Contacts of the helix formed by residues 349 - 362 (chain A) in PDB entry 1R2J
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 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 4.8 4.0 + - - -
344A GLU 3.4 10.8 - - - -
345A ILE* 3.4 21.6 + - - -
348A GLY* 1.3 74.7 - - - +
350A SER* 1.3 55.6 + - - +
351A GLU* 3.3 4.1 + - - -
352A MET* 2.9 24.1 + - - +
353A CYS* 2.7 32.4 + - - -
399A FAD 2.5 35.9 + - - -
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Residues in contact with SER 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LYS* 4.6 2.7 + - - +
305A HIS* 3.5 17.3 + - - -
308A ALA* 5.8 0.3 - - - +
309A GLU* 3.5 31.1 + - - +
344A GLU* 3.0 32.6 + - - +
349A SER* 1.3 72.1 - - - +
351A GLU* 1.3 69.8 + - - +
353A CYS* 3.3 0.6 + - - -
354A ARG* 3.0 38.0 + - - +
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Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU 5.3 0.3 - - - +
349A SER* 3.0 5.4 + - - -
350A SER* 1.3 90.2 + - - +
352A MET* 1.3 62.2 + - - +
354A ARG* 3.2 12.9 + - - +
355A VAL* 3.0 28.7 + - - +
399A FAD 2.7 66.0 + - + +
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.9 34.5 - - - +
348A GLY* 4.4 3.4 - - - -
349A SER* 2.9 30.2 + - - +
351A GLU* 1.3 72.6 - - - +
353A CYS* 1.3 61.9 + - - +
355A VAL* 2.9 23.1 - - + +
356A MET* 2.9 46.5 + - + +
399A FAD 3.9 39.0 - - - +
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Residues in contact with CYS 353 (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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226A ARG* 5.7 1.1 - - - -
301A ILE* 4.0 17.3 - - + -
304A LYS* 4.2 12.6 - - - -
305A HIS* 3.4 42.8 - - + +
347A GLU 4.7 1.1 - - - -
348A GLY* 3.2 32.5 - - - -
349A SER 2.7 12.7 + - - +
350A SER 3.6 0.2 - - - +
352A MET* 1.3 73.6 - - - +
354A ARG* 1.3 57.9 + - - +
356A MET* 3.8 9.2 - - - +
357A LEU* 2.8 37.4 + - + +
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Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A HIS* 3.3 27.0 + - - +
309A GLU* 2.7 41.4 + - - -
350A SER* 3.0 22.9 + - - +
351A GLU* 3.5 13.5 + - - +
352A MET 3.2 0.4 - - - -
353A CYS* 1.3 74.1 - - - +
355A VAL* 1.3 60.4 + - + +
357A LEU* 4.1 4.8 - - + +
358A ALA* 2.8 33.0 + - - +
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Residues in contact with VAL 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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351A GLU 3.0 17.0 + - - +
352A MET* 2.9 41.1 - - + +
354A ARG* 1.3 75.7 - - + +
356A MET* 1.3 64.2 + - + +
358A ALA* 3.5 5.5 - - - +
359A GLN* 2.9 43.1 + - + +
399A FAD 4.4 20.0 - - + +
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Residues in contact with MET 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ARG* 3.7 34.1 - - - +
301A ILE* 4.0 32.3 - - + -
348A GLY* 4.8 2.0 - - - -
352A MET* 2.9 40.5 + - + +
353A CYS* 3.9 12.8 - - - +
355A VAL* 1.3 82.3 - - + +
357A LEU* 1.3 60.5 + - - +
359A GLN* 3.2 17.2 + - - +
360A HIS* 2.9 26.5 + - - +
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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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298A PRO* 3.8 29.2 - - + +
301A ILE* 4.0 16.8 - - + -
302A LEU* 4.1 29.2 - - + +
305A HIS* 4.0 26.0 - - + -
353A CYS 2.8 26.1 + - - +
354A ARG* 4.1 3.8 - - - +
356A MET* 1.3 69.7 - - - +
358A ALA* 1.3 61.3 + - - +
360A HIS* 3.3 11.0 + - + +
361A ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 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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354A ARG 2.8 20.2 + - - +
355A VAL* 3.5 7.4 - - - +
357A LEU* 1.3 75.7 - - - +
359A GLN* 1.3 65.9 + - + +
361A ALA* 3.3 4.4 + - - +
362A LEU* 2.9 42.1 + - + +
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Residues in contact with GLN 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 VAL* 2.9 32.8 + - + +
356A MET* 3.2 20.6 + - - +
358A ALA* 1.3 79.3 - - + +
360A HIS* 1.3 62.2 + - - +
362A LEU* 3.5 10.4 + - + +
363A ALA* 3.4 20.3 + - - +
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Residues in contact with HIS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PRO* 3.9 39.5 - - + +
356A MET 2.9 13.6 + - - +
357A LEU* 3.5 17.3 - - + +
358A ALA 3.2 0.2 - - - -
359A GLN* 1.3 76.1 - - - +
361A ALA* 1.3 65.7 + - + +
363A ALA* 3.1 11.3 + - - +
364A LEU* 3.1 50.8 - - + +
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Residues in contact with ALA 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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357A LEU 2.9 16.7 + - - +
358A ALA* 3.9 5.8 - - - +
360A HIS* 1.3 79.3 - - + +
362A LEU* 1.3 58.4 + - + +
363A ALA 3.0 4.9 + - - -
364A LEU* 3.1 33.3 + - + +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ALA* 2.9 33.2 + - + +
359A GLN* 3.9 9.4 - - + +
360A HIS 3.3 0.4 - - - -
361A ALA* 1.3 75.8 - - + +
363A ALA* 1.3 57.8 + - - +
364A LEU 3.5 2.7 - - - +
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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