Contacts of the helix formed by residues 246 - 268 (chain A) in PDB entry 4XQ2
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 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A HIS* 4.0 7.7 + - - +
242A ARG 5.0 1.5 + - - +
243A GLY 3.1 6.8 + - - -
245A HIS* 1.3 83.3 - - + +
247A LEU* 1.3 65.5 + - - +
248A SER 3.2 3.4 - - - -
249A LEU* 3.1 23.5 + - + +
250A ARG* 2.7 53.8 + - - +
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 6.2 0.2 - - + -
10A LEU* 4.1 8.3 - - + -
177A SER* 4.5 1.6 - - - +
178A PRO* 4.2 20.0 - - + -
179A VAL* 3.6 20.0 - - + -
198A SER* 3.1 37.5 - - - +
199A ILE* 3.9 10.1 - - + -
244A LEU* 3.0 38.6 + - + +
245A HIS 3.5 0.2 - - - -
246A THR* 1.3 76.2 - - - +
248A SER* 1.3 56.3 + - - +
250A ARG* 3.3 16.6 - - - +
251A VAL* 2.9 49.9 + - + +
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 4.2 11.1 - - - -
7A GLY* 5.3 5.6 - - - -
10A LEU* 3.6 22.0 - - - +
179A VAL* 4.0 23.8 - - - +
246A THR 3.1 1.0 + - - -
247A LEU* 1.3 76.3 - - - +
249A LEU* 1.3 69.1 + - - +
251A VAL* 3.4 1.7 + - - +
252A HIS* 3.1 31.2 + - - +
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A HIS 5.6 2.2 - - - +
246A THR* 3.1 28.1 + - + +
248A SER* 1.3 81.3 - - - +
250A ARG* 1.3 61.8 + - + +
252A HIS* 3.6 2.9 + - - +
253A ARG* 3.2 22.3 + - - +
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 2.7 21.8 + - - +
199A ILE 3.1 21.0 + - - -
201A GLY* 3.3 17.7 + - - -
202A HIS* 3.6 8.8 - - - -
243A GLY 3.1 22.8 + - - -
246A THR* 2.7 35.6 + - - +
247A LEU* 3.3 21.6 - - - +
249A LEU* 1.3 74.3 - - + +
251A VAL* 1.3 67.5 + - - +
253A ARG* 3.1 4.9 + - - +
254A GLN* 2.9 34.2 + - - +
325A GLY 4.4 6.1 + - - -
327A VAL* 4.0 23.5 - - - +
363A ILE* 4.1 23.8 - - + -
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA 5.1 0.4 - - - +
177A SER* 3.8 22.4 - - - +
179A VAL* 3.4 27.4 - - + -
180A LEU* 3.7 27.4 - - + -
198A SER* 4.9 4.5 - - - -
247A LEU* 2.9 37.2 + - + +
248A SER 3.8 0.7 - - - +
250A ARG* 1.3 76.0 - - - +
252A HIS* 1.3 61.9 + - + +
254A GLN* 3.1 16.5 + - - +
255A VAL* 2.9 29.3 + - + +
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Residues in contact with HIS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 4.1 12.7 + - + +
180A LEU* 3.9 15.8 - - + +
248A SER* 3.1 21.6 + - - +
249A LEU* 4.4 2.7 - - - +
251A VAL* 1.3 90.8 - - + +
253A ARG* 1.3 60.0 + - - +
255A VAL* 3.9 7.7 - - + +
256A ALA* 3.0 29.6 + - - +
293A SER* 5.0 4.4 + - - -
294A ALA* 4.7 7.9 - - + +
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU 3.2 13.1 + - - +
250A ARG* 3.1 9.3 + - - +
252A HIS* 1.3 74.9 - - - +
254A GLN* 1.3 63.4 + - - +
256A ALA* 3.3 15.6 + - - +
257A THR* 2.8 52.2 + - - +
260A VAL* 5.6 1.2 - - - +
362A GLY 4.5 0.4 - - - +
363A ILE* 3.9 39.3 - - + +
364A GLU 4.5 2.2 + - - -
366A PRO* 3.7 26.1 - - - +
