Contacts of the helix formed by residues 478 - 490 (chain A) in PDB entry 2HRG
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 PRO 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A TRP* 3.4 51.6 - - + +
93A PHE* 4.8 2.9 - - + -
94A LEU 5.4 1.1 - - - +
476A PRO 4.3 0.7 - - - +
477A VAL* 1.3 90.8 - - + +
479A GLN* 1.3 66.9 + - - +
480A ALA* 4.2 6.7 - - + +
481A TRP* 3.0 24.7 + - + +
482A SER* 3.3 8.5 + - - -
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Residues in contact with GLN 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A VAL 3.9 0.6 + - - -
478A PRO* 1.3 72.5 - - - +
480A ALA* 1.3 62.3 + - - +
482A SER* 3.1 22.5 + - - -
483A ASP* 3.1 43.3 + - - +
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Residues in contact with ALA 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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92A ALA 5.6 2.0 - - - +
93A PHE* 3.7 23.9 - - + -
94A LEU* 5.4 4.7 - - + +
478A PRO* 3.2 6.5 - - + +
479A GLN* 1.3 78.0 - - - +
481A TRP* 1.3 62.0 + - - +
483A ASP* 3.4 15.9 + - - +
484A LEU* 3.4 17.3 + - - +
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Residues in contact with TRP 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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75A TRP* 3.4 29.8 + - + +
83A ASN 2.8 30.8 + - - -
84A GLN* 3.5 12.0 - - + +
85A CYS 5.6 0.7 - - - -
93A PHE* 3.5 15.6 - + + -
349A PRO* 5.3 2.0 - - + -
351A LEU* 3.6 14.1 - - + -
352A LEU* 4.0 38.4 - - + -
355A LEU* 3.8 29.4 - - + -
477A VAL* 3.7 19.7 - - + -
478A PRO* 3.0 26.4 + - + +
480A ALA* 1.3 76.3 - - - +
482A SER* 1.3 75.3 + - - +
484A LEU* 3.1 33.2 + - + +
485A CYS* 4.5 3.5 + - - -
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A VAL* 5.0 6.1 - - - -
478A PRO 3.3 7.5 + - - -
479A GLN* 3.1 24.7 + - - -
481A TRP* 1.3 92.3 - - - +
483A ASP* 1.3 59.7 + - - +
485A CYS* 4.3 1.7 + - - +
486A PRO* 3.3 21.0 - - - +
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Residues in contact with ASP 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLN* 3.1 41.1 + - - +
480A ALA* 3.9 8.6 - - - +
481A TRP 3.1 1.0 - - - -
482A SER* 1.3 81.5 + - - +
484A LEU* 1.3 62.1 + - - +
485A CYS 3.5 0.9 - - - -
486A PRO* 3.4 9.9 - - + +
487A THR* 3.0 31.3 + - - +
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Residues in contact with LEU 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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84A GLN* 3.6 15.9 - - + +
85A CYS* 3.6 27.6 - - + +
86A PRO 4.2 2.9 - - - +
87A ILE* 4.1 28.3 - - + -
88A SER* 5.0 0.6 + - - +
91A HIS* 6.5 0.4 - - + -
92A ALA 5.5 1.3 - - - +
93A PHE* 4.0 40.2 - - + -
480A ALA 3.4 12.2 + - - +
481A TRP* 3.1 25.1 + - + +
483A ASP* 1.3 77.4 - - - +
485A CYS* 1.3 59.6 + - - +
487A THR* 3.7 4.8 - - - -
488A TYR* 2.9 30.5 + - - +
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Residues in contact with CYS 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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85A CYS* 2.1 50.3 - - - -
347A THR 5.2 0.4 - - - -
349A PRO* 3.4 23.8 - - - -
352A LEU* 4.0 19.7 - - + -
481A TRP* 4.5 4.1 + - - -
482A SER 4.3 2.7 + - - +
484A LEU* 1.3 76.7 - - - +
486A PRO* 1.4 66.7 - - + +
488A TYR 3.2 0.4 + - - +
489A ASP* 2.8 45.1 + - - +
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Residues in contact with PRO 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER 3.3 21.8 - - - +
483A ASP* 3.4 13.2 - - - +
485A CYS* 1.4 91.4 - - + +
487A THR* 1.3 59.7 + - - +
489A ASP* 4.1 4.7 - - + +
490A ALA* 3.3 23.0 + - - +
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Residues in contact with THR 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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88A SER* 3.6 17.3 - - - +
91A HIS* 3.5 39.6 + - + +
483A ASP* 3.0 22.3 + - - +
484A LEU* 3.7 4.7 - - - -
485A CYS 3.2 0.8 - - - -
486A PRO* 1.3 77.3 - - - +
488A TYR* 1.3 62.9 + - - +
490A ALA* 3.3 16.6 + - - +
491A LEU* 3.7 12.3 + - + +
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Residues in contact with TYR 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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60A SER* 3.4 26.7 - - - -
81A PHE* 3.8 33.5 - + - -
85A CYS* 4.2 7.4 - - + -
86A PRO* 3.7 39.1 - - + +
88A SER* 3.5 8.0 + - - +
112A LEU* 5.3 2.8 - - - +
484A LEU 2.9 18.8 + - - +
485A CYS 3.8 1.8 - - - +
487A THR* 1.3 76.5 - - - +
489A ASP* 1.3 78.3 + - - +
490A ALA 3.1 0.2 - - - -
491A LEU* 3.1 28.9 + - + +
496A GLN* 3.7 41.8 + - + +
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Residues in contact with ASP 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 5.8 0.3 - - - -
85A CYS* 4.8 1.4 - - - -
347A THR* 4.7 24.7 - - - +
485A CYS* 2.8 35.4 + - - +
486A PRO* 4.4 4.4 - - + +
488A TYR* 1.3 88.2 - - - +
490A ALA* 1.3 59.3 + - - +
491A LEU 3.3 5.2 + - - +
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Residues in contact with ALA 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A PRO 3.3 18.6 + - - +
487A THR* 3.6 7.9 - - - +
488A TYR 3.1 0.8 - - - -
489A ASP* 1.3 77.6 - - - +
491A LEU* 1.3 61.6 + - - +
492A SER 3.7 1.0 + - - -
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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