Contacts of the helix formed by residues 293 - 310 (chain A) in PDB entry 1XMK
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A HIS* 2.9 42.5 + - - +
291A MET 3.4 0.4 - - - +
292A ALA* 1.3 81.8 - - - +
294A LEU* 1.4 64.8 + - - +
295A ASP* 3.5 14.4 + - - -
296A MET* 3.0 17.3 + - - +
297A ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 294 (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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292A ALA 4.0 0.6 + - - -
293A SER* 1.4 74.1 - - - +
295A ASP* 1.3 67.2 + - - +
297A ALA* 3.2 10.1 + - + +
298A GLU* 2.9 24.3 + - - +
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A HIS* 4.5 14.3 - - - +
293A SER* 3.1 19.3 + - - +
294A LEU* 1.3 82.7 + - - +
296A MET* 1.3 59.7 + - - +
298A GLU* 3.3 13.5 + - - +
299A ILE* 3.1 31.6 + - + +
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Residues in contact with MET 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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288A GLY 4.0 0.7 - - - +
290A HIS* 3.1 38.1 - - + +
291A MET* 3.8 32.3 - - + +
293A SER* 3.0 12.2 + - - +
295A ASP* 1.3 76.2 - - - +
297A ALA* 1.3 59.6 + - - +
299A ILE* 3.8 5.7 - - - +
300A LYS* 2.9 30.0 + - - +
329A ASP* 3.5 47.3 - - - +
332A ALA* 4.1 7.0 - - + -
333A VAL* 3.8 25.8 - - + +
398A NI 3.9 14.6 - - + -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A MET 4.8 3.5 + - - +
293A SER 3.0 13.1 + - - +
294A LEU* 3.7 13.9 - - + +
296A MET* 1.3 74.8 - - - +
298A GLU* 1.3 58.3 + - - +
300A LYS* 3.4 9.1 + - - +
301A GLU* 3.0 28.4 + - - +
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Residues in contact with GLU 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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294A LEU 2.9 14.7 + - - +
295A ASP* 3.5 14.2 - - - +
297A ALA* 1.3 74.7 - - - +
299A ILE* 1.3 68.6 + - + +
301A GLU* 3.3 5.4 + - - +
302A LYS* 3.0 54.6 + - + +
326A LYS* 5.4 6.3 + - - -
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Residues in contact with ILE 299 (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 ASP* 3.1 17.6 + - + +
296A MET* 3.3 11.9 + - - +
298A GLU* 1.3 78.9 - - + +
300A LYS* 1.3 62.9 + - - +
302A LYS* 3.1 10.1 + - + +
303A ILE* 2.9 32.8 + - + +
322A ILE* 5.2 5.2 - - + -
326A LYS* 4.1 33.9 - - + +
329A ASP* 3.3 34.1 - - + +
330A ILE* 3.8 26.9 - - + +
333A VAL* 4.1 8.7 - - + -
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Residues in contact with LYS 300 (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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291A MET* 5.1 10.9 - - + +
296A MET 2.9 18.3 + - - +
297A ALA* 3.7 8.5 - - - +
298A GLU 3.3 0.2 - - - -
299A ILE* 1.3 76.3 - - - +
301A GLU* 1.3 56.7 + - - +
303A ILE* 3.2 5.5 + - - +
304A CYS* 2.9 26.4 + - - +
333A VAL* 3.8 25.1 - - + -
336A ASP* 5.4 3.2 + - - -
337A MET* 3.9 24.7 - - - +
340A GLN* 4.6 15.4 - - - +
342A ASP* 5.1 5.7 + - - -
399A CL 3.7 25.1 - - + -
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Residues in contact with GLU 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 ALA 3.0 16.3 + - - +
298A GLU* 4.0 4.7 - - - +
300A LYS* 1.3 77.7 - - - +
302A LYS* 1.3 58.6 + - + +
304A CYS* 3.5 7.4 - - - +
305A ASP* 2.8 38.9 + - + +
396A CD 4.0 3.6 - - - -
397A CD 2.3 30.7 - - - -
400A CL 3.7 6.2 - - - +
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Residues in contact with LYS 302 (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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298A GLU* 3.0 47.7 + - + +