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Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 5.0 2.9 - - - -
250A ARG* 2.9 37.1 + - - +
251A VAL* 3.2 17.9 + - - +
253A ARG* 1.3 76.6 - - - +
255A VAL* 1.3 57.0 + - - +
257A THR 3.4 0.3 + - - -
258A ALA* 2.8 30.1 + - - +
297A ALA* 3.5 19.3 - - + +
325A GLY* 3.0 34.9 + - - +
326A GLY 3.4 8.0 + - - -
361A VAL* 3.1 24.0 + - - +
362A GLY 3.1 26.9 - - - +
363A ILE* 3.9 6.5 - - + -
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.0 20.6 - - + -
251A VAL* 2.9 25.2 + - + +
252A HIS* 3.9 8.3 - - + +
253A ARG 3.3 0.2 - - - -
254A GLN* 1.3 76.7 - - - +
256A ALA* 1.3 64.9 + - - +
258A ALA* 3.2 2.8 + - - +
259A ARG* 3.0 47.6 + - - +
276A TYR* 3.8 13.9 - - - +
294A ALA* 3.9 17.7 - - + -
295A PRO* 4.0 1.1 - - + -
296A GLY* 3.7 24.9 - - - +
297A ALA* 4.5 1.8 - - + +
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS 3.0 18.3 + - - +
253A ARG* 3.6 22.2 - - - +
255A VAL* 1.3 77.8 - - - +
257A THR* 1.3 62.6 + - - +
259A ARG* 3.5 11.6 + - - +
260A VAL* 3.3 23.4 + - - +
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Residues in contact with THR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 2.8 43.6 + - - +
256A ALA* 1.3 74.1 - - - +
258A ALA* 1.3 65.4 + - - +
260A VAL* 3.0 8.6 + - - +
261A LEU* 3.0 31.5 + - + +
361A VAL* 3.6 23.3 - - + -
362A GLY 5.0 1.3 - - - -
364A GLU 4.1 3.2 + - - -
366A PRO* 3.5 22.4 - - + +
369A LEU* 3.7 21.5 - - + -
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLN 2.8 19.1 + - - +
255A VAL 3.2 5.4 + - - +
257A THR* 1.3 76.1 - - - +
259A ARG* 1.3 62.7 + - - +
261A LEU* 3.2 4.2 + - - +
262A VAL* 3.0 28.4 + - - +
276A TYR* 3.9 11.0 - - + +
296A GLY 3.8 6.7 - - - +
297A ALA* 3.8 23.1 - - - -
299A VAL* 4.1 6.1 - - + +
361A VAL* 4.0 16.7 - - + +
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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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255A VAL* 3.0 32.5 + - - +
256A ALA* 3.7 12.0 - - - +
257A THR 3.2 0.2 - - - -
258A ALA* 1.3 75.7 - - - +
260A VAL* 1.3 62.9 + - - +
262A VAL* 3.4 15.4 + - - +
263A GLU* 3.5 16.3 + - - +
276A TYR* 4.2 17.4 - - + +
278A GLY* 5.7 1.4 + - - -
293A SER 5.8 0.2 + - - -
294A ALA* 4.7 6.1 - - - +
295A PRO* 3.3 31.4 - - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 5.6 1.1 - - - +
256A ALA 3.3 12.5 + - - +
257A THR* 3.0 13.1 + - - +
259A ARG* 1.3 77.3 - - + +
261A LEU* 1.3 64.5 + - + +
263A GLU* 3.3 14.7 + - - +
264A ARG* 3.5 14.0 + - + +
366A PRO* 4.6 20.0 - - + +
370A ALA* 4.5 19.7 - - + -
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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
----------------------------------------------------------
257A THR* 3.0 25.7 + - + +
258A ALA* 3.7 4.9 - - - +
260A VAL* 1.3 74.3 - - + +
262A VAL* 1.3 67.2 + - - +
264A ARG* 3.4 4.9 + - + +
