Contacts of the helix formed by residues 473 - 489 (chain A) in PDB entry 3RS9
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 THR 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A GLY 5.5 0.4 - - - -
426A LYS* 4.4 17.0 - - + -
429A SER* 6.1 0.2 - - - -
471A GLY 3.5 9.5 + - - +
472A LEU* 1.3 85.4 - - - +
474A ALA* 1.3 60.1 + - - +
475A SER* 3.9 8.5 + - - -
476A GLU* 2.9 28.5 + - - +
477A LEU* 2.9 23.5 + - - +
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 3.8 23.1 - - + -
426A LYS* 5.7 0.2 - - - +
427A GLY 4.5 4.6 + - - +
428A GLY* 3.7 34.8 - - - +
429A SER* 4.3 4.9 + - - +
432A VAL* 4.1 6.0 - - + +
473A THR* 1.3 74.6 - - - +
475A SER* 1.3 57.2 + - - +
477A LEU* 3.2 12.6 + - - +
478A LEU* 3.0 32.1 + - - +
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Residues in contact with SER 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 4.4 10.8 - - - +
278A ARG* 3.7 23.5 + - - -
279A PHE* 5.7 1.7 - - - -
473A THR* 3.2 8.6 + - - -
474A ALA* 1.3 74.3 - - - +
476A GLU* 1.3 70.4 + - - +
478A LEU* 3.5 14.7 + - - +
479A ARG* 3.3 18.7 + - - +
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Residues in contact with GLU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A PHE* 4.1 18.4 - - + -
471A GLY 5.4 1.3 - - - +
472A LEU* 3.8 15.5 - - + -
473A THR* 2.9 23.3 + - - +
475A SER* 1.3 78.7 - - - +
477A LEU* 1.3 67.6 + - - +
479A ARG* 2.5 59.5 + - - +
480A LEU* 3.1 17.5 + - - +
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 3.7 24.0 - - + -
429A SER* 4.6 8.1 - - - +
432A VAL* 4.2 21.1 - - + -
458A HIS* 3.6 33.9 - - + +
461A ALA* 3.8 9.9 - - + -
462A ALA* 3.6 34.3 - - + +
472A LEU* 4.0 10.5 - - + +
473A THR 2.9 12.1 + - - +
474A ALA* 3.2 11.0 + - - +
476A GLU* 1.3 77.4 - - - +
478A LEU* 1.3 63.6 + - - +
480A LEU* 3.0 15.7 + - - +
481A ILE* 3.1 15.9 + - + +
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Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 3.9 30.3 - - + +
253A MET* 3.6 25.8 - - + +
254A GLY* 3.4 34.5 - - - +
257A LYS* 3.5 31.6 - - + +
279A PHE* 4.5 16.8 - - + -
432A VAL* 3.9 16.8 - - + -
474A ALA 3.0 14.9 + - - +
475A SER* 3.6 13.0 - - - +
476A GLU 3.3 0.2 - - - -
477A LEU* 1.3 78.6 - - - +
479A ARG* 1.3 62.0 + - - +
480A LEU 3.3 0.7 + - - -
481A ILE* 3.4 17.0 + - + +
482A PRO* 3.6 0.9 - - - +
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Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LYS* 4.5 11.8 + - - +
465A PHE* 4.1 8.5 - - - -
466A GLU* 3.0 40.4 + - - -
475A SER 3.3 9.9 + - - +
476A GLU* 2.5 39.0 + - - +
478A LEU* 1.3 79.4 - - - +
480A LEU* 1.3 80.8 + - - +
482A PRO* 3.5 11.8 - - - +
483A GLU* 4.9 2.8 + - - +
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Residues in contact with LEU 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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461A ALA* 3.4 29.3 - - + +
464A LEU* 3.9 19.2 - - + +
465A PHE* 3.6 35.2 - - + -
466A GLU* 4.0 6.3 - - - +
472A LEU* 4.3 7.2 - - + -
476A GLU 3.1 14.8 + - - +
477A LEU* 3.0 10.1 + - - +
479A ARG* 1.3 101.5 - - - +
481A ILE* 1.3 63.4 + - - +
482A PRO 3.4 0.7 - - - -
483A GLU* 3.1 30.8 + - - +
484A ALA* 3.0 21.1 + - - +
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Residues in contact with ILE 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLY* 4.8 0.7 - - - -
257A LYS* 3.7 31.6 - - + +
258A VAL* 4.0 15.3 - - + -
432A VAL* 3.8 17.9 - - + -
436A MET* 3.8 38.1 - - + -
457A LEU* 5.3 2.2 - - + +
