Contacts of the helix formed by residues 353 - 368 (chain A) in PDB entry 5MQI
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 CYS 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.6 38.1 - - - -
206A ALA* 3.5 22.7 - - + +
207A SER* 3.9 10.8 - - - +
348A GLU* 4.2 1.1 - - - -
349A PHE* 2.7 37.1 + - + +
350A LEU 4.2 0.4 + - - -
351A GLU 3.9 0.2 - - - -
352A ASN* 1.3 86.0 - - - +
354A TYR* 1.3 58.9 + - - +
355A ASN 3.4 2.2 - - - -
356A ARG* 3.3 6.2 + - - +
357A LEU* 2.9 30.4 + - - +
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Residues in contact with TYR 354 (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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349A PHE* 2.9 42.0 + + + +
350A LEU* 4.0 17.3 + - + -
353A CYS* 1.3 75.7 - - - +
355A ASN* 1.3 63.1 + - - +
357A LEU* 4.8 0.2 - - - -
358A MET* 2.8 65.7 + - + +
381A ALA 4.2 3.8 - - - -
382A LEU* 3.6 18.0 - - - -
385A PHE* 3.6 24.9 - + + -
386A MET* 3.7 5.5 - - + +
398A LEU 3.5 19.3 - - - +
399A VAL* 3.8 19.5 - - + -
401A GLU* 5.3 0.2 - - + -
402A THR* 2.8 37.7 + - + +
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Residues in contact with ASN 355 (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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350A LEU 5.4 1.0 + - - -
353A CYS 3.4 0.6 - - - -
354A TYR* 1.3 79.4 - - - +
356A ARG* 1.3 64.2 + - - +
359A GLY* 3.0 20.1 + - - -
397A GLY 3.0 25.7 + - - -
398A LEU* 3.2 21.1 + - - +
399A VAL* 3.4 2.8 - - - -
400A SER* 3.2 13.8 + - - -
401A GLU* 2.9 40.0 + - + +
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Residues in contact with ARG 356 (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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206A ALA 3.8 10.5 - - - +
207A SER* 3.2 34.1 + - - -
208A SER* 3.9 2.9 - - - +
209A SER* 3.7 35.4 + - - +
352A ASN 5.1 2.7 - - - +
353A CYS* 3.3 9.5 + - - +
354A TYR 3.3 0.4 - - - -
355A ASN* 1.3 80.1 - - - +
357A LEU* 1.4 58.4 + - - +
359A GLY* 3.8 0.9 - - - -
360A SER* 2.9 31.4 + - - -
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Residues in contact with LEU 357 (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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205A LEU 5.6 0.2 - - - +
206A ALA* 3.9 28.5 + - + +
215A SER* 3.4 42.6 - - - +
218A VAL* 4.4 5.6 - - + -
219A LEU* 3.7 39.5 - - + +
222A VAL* 5.3 0.7 - - + -
349A PHE* 3.7 26.2 - - + -
353A CYS 2.9 20.8 + - - +
354A TYR* 4.1 2.2 - - - +
356A ARG* 1.4 71.4 - - - +
358A MET* 1.3 59.1 + - + +
360A SER* 3.3 3.7 + - - -
361A VAL* 2.9 29.2 + - + +
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Residues in contact with MET 358 (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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219A LEU* 4.0 34.3 - - - -
349A PHE* 5.7 0.7 - - + -
354A TYR* 2.8 60.4 + - + +
357A LEU* 1.3 77.1 - - + +
359A GLY* 1.3 62.7 + - - +
361A VAL* 4.5 1.8 - - - +
362A LYS* 3.1 26.3 + - - +
378A TYR* 3.5 48.9 - - + +
381A ALA* 4.1 2.0 - - - -
382A LEU* 3.8 9.4 - - + +
401A GLU* 4.2 14.5 - - + +
402A THR* 4.0 11.7 - - + -
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Residues in contact with GLY 359 (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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355A ASN 3.0 18.1 + - - -
356A ARG 3.8 1.1 - - - -
358A MET* 1.3 77.2 - - - +
360A SER* 1.3 60.6 + - - +
362A LYS* 3.5 2.8 + - - +
363A ASP* 3.2 22.2 + - - +
401A GLU* 3.7 23.0 - - - +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 3.5 26.6 + - - +
215A SER* 2.8 25.9 + - - -
356A ARG* 2.9 20.7 + - - -
357A LEU* 3.8 3.8 - - - -
359A GLY* 1.3 73.3 - - - +
361A VAL* 1.4 61.7 + - - +
