Contacts of the helix formed by residues 349 - 363 (chain A) in PDB entry 1RO9
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 LYS 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLU* 5.7 2.8 + - - -
301A SER* 4.1 17.9 + - - -
343A LEU* 4.1 9.2 - - - +
344A ALA* 4.7 6.7 - - - +
346A ASP* 2.7 23.5 + - + +
348A SER* 1.3 94.2 + - - +
350A HIS* 1.3 65.8 + - - +
351A MET 3.5 1.6 - - - -
352A SER* 3.0 18.6 + - - +
353A LEU* 2.9 31.5 + - + +
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Residues in contact with HIS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ASP 3.8 1.8 + - - -
347A MET* 3.2 26.1 + - + +
348A SER 3.4 0.4 - - - -
349A LYS* 1.3 75.3 - - - +
351A MET* 1.3 72.9 + - + +
353A LEU* 2.8 25.4 + - - +
354A LEU* 2.8 28.2 + - + +
389A HIS* 2.7 38.2 + + + +
449A TYR 4.6 1.4 + - - -
450A ILE* 3.6 60.9 + - + +
454A LEU* 4.0 19.1 - - + -
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Residues in contact with MET 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A SER 5.3 1.5 + - - +
349A LYS 3.5 0.6 - - - -
350A HIS* 1.3 99.4 - - + +
352A SER* 1.3 57.8 + - - +
354A LEU* 3.3 12.5 + - - +
355A ALA* 2.8 31.1 + - - +
449A TYR* 4.4 9.4 - - + +
450A ILE* 4.0 16.6 - - + -
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LYS* 3.0 27.3 + - - +
350A HIS 3.2 0.2 - - - -
351A MET* 1.3 78.9 - - - +
353A LEU* 1.3 63.2 + - - +
355A ALA* 4.2 6.3 - - - -
356A ASP* 2.7 35.6 + - - +
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ALA* 3.3 35.4 - - + +
349A LYS* 2.9 20.5 + - + +
350A HIS* 2.8 10.1 + - - +
352A SER* 1.3 81.6 + - - +
354A LEU* 1.3 57.5 + - - +
356A ASP* 3.8 4.8 - - + +
357A LEU* 2.8 28.9 + - - +
385A ARG* 3.3 36.1 - - + +
386A ASN* 3.4 18.0 + - - +
389A HIS* 3.8 31.9 - - + +
454A LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 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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350A HIS* 2.8 31.9 + - + +
351A MET* 3.7 16.4 - - - +
353A LEU* 1.3 74.2 - - - +
355A ALA* 1.3 66.2 + - - +
357A LEU* 3.1 5.9 + - + +
358A LYS* 2.8 44.9 + - + +
386A ASN* 4.5 1.1 + - - -
449A TYR 5.9 0.4 - - - +
453A PRO* 3.5 32.1 - - + +
454A LEU* 4.1 14.8 - - + +
457A THR* 3.3 33.4 - - + +
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Residues in contact with ALA 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 MET 2.8 19.8 + - - +
352A SER* 3.8 8.5 - - - +
354A LEU* 1.3 78.0 - - - +
356A ASP* 1.3 66.5 + - - +
358A LYS* 3.2 8.4 + - - +
359A THR* 3.0 27.9 + - - +
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Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A SER* 2.7 29.5 + - - +
353A LEU* 3.8 5.6 - - + +
355A ALA* 1.3 78.4 - - - +
357A LEU* 1.3 60.8 + - - +
359A THR* 3.4 10.9 + - - -
360A MET* 3.1 16.8 + - - +
382A GLN* 2.8 29.2 + - + +
385A ARG* 5.8 2.1 + - - +
386A ASN* 5.8 0.2 - - - +
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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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353A LEU 2.8 19.0 + - - +
354A LEU* 3.1 7.6 + - + +
356A ASP* 1.3 74.9 - - - +
358A LYS* 1.3 63.8 + - - +
360A MET* 3.2 12.7 + - - +
361A VAL* 3.1 27.8 + - + +
382A GLN* 3.4 8.5 + - + +
383A VAL* 5.5 2.0 - - - -
386A ASN* 3.7 37.0 - - + +
390A CYS* 5.5 0.2 - - - -
454A LEU* 4.3 16.8 - - + +
457A THR* 3.6 28.3 - - + -
458A TRP* 4.4 14.8 - - + +
461A LEU* 4.4 23.1 - - + -
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Residues in contact with LYS 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 LEU* 2.8 38.8 + - + +
355A ALA* 3.6 8.5 - - - +
357A LEU* 1.3 70.1 - - - +
359A THR* 1.3 56.5 + - - +
360A MET 2.7 6.0 + - - -
361A VAL* 2.7 28.9 + - - +
362A GLU* 3.2 15.4 + - + +
453A PRO* 4.8 3.3 - - - +
456A GLU* 5.0 7.7 + - - -
457A THR* 3.7 32.8 - - + -
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Residues in contact with THR 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 ALA* 3.0 15.6 + - - +
356A ASP* 3.5 14.0 - - - -
358A LYS* 1.3 75.9 - - - +
360A MET* 1.3 58.3 + - - +
362A GLU* 3.6 31.8 + - - +
363A THR* 3.9 12.3 + - + +
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Residues in contact with MET 360 (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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356A ASP 3.1 12.3 + - - +
357A LEU* 3.4 14.6 - - - +
358A LYS 2.7 4.6 + - - -
359A THR* 1.3 73.0 - - - +
361A VAL* 1.3 57.0 + - + +
362A GLU 2.9 5.7 + - - -
363A THR* 3.1 12.6 + - - +
364A LYS* 2.9 26.1 + - - -
374A LEU* 4.6 7.4 - - + -
379A ASP* 2.9 55.4 - - + +
382A GLN* 3.6 26.7 - - - +
383A VAL* 3.9 22.9 - - - -
461A LEU* 5.1 12.1 - - + -
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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
----------------------------------------------------------
357A LEU* 3.1 18.6 + - + +
358A LYS* 2.7 12.7 + - - +
360A MET* 1.3 71.5 - - + +
362A GLU* 1.3 59.1 + - + +
364A LYS* 3.0 28.7 - - + +
457A THR* 3.9 28.5 - - + +
460A ASP* 2.9 38.4 - - + +
461A LEU* 4.0 22.4 - - + +
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Residues in contact with GLU 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 LYS* 3.5 13.5 - - + +
359A THR* 3.6 27.3 + - - +
360A MET 2.9 0.2 - - - -
361A VAL* 1.3 76.8 - - - +
363A THR* 1.3 62.4 + - + +
364A LYS* 3.0 10.2 + - - +
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Residues in contact with THR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A THR* 4.0 11.6 + - + +
360A MET* 3.1 18.6 + - - +
362A GLU* 1.3 76.8 - - + +
364A LYS* 1.3 66.4 + - - +
365A LYS* 3.2 23.1 + - - +
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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