458A HIS* 5.6 0.4 - - - -
461A ALA* 4.1 15.5 - - + -
477A LEU* 3.1 12.4 + - + +
478A LEU* 3.6 19.1 - - + +
480A LEU* 1.3 75.4 - - - +
482A PRO* 1.3 68.0 - - + +
484A ALA* 3.0 5.7 + - - +
485A ILE* 3.0 27.6 + - + +
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Residues in contact with PRO 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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257A LYS* 4.0 31.2 - - + +
478A LEU 3.6 6.5 - - - +
479A ARG 3.5 17.0 - - - +
481A ILE* 1.3 92.6 - - + +
483A GLU* 1.3 55.9 + - - +
485A ILE* 3.6 13.3 + - + +
486A ARG* 3.0 26.7 + - - +
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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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464A LEU* 3.9 17.4 - - + +
466A GLU* 4.9 3.5 - - - +
479A ARG* 4.9 2.1 + - - +
480A LEU* 3.1 32.1 + - - +
482A PRO* 1.3 76.1 - - - +
484A ALA* 1.3 59.6 + - - +
486A ARG* 3.2 18.8 + - - +
487A ARG* 2.8 64.7 + - - +
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LEU* 3.9 16.8 - - + +
460A PHE* 3.6 26.5 - - + -
461A ALA* 3.8 24.2 - - + +
464A LEU* 3.6 10.4 - - + +
480A LEU 3.0 11.5 + - - +
481A ILE* 3.4 8.1 - - - +
483A GLU* 1.3 74.6 - - - +
485A ILE* 1.3 63.5 + - - +
487A ARG 3.2 1.4 + - - -
488A LEU* 3.0 23.0 + - - +
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Residues in contact with ILE 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 4.1 25.4 - - + -
257A LYS 3.9 21.8 - - - +
258A VAL* 4.2 15.5 - - + +
440A PHE* 5.0 3.4 - - + -
457A LEU* 4.1 30.5 - - + -
481A ILE* 3.0 20.6 + - + +
482A PRO* 3.8 10.1 - - + +
484A ALA* 1.3 75.3 - - - +
486A ARG* 1.3 64.7 + - - +
488A LEU* 3.2 18.2 + - - +
489A LYS* 3.6 13.7 + - + +
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A PRO 3.0 17.9 + - - +
483A GLU* 3.2 17.3 + - - +
485A ILE* 1.3 76.3 - - - +
487A ARG* 1.3 104.1 + - - +
489A LYS* 3.1 29.0 + - - +
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Residues in contact with ARG 487 (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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213A ARG* 3.2 21.7 + - - +
460A PHE* 3.7 19.7 - - + -
464A LEU* 3.6 27.6 - - - +
483A GLU* 2.8 45.3 + - - +
485A ILE 3.2 0.2 - - - -
486A ARG* 1.3 101.0 - - - +
488A LEU* 1.3 63.6 + - - +
489A LYS 3.2 4.7 + - - -
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Residues in contact with LEU 488 (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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213A ARG* 3.8 38.0 + - + +
216A VAL* 3.4 35.4 - - + -
217A ARG* 3.3 32.8 + - + +
220A LEU* 4.0 25.1 - - + -
456A TYR* 3.9 17.0 - - + -
457A LEU* 3.6 18.8 - - + -
460A PHE* 4.4 3.5 - - + -
484A ALA 3.0 16.2 + - - +
485A ILE* 3.2 8.7 + - - +
487A ARG* 1.3 76.9 - - - +
489A LYS* 1.3 63.5 + - + +
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Residues in contact with LYS 489 (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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217A ARG* 4.3 17.0 - - + +
220A LEU* 3.5 27.6 - - + -
221A PRO 6.0 0.7 - - - -
223A ARG* 6.6 0.2 - - - -
485A ILE* 3.8 21.1 - - + +
486A ARG* 3.1 19.9 + - - +
487A ARG* 4.1 4.2 - - - +
488A LEU* 1.3 85.7 - - + +
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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
------------------------------------------------------------
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