Contacts of the helix formed by residues 295 - 310 (chain A) in PDB entry 2X96
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 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLY 3.6 9.2 + - - +
294A TYR* 1.3 79.7 - - - +
296A PRO* 1.3 77.3 - - + +
297A LEU* 3.7 9.3 + - - +
298A LYS* 3.1 25.1 + - - +
299A MET* 3.0 28.6 + - - +
326A GLU* 5.5 1.3 - - - -
357A VAL* 4.3 1.1 - - - -
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Residues in contact with PRO 296 (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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295A THR* 1.3 87.3 - - + +
297A LEU* 1.3 61.8 + - - +
299A MET* 3.2 13.2 + - - +
300A PHE* 3.0 28.3 + - - -
325A ILE* 3.4 26.0 - - + +
326A GLU* 3.5 33.7 - - + +
355A THR* 3.7 27.6 - - + +
356A ARG* 5.5 0.2 - - - -
357A VAL* 4.3 11.4 - - + -
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Residues in contact with LEU 297 (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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295A THR* 3.2 8.4 + - - +
296A PRO* 1.3 79.7 - - - +
298A LYS* 1.3 56.0 + - - +
300A PHE* 3.3 2.1 + - - +
301A GLN* 2.9 59.5 + - - +
320A TRP* 3.8 26.0 - - + -
325A ILE* 3.6 19.3 - - + +
326A GLU* 5.2 2.6 + - - +
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Residues in contact with LYS 298 (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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293A GLY 5.6 0.7 - - - +
294A TYR* 4.5 22.4 - - + -
295A THR* 3.1 27.6 + - - +
297A LEU* 1.3 76.0 - - - +
299A MET* 1.3 57.9 + - - +
301A GLN* 3.3 19.1 + - + +
302A MET* 2.9 59.6 + - + +
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Residues in contact with MET 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MET* 3.9 16.6 - - + -
294A TYR* 4.0 18.4 - - + -
295A THR 3.0 21.7 + - - +
296A PRO* 3.4 9.0 - - + +
298A LYS* 1.3 75.6 - - - +
300A PHE* 1.3 57.8 + - - +
302A MET* 3.2 9.1 + - - +
303A GLY* 3.0 23.2 + - - -
355A THR* 4.1 14.6 - - + -
356A ARG 3.5 25.6 - - - +
357A VAL* 4.1 9.4 - - - -
361A GLN* 3.7 7.9 - - + +
362A LEU* 3.6 48.1 - - + +
365A VAL* 3.8 16.0 - - + +
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PRO 3.0 27.0 + - - +
297A LEU* 3.8 4.5 - - - +
299A MET* 1.3 72.1 - - - +
301A GLN* 1.3 60.8 + - - +
303A GLY* 3.2 1.9 + - - -
304A ASP* 2.9 28.2 + - - +
315A LEU* 4.5 0.3 - - - +
319A PHE* 3.9 18.2 - + - -
320A TRP* 3.8 20.5 - + + -
325A ILE* 3.6 26.9 - - + -
351A ILE* 3.7 34.3 - - + -
353A GLN* 3.4 22.9 - - + -
355A THR* 3.5 22.9 - - + -
365A VAL* 3.8 30.3 - - + -
369A LEU* 3.8 12.1 - - + +
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Residues in contact with GLN 301 (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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297A LEU* 2.9 47.4 + - - +
298A LYS* 3.6 21.6 + - + +
300A PHE* 1.3 75.2 - - - +
302A MET* 1.3 57.7 + - + +
304A ASP* 3.4 6.0 - - - +
305A ASP* 2.9 26.5 + - - +
320A TRP* 3.8 21.9 - - + -
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Residues in contact with MET 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 3.3 44.9 - - + +
298A LYS* 2.9 41.9 + - - +
299A MET* 3.5 7.0 - - - +
300A PHE 3.2 0.2 - - - -
301A GLN* 1.3 74.8 - - - +
303A GLY* 1.3 59.5 + - - +
305A ASP* 3.3 12.4 - - - +
306A PHE* 3.0 27.2 + - - +
362A LEU* 5.0 11.7 - - + -
366A HIS* 4.3 5.6 + - + -
410A HIS* 5.8 1.1 - - - +
414A ILE* 3.8 34.3 - - + -
543A TYR* 5.6 0.3 - - - -
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Residues in contact with GLY 303 (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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299A MET 3.0 14.0 + - - -
