Contacts of the helix formed by residues 470 - 486 (chain A) in PDB entry 4RS6
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 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A VAL* 1.3 66.9 + - - +
472A ALA* 3.2 7.7 - - - +
473A ASP* 3.4 33.3 + - - +
474A THR* 2.8 30.2 + - - -
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A SER* 1.3 74.9 - - - +
472A ALA* 1.3 62.9 + - - +
474A THR* 3.2 17.2 + - - -
475A VAL* 3.3 14.0 + - - +
603A LEU* 4.2 17.0 - - + -
615A LEU* 4.1 12.8 - - + -
616A PHE 3.8 11.0 - - - +
617A ASN 3.9 15.5 - - - +
618A ASP 5.7 0.2 - - - -
619A GLY* 3.6 30.3 - - - +
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Residues in contact with ALA 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A SER 4.0 4.9 - - - +
471A VAL* 1.3 78.2 - - - +
473A ASP* 1.3 70.7 + - - +
475A VAL* 3.2 4.5 + - - +
476A ALA* 3.0 25.1 + - - +
604A GLN* 4.8 6.1 - - - +
615A LEU* 3.6 23.5 - - + +
680A LEU* 3.9 20.8 - - + +
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Residues in contact with ASP 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A SER* 3.2 32.7 + - - +
472A ALA* 1.3 79.8 - - - +
474A THR* 1.3 63.3 + - - +
476A ALA* 3.4 5.3 + - - +
477A ARG* 2.9 27.5 + - - +
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Residues in contact with THR 474 (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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470A SER* 2.8 17.0 + - - -
471A VAL* 3.4 10.0 + - - -
472A ALA 3.1 0.2 - - - -
473A ASP* 1.3 78.6 - - - +
475A VAL* 1.3 63.7 + - - +
477A ARG* 3.7 6.2 - - + +
478A VAL* 3.1 26.4 + - + +
641A TYR* 3.4 24.5 - - + +
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Residues in contact with VAL 475 (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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471A VAL 3.6 13.9 - - - +
472A ALA* 3.2 6.3 + - - +
474A THR* 1.3 80.2 - - + +
476A ALA* 1.3 61.5 + - - +
478A VAL* 3.5 6.3 + - - +
479A LEU* 3.0 22.8 + - + +
615A LEU* 4.3 9.6 - - + -
619A GLY* 3.5 28.7 - - - +
621A PHE* 3.9 32.5 - - + -
634A ILE* 4.4 18.6 - - + -
641A TYR* 5.4 9.9 - - + +
680A LEU* 4.0 10.5 - - + -
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Residues in contact with ALA 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ALA 3.0 16.2 + - - +
473A ASP* 3.7 6.1 - - - +
475A VAL* 1.3 73.8 - - - +
477A ARG* 1.3 59.5 + - - +
479A LEU* 4.0 0.2 - - - +
480A ARG* 2.7 43.5 + - - +
677A LEU* 4.0 8.9 - - + +
680A LEU* 3.3 20.0 - - + +
681A LEU* 4.2 23.8 - - + -
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Residues in contact with ARG 477 (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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473A ASP 2.9 19.7 + - - +
474A THR* 3.7 6.3 - - + +
476A ALA* 1.3 74.7 - - - +
478A VAL* 1.3 72.2 + - + +
480A ARG* 3.8 12.0 - - - +
481A GLY* 2.9 32.4 + - - -
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A THR* 3.1 15.7 + - + +
475A VAL* 3.5 10.5 - - - +
477A ARG* 1.3 86.3 - - + +
479A LEU* 1.3 65.6 + - + +
481A GLY* 3.2 2.9 + - - -
482A CYS* 3.1 21.8 + - - +
634A ILE* 5.1 6.5 - - + -
641A TYR* 3.5 45.3 - - + +
657A LEU* 3.2 31.2 - - + +
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Residues in contact with LEU 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 VAL 3.0 17.7 + - - +
476A ALA 4.0 1.8 - - - +
478A VAL* 1.3 76.5 - - + +
480A ARG* 1.3 66.3 + - - +
482A CYS* 3.4 4.5 + - + +
483A LEU* 3.0 34.1 + - + +
621A PHE* 4.4 13.2 - - + -
632A ILE* 6.5 0.4 - - + -
634A ILE* 3.9 28.7 - - + -
643A LEU* 4.8 1.3 - - + -
657A LEU* 5.1 2.9 - - + -
673A MET* 3.8 37.5 - - + +
676A ALA* 4.6 2.0 - - + -
677A LEU* 3.9 35.2 - - + +
680A LEU* 5.2 2.7 - - + -
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Residues in contact with ARG 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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476A ALA* 2.7 28.2 + - - +
477A ARG* 3.8 9.5 + - - +
479A LEU* 1.3 70.3 - - - +
481A GLY* 1.3 68.0 + - - +
483A LEU* 3.1 3.2 + - + +
484A GLU* 2.8 63.9 + - + +
677A LEU* 4.0 23.1 - - + +
681A LEU* 4.6 29.9 - - - +
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Residues in contact with GLY 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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477A ARG* 2.9 25.9 + - - -
478A VAL 3.5 4.9 - - - -
480A ARG* 1.3 79.2 - - - +
482A CYS* 1.3 60.7 + - - +
484A GLU* 5.2 2.5 - - - -
485A ASN* 2.8 38.5 + - - +
661A LEU* 4.7 2.5 - - - -
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Residues in contact with CYS 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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478A VAL 3.1 12.4 + - - +
479A LEU* 3.9 6.3 - - - +
481A GLY* 1.3 71.3 - - - +
483A LEU* 1.3 62.4 + - - +
486A MET* 2.9 45.5 + - - +
657A LEU* 4.2 27.6 - - + -
660A LEU* 3.9 15.7 - - - -
661A LEU* 3.8 37.9 - - + -
673A MET* 4.3 9.0 - - + -
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Residues in contact with LEU 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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479A LEU* 3.0 31.4 + - + +
480A ARG* 3.5 4.9 - - - +
482A CYS* 1.3 78.6 - - - +
484A GLU* 1.3 64.2 + - + +
485A ASN 3.3 0.3 + - - -
486A MET* 3.9 19.3 + - - +
670A LYS* 4.0 35.7 + - + +
673A MET* 3.9 35.2 - - + +
674A GLU* 3.9 29.2 - - + +
677A LEU* 3.8 24.7 - - + -
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Residues in contact with GLU 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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480A ARG* 2.8 57.0 + - + +
481A GLY* 4.3 3.5 - - - +
483A LEU* 1.3 74.5 - - + +
485A ASN* 1.3 65.6 + - - +
486A MET 5.0 1.2 - - - +
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Residues in contact with ASN 485 (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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481A GLY* 2.8 32.0 + - - +
484A GLU* 1.3 86.0 + - - +
486A MET* 1.3 66.4 + - - +
487A PRO* 4.2 1.7 - - - +
661A LEU* 3.6 23.5 - - + +
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Residues in contact with MET 486 (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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482A CYS* 2.9 29.4 + - - +
483A LEU* 3.9 23.0 - - - +
484A GLU 3.8 1.6 - - - +
485A ASN* 1.3 79.6 - - - +
487A PRO* 1.3 74.1 - - + +
660A LEU* 3.4 32.3 - - + +
661A LEU* 3.3 6.7 - - - +
664A GLY* 3.6 17.5 - - - -
665A CYS* 3.4 34.8 - - - +
670A LYS* 4.3 24.2 - - + -
673A MET* 4.5 6.5 - - + -
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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