Contacts of the helix formed by residues 472 - 484 (chain A) in PDB entry 1R4L
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 GLN 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A ILE* 3.0 18.8 - - + +
469A PRO* 2.5 38.9 + - + +
471A ASP* 1.3 116.1 + - - +
473A TRP* 1.3 58.9 + - - +
475A LYS* 3.0 53.4 - - + +
476A LYS* 3.3 16.0 + - - +
495A GLU* 4.0 0.4 - - - -
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Residues in contact with TRP 473 (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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177A ARG* 3.6 41.7 - - - +
180A TYR* 3.6 22.0 - + + -
181A GLU* 3.7 24.5 - - + -
184A VAL* 3.6 23.1 - - + -
459A TRP* 3.0 45.5 + + + -
463A VAL* 3.6 24.3 - - + +
468A ILE* 3.2 35.8 + - + -
469A PRO 3.7 6.1 - - - -
470A LYS* 3.5 33.3 + - + +
472A GLN* 1.3 74.7 - - - +
474A MET* 1.3 68.5 + - - +
475A LYS 2.9 5.5 + - - -
477A TRP* 3.1 9.7 + - - +
495A GLU* 3.2 3.8 + - - -
498A CYS* 4.7 3.1 - - - -
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Residues in contact with MET 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 3.9 16.8 - - - +
473A TRP* 1.3 76.0 - - - +
475A LYS* 1.3 68.2 + - - +
477A TRP* 4.0 5.2 - - + -
478A TRP* 3.2 31.5 + - + +
493A HIS* 3.7 20.5 - - + +
494A ASP 3.6 18.2 - - - +
495A GLU* 2.9 15.5 + - - +
497A TYR* 4.0 5.4 - - + -
498A CYS* 3.8 19.3 - - - +
499A ASP* 3.1 51.6 - - + +
500A PRO* 3.8 12.6 - - + -
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Residues in contact with LYS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A GLN* 3.0 46.2 - - + +
473A TRP 2.9 0.8 - - - -
474A MET* 1.3 82.3 - - - +
476A LYS* 1.3 77.3 + - - +
477A TRP 3.0 0.2 + - - -
478A TRP* 3.1 8.1 + - - +
479A GLU* 2.8 50.7 + - - +
482A ARG* 5.5 0.5 + - - -
495A GLU* 3.3 20.1 + - - +
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Residues in contact with LYS 476 (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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459A TRP* 4.1 2.9 - - + -
462A MET* 5.1 9.2 - - + -
467A GLU 4.6 13.1 + - - -
468A ILE* 3.7 34.7 - - + +
469A PRO* 5.6 1.6 - - - +
472A GLN* 3.3 24.5 + - - +
475A LYS* 1.3 86.4 - - - +
477A TRP* 1.3 52.6 + - - +
479A GLU* 3.8 20.6 + - + +
480A MET* 2.7 50.9 + - + +
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Residues in contact with TRP 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A PHE* 5.7 0.7 - + - -
455A MET* 4.2 4.8 - - + +
456A LEU* 3.9 38.4 - - + -
459A TRP* 3.3 49.1 - + + +
473A TRP 3.1 19.3 + - - +
474A MET* 4.0 16.6 - - + -
475A LYS 3.0 0.6 + - - -
476A LYS* 1.3 78.9 - - - +
478A TRP* 1.3 84.9 + + - +
480A MET* 3.6 2.7 - - - +
481A LYS* 2.8 54.7 + - + +
499A ASP* 3.9 1.8 - - - +
500A PRO* 3.3 39.5 - - + -
802A CL 3.9 22.8 - - + +
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Residues in contact with TRP 478 (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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165A TRP* 3.5 30.1 - + - -
264A ALA* 4.1 8.1 - - + -
474A MET* 3.2 31.0 - - + +
475A LYS 3.1 4.3 + - - +
477A TRP* 1.3 89.8 - + - +
479A GLU* 1.3 68.6 + - - +
480A MET 3.1 0.9 - - - -
481A LYS* 3.7 25.7 - - + +
482A ARG* 3.1 33.6 + - - +
487A VAL* 4.4 2.6 - - + +
