Contacts of the helix formed by residues 255 - 269 (chain A) in PDB entry 1JQO
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 GLY 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A THR 3.3 18.9 + - - -
252A VAL* 3.1 4.3 + - - -
254A LYS* 1.3 77.5 - - - +
256A VAL* 1.3 68.2 + - - +
258A LYS* 2.7 22.5 + - - +
259A PHE* 2.9 11.9 + - - +
684A GLU* 5.7 4.3 - - - -
687A CYS* 4.9 7.6 - - - -
688A PHE* 5.9 0.5 - - - -
691A LEU* 4.9 3.6 - - - -
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Residues in contact with VAL 256 (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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252A VAL* 3.1 26.9 + - + +
255A GLY* 1.3 72.5 - - - +
257A PRO* 1.3 72.4 - - + +
259A PHE* 3.0 19.2 + - - +
260A LEU* 3.0 30.8 + - + +
283A ILE* 4.3 13.2 - - + -
285A PHE* 4.0 13.7 - - + -
441A ARG* 5.6 2.2 - - + +
442A GLN* 5.9 0.2 - - - -
445A THR* 3.8 22.9 - - + +
446A PHE* 3.3 22.7 - - + -
691A LEU* 4.5 10.0 - - + +
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Residues in contact with PRO 257 (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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253A TRP 3.1 16.6 - - - +
254A LYS* 3.8 7.6 - - - +
255A GLY 3.4 3.6 - - - -
256A VAL* 1.3 93.3 - - + +
258A LYS* 1.3 61.1 + - + +
260A LEU* 3.5 12.3 + - + +
261A ARG* 3.1 26.6 + - - +
438A ASP* 4.2 30.6 - - + +
441A ARG* 4.8 4.0 + - + -
442A GLN* 3.4 38.4 - - + +
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Residues in contact with LYS 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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254A LYS* 3.4 25.5 + - - +
255A GLY* 2.7 15.2 + - - +
257A PRO* 1.3 71.5 - - + +
259A PHE* 1.3 66.0 + - - +
261A ARG* 3.2 20.1 + - + +
262A ARG* 3.3 12.1 + - - +
684A GLU* 3.6 24.9 + - - +
688A PHE* 4.6 9.5 - - + -
212B GLU* 5.0 1.2 - - - +
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Residues in contact with PHE 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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143A ILE* 3.6 15.0 - - + -
255A GLY 2.9 7.4 + - - +
256A VAL 3.3 8.1 - - - +
258A LYS* 1.3 76.9 - - - +
260A LEU* 1.3 82.7 + - + +
262A ARG* 3.1 7.8 + - - +
263A VAL* 3.0 34.0 + - + +
282A LEU* 4.5 8.3 - - + -
283A ILE* 4.5 10.5 - - + -
688A PHE* 4.0 23.4 - + + -
691A LEU* 3.6 39.0 - - + -
692A GLN* 3.3 39.7 - - - -
695A THR* 3.2 30.5 - - + -
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Residues in contact with LEU 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 VAL* 3.0 30.6 + - + +
257A PRO* 3.7 6.5 - - + +
259A PHE* 1.3 97.9 - - + +
261A ARG* 1.3 58.6 + - - +
263A VAL* 2.6 31.7 + - + +
264A ASP* 2.8 15.8 + - - +
276A LEU* 5.6 7.0 - - + -
280A VAL 6.0 1.8 - - - +
282A LEU* 4.6 10.5 - - + -
283A ILE* 4.4 12.6 - - + -
441A ARG* 3.5 50.7 - - + +
445A THR* 5.1 2.5 - - - +
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Residues in contact with ARG 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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257A PRO 3.1 17.2 + - - +
258A LYS* 3.3 14.4 - - + +
260A LEU* 1.3 78.1 - - - +
262A ARG* 1.3 57.2 + - - +
264A ASP* 3.3 12.8 + - - +
265A THR* 3.0 28.6 + - - -
275A ARG* 3.8 16.5 + - - +
433A ASP 2.5 30.4 + - - -
434A GLY* 2.9 23.8 + - - -
437A LEU* 4.1 8.8 - - - +
438A ASP* 3.3 22.2 + - - +
441A ARG* 4.3 4.5 - - - +
212B GLU* 3.8 20.6 - - - +
215B GLU* 3.4 23.5 + - - -
219B ARG* 3.4 12.6 - - - +
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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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122A ARG* 4.3 6.5 - - - +
142A ASP* 5.9 1.6 - - - +
144A GLU* 5.1 4.2 - - - +
258A LYS 3.3 6.0 + - - +
259A PHE* 3.1 11.1 + - + +