300A PHE 3.2 0.2 + - - -
302A MET* 1.3 73.4 - - - +
304A ASP* 1.3 63.9 + - - +
306A PHE* 3.0 13.9 + - - +
307A PHE* 3.2 17.2 + - - -
365A VAL* 4.8 0.4 - - - -
366A HIS* 3.6 23.4 + - - -
369A LEU* 3.6 23.1 - - - -
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Residues in contact with ASP 304 (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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300A PHE 2.9 13.4 + - - +
301A GLN* 3.4 13.0 - - - +
303A GLY* 1.3 73.2 - - - +
305A ASP* 1.3 63.5 + - - +
307A PHE* 3.3 7.3 + - - +
308A THR* 3.0 27.7 + - - +
313A THR 4.4 2.1 - - - +
314A LYS* 3.7 14.6 - - - +
315A LEU* 3.1 48.8 + - + +
320A TRP* 3.8 14.5 + - + -
369A LEU* 3.7 3.1 - - - +
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Residues in contact with ASP 305 (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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301A GLN 2.9 15.2 + - - +
302A MET* 3.3 16.4 - - - +
303A GLY 3.2 0.2 - - - -
304A ASP* 1.3 75.4 - - - +
306A PHE* 1.3 56.1 + - - +
308A THR* 3.2 8.7 + - - -
309A SER* 2.9 28.8 + - - -
543A TYR* 2.7 32.2 + - - -
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Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET 3.0 12.6 + - - +
303A GLY 3.0 8.9 + - - +
305A ASP* 1.3 74.7 - - - +
307A PHE* 1.3 62.1 + - - +
309A SER* 2.6 22.9 + - - -
310A MET* 3.4 19.8 + - - +
366A HIS* 4.2 9.4 - + + +
401A LEU* 3.4 25.8 - - + -
404A SER* 3.1 25.1 - - - -
405A VAL* 3.5 26.5 - - + -
410A HIS* 3.5 29.4 - + - -
541A ASP* 3.6 1.3 - - - -
542A ILE* 4.0 4.3 - - + -
543A TYR* 3.6 42.0 - + + -
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Residues in contact with PHE 307 (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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303A GLY 3.2 22.5 + - - -
304A ASP* 3.8 7.4 - - - +
306A PHE* 1.3 78.2 - - - +
308A THR* 1.3 62.8 + - - +
310A MET* 3.0 13.9 + - - +
312A LEU* 3.1 37.4 + - + +
313A THR 4.5 4.7 - - - +
366A HIS* 4.2 9.0 - + - -
369A LEU* 3.5 40.2 - - + -
370A GLY* 3.6 15.3 - - - -
373A GLN* 3.7 43.1 - - + +
397A VAL* 4.5 9.0 - - + -
398A GLY* 4.7 0.9 - - - -
401A LEU* 3.6 33.7 - - + -
552A PHE* 6.3 0.4 - + - -
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Residues in contact with THR 308 (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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304A ASP* 3.0 24.1 + - - +
305A ASP* 3.2 18.2 + - - -
307A PHE* 1.3 74.9 - - - +
309A SER* 1.3 56.0 + - - +
311A ASN* 2.9 20.4 + - - -
312A LEU 3.7 8.7 - - - +
313A THR 4.3 1.1 - - - -
314A LYS* 3.6 42.2 - - + +
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Residues in contact with SER 309 (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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305A ASP* 2.9 17.9 + - - -
306A PHE 2.6 18.2 + - - -
308A THR* 1.3 76.1 + - - +
310A MET* 1.3 57.0 + - - +
311A ASN 3.2 2.0 + - - -
543A TYR* 3.3 31.0 - - - -
544A GLY* 2.9 43.8 + - - +
545A SER 4.5 0.7 - - - -
546A ALA* 4.6 1.4 + - - +
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Residues in contact with MET 310 (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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306A PHE* 3.5 26.9 - - + +
307A PHE* 3.0 9.6 + - - +
309A SER* 1.3 79.8 - - - +
311A ASN* 1.3 70.2 + - - +
312A LEU* 3.2 10.3 - - + -
401A LEU* 3.8 23.1 - - + -
542A ILE* 3.6 38.6 - - + +
544A GLY 4.3 0.2 - - - +
545A SER 3.4 14.8 - - - +
546A ALA* 3.6 3.5 - - - -
548A ALA* 3.8 21.3 - - + -
549A GLY* 3.3 28.5 - - - +
552A PHE* 3.9 18.6 - - + -
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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