299A ILE* 3.1 8.9 + - + +
301A GLU* 1.3 76.7 - - + +
303A ILE* 1.3 63.2 + - - +
305A ASP* 3.6 6.2 + - - +
306A TYR* 3.0 24.6 + - - +
322A ILE* 3.8 48.7 + - + +
326A LYS* 5.2 10.5 - - + +
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Residues in contact with ILE 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 ILE* 2.9 27.6 + - + +
300A LYS* 3.2 6.9 + - - +
302A LYS* 1.3 74.7 - - - +
304A CYS* 1.4 60.2 + - - +
306A TYR* 3.3 1.7 + - - +
307A LEU* 2.9 53.4 + - + +
318A LEU* 4.5 9.4 - - + -
322A ILE* 3.9 18.2 - - + -
330A ILE* 3.9 28.7 - - + +
333A VAL* 3.8 26.7 - - + -
334A LEU* 3.9 16.6 - - + -
337A MET* 4.4 11.4 - - + -
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Residues in contact with CYS 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 LYS 2.9 17.4 + - - +
301A GLU* 3.5 11.7 - - - +
303A ILE* 1.4 74.2 - - - +
305A ASP* 1.3 56.6 + - - +
307A LEU* 3.8 3.4 - - - +
308A PHE* 2.9 35.4 + - - +
337A MET* 5.3 2.4 - - + +
355A LEU* 4.9 6.9 - - - +
359A LYS* 3.9 5.2 - - - +
363A MET* 3.6 19.3 - - - -
396A CD 2.5 31.0 - - - -
397A CD 2.6 22.9 - - - -
399A CL 3.6 7.0 - - + -
400A CL 4.0 0.7 - - - -
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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 GLU* 2.8 31.7 + - + +
302A LYS* 3.8 7.6 - - - +
304A CYS* 1.3 73.7 - - - +
306A TYR* 1.3 57.1 + - - +
309A ASN* 2.8 64.2 + - - +
310A VAL* 4.7 1.3 - - - +
400A CL 4.7 1.6 - - - -
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Residues in contact with TYR 306 (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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302A LYS 3.0 18.5 + - - +
303A ILE 3.3 2.9 + - - +
305A ASP* 1.3 76.7 - - - +
307A LEU* 1.3 58.9 + - - +
310A VAL* 2.9 62.4 + - + +
311A SER* 3.0 30.0 + - - -
313A SER* 3.9 6.1 - - - -
317A ASN* 2.9 31.7 + - - -
318A LEU* 3.7 24.9 - - + -
321A ASN* 3.5 39.4 + - + -
322A ILE* 5.3 3.8 - - + -
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Residues in contact with LEU 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 ILE* 2.9 42.9 + - + +
304A CYS 4.1 0.4 - - - +
306A TYR* 1.3 71.9 - - - +
308A PHE* 1.3 59.0 + - - +
311A SER* 3.5 29.0 - - - +
312A ASP* 4.0 2.8 + - - -
313A SER* 3.8 15.5 - - - +
318A LEU* 4.4 8.1 - - + -
334A LEU* 4.6 1.6 - - + -
343A VAL* 3.9 25.8 - - + -
353A TRP* 3.5 34.8 - - + +
354A HIS* 5.5 0.2 - - - -
355A LEU* 3.9 32.1 + - + +
360A ARG* 4.2 9.0 + - - -
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Residues in contact with PHE 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 CYS* 2.9 18.5 + - - +
305A ASP* 4.2 1.1 - - - +
307A LEU* 1.3 78.9 - - - +
309A ASN* 1.3 89.6 + - - +
310A VAL 3.6 1.0 - - - -
311A SER* 5.9 0.2 - - - -
355A LEU* 3.7 23.3 - - + -
360A ARG* 3.7 12.8 + - + +
363A MET* 3.8 40.4 - - + -
364A GLN* 3.6 45.1 - - + -
400A CL 4.3 4.0 - - + -
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Residues in contact with ASN 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* 2.8 43.0 + - - +
308A PHE* 1.3 102.4 - - - +
310A VAL* 1.3 67.6 + - + +
400A CL 4.1 9.5 - - - +
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Residues in contact with VAL 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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305A ASP* 4.7 1.8 - - - +
306A TYR* 2.9 60.4 + - + +
308A PHE 5.1 1.1 - - - -
309A ASN* 1.3 86.4 - - + +
311A SER* 1.3 66.6 + - - +
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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