363A ASP* 3.3 7.8 + - - +
364A HIS* 3.1 29.1 + - - -
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Residues in contact with VAL 361 (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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215A SER* 3.6 34.1 - - - +
216A LEU* 3.7 20.9 - - + +
219A LEU* 4.1 27.1 - - + -
357A LEU* 2.9 21.6 + - + +
358A MET* 4.0 4.0 - - - +
360A SER* 1.4 74.2 - - - +
362A LYS* 1.3 59.6 + - - +
364A HIS* 3.2 4.4 + - - +
365A LEU* 2.9 36.4 + - + +
378A TYR* 3.9 21.3 - - + +
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Residues in contact with LYS 362 (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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358A MET 3.1 18.1 + - - +
359A GLY* 4.0 4.7 - - - +
361A VAL* 1.3 77.4 - - - +
363A ASP* 1.3 63.4 + - - +
365A LEU* 3.0 18.1 + - - +
366A LEU* 3.0 32.8 + - + +
378A TYR* 3.9 25.3 + - + +
401A GLU* 4.5 12.9 + - - +
406A ARG* 3.8 34.1 + - - +
407A THR* 4.5 5.9 + - - +
410A PHE* 3.8 36.2 - - + +
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Residues in contact with ASP 363 (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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359A GLY 3.2 14.1 + - - +
360A SER* 3.4 12.9 - - - +
362A LYS* 1.3 77.4 - - - +
364A HIS* 1.3 65.0 + - - +
366A LEU* 3.3 5.7 + - - +
367A ARG* 2.7 89.9 + - - +
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Residues in contact with HIS 364 (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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212A GLU* 2.9 30.0 + - + +
213A GLN* 4.3 14.7 - - - -
215A SER* 3.1 17.7 + - - -
216A LEU* 4.2 24.1 - - + +
360A SER* 3.1 25.2 + - - -
361A VAL* 3.2 6.7 + - - +
363A ASP* 1.3 84.8 + - - +
365A LEU* 1.3 62.2 + - - +
367A ARG* 4.6 0.9 - - - +
368A GLU* 3.0 62.9 + - - +
373A HIS* 3.9 2.3 - - - -
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Residues in contact with LEU 365 (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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216A LEU* 4.2 12.8 - - + -
361A VAL* 2.9 32.6 + - + +
362A LYS* 3.0 9.3 + - - +
364A HIS* 1.3 79.7 - - - +
366A LEU* 1.3 59.3 + - - +
368A GLU 4.4 0.2 - - - -
369A LYS* 3.1 33.1 + - - +
373A HIS* 3.7 29.8 - - + -
374A ASP 4.5 1.3 - - - +
375A GLU* 3.5 38.8 - - + +
378A TYR* 4.1 13.5 - - + -
410A PHE* 4.3 22.0 - - + -
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Residues in contact with LEU 366 (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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362A LYS* 3.0 41.4 + - + +
363A ASP* 4.0 4.7 - - - +
365A LEU* 1.3 81.1 - - - +
367A ARG* 1.3 64.5 + - + +
368A GLU 3.6 0.5 + - - -
369A LYS* 3.7 32.7 + - - +
410A PHE* 3.9 26.0 - - + -
413A GLN* 5.5 3.4 - - - +
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Residues in contact with ARG 367 (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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363A ASP* 2.7 53.4 + - - +
364A HIS* 4.9 0.7 - - - -
366A LEU* 1.3 81.0 - - + +
368A GLU* 1.3 68.6 + - + +
369A LYS 3.6 1.6 + - - -
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Residues in contact with GLU 368 (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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216A LEU* 4.7 0.3 - - - +
364A HIS* 3.0 49.0 + - - +
365A LEU 4.4 1.6 - - - -
367A ARG* 1.3 87.1 - - + +
369A LYS* 1.3 65.4 + - - +
370A ALA* 3.1 3.6 - - - +
371A GLN* 2.9 44.0 + - - +
372A GLN 4.0 1.2 + - - -
373A HIS* 2.7 39.0 + - - +
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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