265A LEU* 3.0 28.7 + - + +
299A VAL* 5.3 2.7 - - + -
318A PHE* 3.9 20.9 - - + -
359A LEU* 4.4 10.3 - - + -
361A VAL* 3.7 29.8 - - + -
366A PRO 4.7 2.2 - - - +
369A LEU* 4.0 7.4 - - + +
370A ALA* 3.7 39.7 - - + +
373A LEU* 4.2 17.6 - - + +
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA 3.0 18.9 + - - +
259A ARG* 3.6 9.6 - - - +
260A VAL 3.3 0.2 - - - -
261A LEU* 1.3 76.7 - - - +
263A GLU* 1.3 71.9 + - - +
265A LEU* 3.3 8.8 + - - +
266A ARG* 3.0 33.8 + - - +
274A VAL* 4.5 5.6 - - + -
276A TYR* 3.7 35.0 - - + -
279A LEU* 3.7 26.2 - - + -
299A VAL* 3.9 17.9 - - + -
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Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG 3.5 8.8 + - - +
260A VAL* 3.3 9.0 + - - +
261A LEU 3.2 1.2 - - - -
262A VAL* 1.3 95.2 - - - +
264A ARG* 1.3 61.5 + - + +
266A ARG* 3.0 31.5 + - - +
267A ALA* 2.9 30.4 + - - +
279A LEU* 4.4 3.1 - - - +
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Residues in contact with ARG 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 VAL* 3.5 11.0 + - + +
261A LEU* 3.4 9.8 + - - +
263A GLU* 1.3 77.5 - - - +
265A LEU* 1.3 60.6 + - - +
267A ALA* 3.3 8.0 + - + +
268A SER* 3.1 23.2 + - - -
367A GLN* 4.5 8.7 + - - +
370A ALA* 3.1 48.2 + - + +
371A GLU* 3.5 13.9 - - - +
373A LEU* 5.3 7.4 - - + -
374A SER* 3.3 30.4 + - - -
377A LEU* 5.1 3.4 - - + +
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU 3.0 23.3 + - - +
262A VAL* 3.5 5.4 - - - +
264A ARG* 1.3 76.9 - - - +
266A ARG* 1.3 56.0 + - - +
268A SER* 2.9 23.9 + - - +
271A VAL* 3.5 21.7 - - + +
274A VAL* 4.0 16.4 - - + -
299A VAL* 3.7 30.1 - - + -
301A PHE* 3.7 48.2 - - + -
359A LEU* 4.1 9.9 - - + -
373A LEU* 3.7 18.2 - - + -
377A LEU* 4.0 6.3 - - + -
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Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A VAL* 3.0 25.0 + - - +
263A GLU* 3.0 34.0 + - - +
265A LEU* 1.3 74.4 - - - +
267A ALA* 1.3 58.4 + - - +
268A SER 3.4 2.2 - - - +
271A VAL* 5.4 0.2 - - - -
272A GLY 5.6 1.6 - - - -
274A VAL* 3.4 26.0 - - + +
279A LEU* 3.7 32.1 - - - +
280A PRO* 5.5 1.6 - - - +
281A GLU* 3.1 31.1 + - - -
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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
----------------------------------------------------------
263A GLU 2.9 16.3 + - - +
264A ARG* 3.7 10.5 - - + +
265A LEU 3.1 0.2 - - - -
266A ARG* 1.3 78.0 - - - +
268A SER* 1.3 60.6 + - - +
269A PRO* 3.7 5.4 - - - +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG 3.1 11.4 + - - -
265A LEU 2.9 15.5 + - - +
266A ARG 4.7 2.1 - - - +
267A ALA* 1.3 78.9 - - - +
269A PRO* 1.3 69.8 - - - +
270A VAL* 3.3 23.0 + - - +
271A VAL* 3.2 32.8 + - - +
377A LEU* 3.9 13.0 - - - +
379A GLY* 5.2 1.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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