260A LEU 2.9 0.6 - - - -
261A ARG* 1.3 76.0 - - - +
263A VAL* 1.3 57.1 + - + +
264A ASP 2.9 4.5 - - - -
265A THR* 3.1 5.2 + - - -
266A ALA* 2.8 31.8 + - + +
688A PHE* 3.9 30.6 - - + -
692A GLN* 5.3 6.3 - - - +
206B THR* 4.6 2.8 + - - +
208B ASP* 3.6 33.0 + - - +
209B ASP* 2.8 37.4 + - - +
212B GLU* 2.8 28.8 + - - -
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Residues in contact with VAL 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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143A ILE* 3.7 32.5 - - + -
165A LEU* 4.0 20.9 - - + -
259A PHE* 3.0 33.6 + - + +
260A LEU* 2.6 18.9 + - + +
262A ARG* 1.3 73.0 - - + +
264A ASP* 1.3 57.9 + - - +
266A ALA* 3.8 7.3 - - - +
267A LEU* 3.1 25.4 + - + +
276A LEU* 4.2 11.2 - - + -
282A LEU* 3.9 21.8 - - + -
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Residues in contact with ASP 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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260A LEU 2.8 10.6 + - - +
261A ARG* 3.3 12.9 - - - +
263A VAL* 1.3 74.6 - - - +
265A THR* 1.3 67.4 + - - +
266A ALA 3.0 1.1 - - - -
267A LEU* 2.9 18.1 + - - +
268A LYS* 3.0 19.8 + - - +
275A ARG* 3.1 38.2 + - + +
276A LEU* 2.8 34.1 + - - +
441A ARG* 3.0 34.0 + - - -
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Residues in contact with THR 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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144A GLU* 5.1 0.4 - - - +
261A ARG 3.0 8.2 + - - -
262A ARG* 3.5 9.0 - - - -
264A ASP* 1.3 77.2 - - - +
266A ALA* 1.3 61.4 + - - +
268A LYS* 3.5 7.7 + - - +
269A ASN* 2.8 41.5 + - - +
275A ARG* 5.1 2.4 + - - +
208B ASP* 3.8 20.6 - - + +
211B GLN* 3.9 30.4 + - - +
212B GLU* 2.9 35.2 + - + +
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Residues in contact with ALA 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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143A ILE* 4.4 3.6 - - + -
144A GLU* 4.0 27.2 + - + +
147A LEU* 3.6 23.6 - - + -
262A ARG* 2.8 17.6 + - + +
263A VAL* 3.8 9.0 - - - +
265A THR* 1.3 74.0 - - - +
267A LEU* 1.3 67.7 + - - +
269A ASN* 2.7 27.8 + - - +
270A ILE* 3.3 8.3 + - - +
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Residues in contact with LEU 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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147A LEU* 4.6 12.8 - - + -
161A VAL* 5.7 2.0 - - + -
162A PHE* 3.9 23.3 - - + +
165A LEU* 4.0 24.2 - - + -
263A VAL 3.1 19.3 + - - +
264A ASP* 2.9 9.4 + - - +
266A ALA* 1.3 78.1 - - - +
268A LYS* 1.3 57.2 + - - +
270A ILE* 2.9 22.7 + - + +
271A GLY 3.4 0.2 + - - -
272A ILE* 3.3 47.8 + - + +
274A GLU 3.8 17.7 - - - +
275A ARG 4.3 0.2 - - - -
276A LEU* 4.0 23.1 - - + +
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Residues in contact with LYS 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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264A ASP 3.0 15.9 + - - +
265A THR* 3.9 8.7 - - - +
267A LEU* 1.3 76.9 - - - +
269A ASN* 1.3 60.4 + - - +
270A ILE 3.0 0.2 - - - -
271A GLY* 3.1 18.0 + - - +
272A ILE 3.1 17.9 - - - +
273A ASN* 4.2 18.8 - - - +
274A GLU 4.5 3.6 - - - +
275A ARG* 4.1 41.0 - - - +
211B GLN* 5.1 12.5 - - - +
215B GLU* 4.2 11.7 + - - +
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Residues in contact with ASN 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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144A GLU* 2.9 30.9 + - + -
148A LYS* 3.5 25.1 - - - +
265A THR* 2.8 33.0 + - - +
266A ALA* 2.7 14.4 + - - +
268A LYS* 1.3 73.1 - - - +
270A ILE* 1.3 64.6 + - + +
271A GLY 3.4 1.6 - - - -
208B ASP* 3.9 3.2 + - - -
211B GLN* 4.5 9.7 - - - +
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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