488A VAL* 3.9 6.1 - - - -
489A GLU* 3.3 60.3 - - + +
493A HIS* 3.8 12.8 - + + +
499A ASP* 2.9 30.2 + - - -
802A CL 3.9 16.6 - - + -
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Residues in contact with GLU 479 (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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475A LYS* 2.8 46.9 + - - +
476A LYS* 3.5 28.2 + - + +
478A TRP* 1.3 74.2 - - - +
480A MET* 1.3 59.0 + - + +
482A ARG* 2.9 41.2 + - - +
483A GLU* 3.0 20.3 + - + +
608A THR* 4.7 3.7 + - - +
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Residues in contact with MET 480 (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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455A MET* 3.9 21.1 - - + +
458A LYS* 3.9 26.5 - - + -
459A TRP* 3.8 32.5 - - - -
462A MET* 5.0 11.4 - - + -
476A LYS* 2.7 35.1 + - + +
477A TRP 3.6 4.3 - - - +
479A GLU* 1.3 73.9 - - + +
481A LYS* 1.3 56.4 + - - +
482A ARG 2.6 16.2 + - - -
483A GLU* 3.1 17.2 + - - +
484A ILE* 3.2 42.4 + - + +
485A VAL 3.8 3.5 + - - -
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Residues in contact with LYS 481 (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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264A ALA* 6.2 1.3 - - - -
267A LEU* 6.3 0.2 - - - -
271A TRP 4.6 7.0 - - - -
452A PHE* 3.6 32.4 - - - -
455A MET* 2.7 39.6 - - + +
456A LEU* 5.5 0.2 - - - +
477A TRP* 2.8 45.6 + - - +
478A TRP* 3.5 27.6 + - + +
480A MET* 1.3 73.5 - - - +
482A ARG* 1.3 50.3 + - - +
485A VAL* 3.4 14.2 - - + +
486A GLY 2.9 9.2 + - - -
487A VAL* 2.6 62.8 + - + +
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Residues in contact with ARG 482 (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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261A CYS* 4.1 14.6 - - - -
475A LYS 5.5 0.6 + - - -
478A TRP* 3.1 26.8 + - - +
479A GLU* 2.9 25.4 + - - +
480A MET 2.6 5.5 + - - -
481A LYS* 1.3 74.0 - - - +
483A GLU* 1.3 58.3 + - - +
486A GLY* 3.4 5.9 - - - -
487A VAL 3.3 16.2 - - - +
488A VAL* 3.7 18.3 - - + +
489A GLU* 3.3 31.9 + - - -
606A TRP* 2.9 26.7 + - - -
607A SER 5.1 0.2 - - - -
608A THR* 4.0 33.2 + - - +
609A ASP* 5.1 1.7 - - - +
610A TRP 4.9 8.9 + - - +
611A SER* 5.8 1.4 - - - -
613A TYR* 4.7 5.1 + - - -
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Residues in contact with GLU 483 (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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234A LYS* 5.9 0.6 + - - -
479A GLU* 3.0 19.0 + - + +
480A MET* 3.1 6.4 + - - +
482A ARG* 1.3 73.4 - - - +
484A ILE* 1.3 69.1 + - + +
606A TRP* 2.8 33.7 + - - +
608A THR* 3.9 21.7 + - + +
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Residues in contact with ILE 484 (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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230A PHE* 3.8 33.8 - - + -
234A LYS* 5.6 8.7 - - - +
237A TYR* 3.9 5.4 - - - -
451A PRO* 4.4 5.4 - - - +
454A TYR* 4.6 13.9 - - + +
455A MET* 3.8 22.7 - - + -
458A LYS* 5.4 1.6 - - + -
480A MET* 3.2 43.8 + - + +
483A GLU* 1.3 83.3 - - + +
485A VAL* 1.3 69.7 + - - +
486A GLY 3.2 1.1 + - - -
606A TRP* 3.4 11.4 - - - -
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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