.3 57.1 + - - +
265A PHE* 2.9 21.5 + - - +
266A GLU* 3.0 19.8 + - - +
286A TRP 4.3 0.3 - - - +
287A SER* 5.1 5.1 - - - -
288A GLY* 3.7 26.6 + - - +
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Residues in contact with GLY 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 ARG* 2.8 14.7 + - - -
260A ALA* 2.9 6.6 + - - -
262A GLU* 1.3 77.6 - - - +
264A ILE* 1.3 52.5 + - - +
266A GLU* 3.4 15.3 + - - +
267A ALA* 2.7 36.8 + - - +
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Residues in contact with ILE 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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159A ARG* 4.1 21.8 - - - +
160A ASN* 3.8 47.8 - - + +
163A PHE* 3.8 35.0 - - + -
164A LEU* 4.2 6.7 - - + -
239A PHE* 6.2 0.7 - - + -
256A LEU* 4.9 2.9 - - + -
260A ALA 3.1 13.9 + - - +
261A LEU* 3.4 24.0 - - + +
262A GLU 3.1 0.4 - - - -
263A GLY* 1.3 72.8 - - - +
265A PHE* 1.3 62.1 + - - +
267A ALA* 4.1 4.6 - - - +
268A THR* 2.9 37.4 + - - +
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Residues in contact with PHE 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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137A PHE* 4.2 12.3 - + - -
163A PHE* 3.5 21.8 - + - -
164A LEU* 3.8 20.6 - - + -
167A ALA* 4.0 10.3 - - + -
174A ILE* 4.8 0.4 - - + -
261A LEU 3.4 16.1 + - - -
262A GLU 2.9 8.6 + - - +
264A ILE* 1.3 79.1 - - - +
266A GLU* 1.3 66.3 + - - +
268A THR* 3.8 2.0 - - - -
269A HIS* 3.2 12.3 + - - +
286A TRP* 3.5 50.3 - + + +
287A SER 3.5 20.2 - - - +
288A GLY* 3.8 15.9 - - - -
290A SER* 4.3 0.9 - - - -
291A ALA* 3.6 41.5 - - + -
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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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259A ARG* 3.3 36.4 + - - -
262A GLU* 3.0 12.2 + - + +
263A GLY* 3.4 19.2 + - - +
265A PHE* 1.3 73.1 - - - +
267A ALA* 1.3 57.5 + - - +
269A HIS* 2.7 30.4 + - - +
270A ARG* 2.9 12.9 + - - +
285A ALA* 4.7 9.8 - - + +
286A TRP 3.5 17.5 - - - +
287A SER* 5.4 0.4 - - - -
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Residues in contact with ALA 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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160A ASN* 5.7 6.1 - - - +
263A GLY 2.7 22.3 + - - +
264A ILE* 4.1 4.9 - - - +
266A GLU* 1.3 72.1 - - - +
268A THR* 1.3 65.4 + - - +
270A ARG* 2.9 26.8 + - - +
271A LEU* 2.8 23.4 + - - +
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Residues in contact with THR 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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137A PHE* 5.1 0.2 - - + -
145A VAL* 3.8 25.8 - - + -
149A MET* 4.6 11.1 - - - +
160A ASN* 4.9 5.0 + - - +
164A LEU* 3.7 22.8 - - + +
264A ILE* 2.9 26.0 + - - +
265A PHE* 3.8 3.6 - - - -
267A ALA* 1.3 78.2 - - - +
269A HIS* 1.3 62.2 + - - +
271A LEU* 3.2 22.1 - - + +
272A ILE* 3.4 10.4 + - + +
286A TRP* 3.6 20.6 - - + -
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Residues in contact with HIS 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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135A LEU* 3.6 18.4 - - + +
265A PHE 3.2 10.3 + - - +
266A GLU 2.7 16.7 + - - +
268A THR* 1.3 70.0 - - - +
270A ARG* 1.3 58.2 + - - +
271A LEU 2.9 4.3 - - - -
272A ILE* 2.9 5.7 + - - -
273A TYR* 2.8 65.8 + + + +
274A GLY 5.0 2.6 + - - -
284A LEU 3.9 15.9 - - - -
285A ALA* 3.8 18.6 - - + +
286A TRP* 3.5 40.3 - + + -
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Residues in contact with ARG 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 2.9 9.1 + - - +
267A ALA* 2.9 24.5 + - - +
269A HIS* 1.3 77.4 + - - +
271A LEU* 1.3 62.2 + - - +
274A GLY* 2.8 33.3 + - - +
275A ALA* 3.5 41.3 - - - +
285A ALA* 5.9 0.2 - - - +
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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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145A VAL* 6.4 2.7 - - + -
148A LEU* 4.0 26.0 - - + -
149A MET* 5.9 9.0 - - + -
267A ALA 2.8 10.5 + - - +
268A THR* 3.2 16.8 - - + +
270A ARG* 1.3 85.8 - - - +
272A ILE* 1.3 75.7 + - + +
274A GLY 4.6 0.5 + - - -
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Residues in contact with ILE 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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141A ASP* 5.1 0.7 - - - +
144A GLN* 3.3 44.2 - - + +
145A VAL* 3.7 24.2 - - + -
148A LEU* 4.3 10.5 - - + -
268A THR 3.4 7.6 + - - +
269A HIS 2.9 4.6 + - - +
271A LEU* 1.3 94.4 - - + +
273A TYR* 1.3 92.4 + - + +
274A GLY 3.7 0.4 - - - -
286A TRP* 4.5 8.1 - - + -
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Residues in contact with TYR 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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141A ASP* 4.0 15.6 + - - -
144A GLN* 4.6 8.9 + - - -
269A HIS* 2.8 57.2 + + + +
272A ILE* 1.3 105.8 - - + +
274A GLY* 1.3 65.2 + - - +
275A ALA 4.9 0.7 - - - +
286A TRP* 4.7 6.0 - + - -
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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