Contacts of the helix formed by residues 259 - 267 (chain A) in PDB entry 1JQP
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 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 3.4 8.6 - - - +
258A LEU* 1.3 72.3 - - - +
260A PRO* 1.3 62.7 - - - +
262A GLU* 2.9 33.3 + - - +
263A VAL* 3.6 6.9 + - - +
291A VAL* 5.5 1.2 - - - +
292A VAL* 2.7 22.1 + - - +
293A GLU 3.3 23.6 - - - -
294A GLU* 3.6 4.5 - - - +
297A PHE* 3.0 21.4 + - - +
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Residues in contact with PRO 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ARG* 3.3 15.0 - - - +
235A SER* 3.2 26.8 + - - +
236A PHE* 3.7 43.3 - - + -
239A LEU* 3.4 11.4 - - + -
258A LEU 3.1 12.1 - - - +
259A SER* 1.3 83.1 - - - +
261A GLN* 1.3 57.5 + - - +
263A VAL* 3.1 2.0 + - + -
264A VAL* 2.9 29.5 + - - +
294A GLU* 3.4 4.3 - - - +
299A TYR* 3.8 16.2 - - + -
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Residues in contact with GLN 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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259A SER 3.2 1.0 - - - -
260A PRO* 1.3 80.1 - - - +
262A GLU* 1.3 60.1 + - - +
264A VAL* 3.9 6.9 - - - +
265A SER* 2.8 51.0 + - - -
297A PHE* 3.3 37.7 - - + +
298A PRO 3.4 16.8 - - - +
299A TYR* 3.3 18.4 - - - -
300A THR* 2.8 35.3 + - - +
301A ALA 3.4 4.3 + - - -
302A THR 2.8 25.1 + - - +
304A ALA* 3.9 4.6 - - - +
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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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259A SER* 2.9 23.1 + - - +
261A GLN* 1.3 76.6 - - - +
263A VAL* 1.3 63.1 + - - +
266A CYS* 2.8 50.5 + - - +
285A TYR* 2.6 39.3 + - - -
290A GLY 4.3 1.8 - - - +
291A VAL* 4.3 5.4 - - - -
292A VAL* 3.5 26.7 - - + +
297A PHE* 3.6 19.6 - - + -
308A PRO* 4.9 5.6 - - + -
314A ARG* 3.0 21.3 + - - +
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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
----------------------------------------------------------
234A TYR* 3.9 16.1 + - + -
235A SER* 3.6 15.5 - - - +
239A LEU* 4.4 6.7 - - + -
259A SER 3.9 11.4 - - - +
260A PRO 3.1 8.4 + - - +
262A GLU* 1.3 86.3 - - - +
264A VAL* 1.3 65.1 + - - +
267A SER* 3.1 28.4 + - - +
270A ALA* 5.1 1.0 - - - +
272A GLY* 5.4 0.5 + - - -
281A ILE* 3.8 46.2 - - + -
285A TYR* 4.6 2.9 - - + -
291A VAL* 4.3 14.6 - - + -
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Residues in contact with VAL 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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230A CYS* 4.3 3.8 - - - -
232A SER* 3.6 31.0 - - - -
234A TYR* 4.1 11.2 - - - +
235A SER* 4.7 2.9 - - - +
260A PRO 2.9 21.2 + - - +
261A GLN* 3.7 8.5 - - - +
263A VAL* 1.3 79.3 - - - +
265A SER* 1.3 59.7 + - - +
267A SER 4.9 2.6 + - - +
272A GLY* 3.3 27.1 + - - +
273A CYS* 4.0 5.8 - - - +
299A TYR* 4.7 3.8 - - + -
302A THR 3.6 23.6 - - - +
303A ASP* 3.7 19.7 - - - +
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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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261A GLN* 2.8 43.8 + - - -
264A VAL* 1.3 76.0 - - - +
266A CYS* 1.3 59.2 + - - +
267A SER 5.4 0.4 - - - -
297A PHE* 3.8 11.4 - - - -
303A ASP 5.5 0.9 - - - -
304A ALA* 2.6 32.7 + - - +
305A PRO 3.7 12.6 - - - -
306A CYS* 3.6 11.6 + - - +
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Residues in contact with CYS 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 GLU* 2.8 43.5 + - - +
265A SER* 1.3 76.2 - - - +
267A SER* 1.3 62.1 + - - +
268A PRO* 3.3 12.0 - - - +
285A TYR* 3.9 4.6 + - - +
297A PHE* 4.1 14.4 - - - -
306A CYS* 2.0 50.9 - - - -
308A PRO* 4.4 4.3 - - - -
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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
----------------------------------------------------------
262A GLU 3.7 1.4 + - - -
263A VAL* 3.1 24.0 + - - +
264A VAL 5.0 3.1 - - - +
265A SER 3.9 0.5 - - - +
266A CYS* 1.3 76.3 - - - +
268A PRO* 1.3 64.2 - - - +
269A TYR* 3.2 11.0 + - - +
270A ALA* 3.5 16.8 + - - +
272A GLY 5.4 0.9 + - - -
281A ILE* 3.4 20.9 - - - +
285A TYR* 3.1 36.4 + - - -
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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