Contacts of the helix formed by residues 65 - 79 (chain G) in PDB entry 2R9R
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 65 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64G ILE* 1.3 81.7 - - - +
66G ASP* 1.3 60.0 + - - +
67G GLU* 3.5 13.1 + - - +
68G MET* 3.1 25.5 + - - +
69G ALA* 2.9 23.8 + - - +
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Residues in contact with ASP 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLY* 4.6 8.1 + - - -
64G ILE 4.7 1.0 - - - +
65G THR* 1.3 71.4 - - - +
67G GLU* 1.3 60.7 + - - +
69G ALA* 3.6 8.1 - - - +
70G GLU* 2.9 29.5 + - - +
98G VAL* 3.6 31.4 - - + +
102G ILE* 4.7 2.4 - - - +
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Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G THR* 3.5 10.2 + - - +
66G ASP* 1.3 80.4 - - - +
68G MET* 1.3 62.9 + - - +
70G GLU* 3.4 10.4 + - - +
71G HIS* 3.1 22.1 + - + +
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Residues in contact with MET 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ILE* 3.9 14.6 - - + -
65G THR* 3.1 26.4 + - - +
67G GLU* 1.3 76.3 - - - +
69G ALA* 1.3 60.8 + - - +
71G HIS* 3.0 16.1 + - - +
72G LEU* 2.8 45.8 + - + +
325G SER 3.8 14.8 - - - +
326G ASN* 3.9 34.3 - - + -
327G ALA* 4.1 4.3 - - + +
328G GLU* 5.9 0.4 - - - +
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Residues in contact with ALA 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G PHE* 3.9 17.3 - - + -
61G GLY 5.7 0.2 - - - +
64G ILE* 3.7 19.7 - - + +
65G THR 2.9 14.0 + - - +
66G ASP* 3.6 8.5 - - - +
67G GLU 3.3 0.2 - - - -
68G MET* 1.3 75.3 - - - +
70G GLU* 1.3 64.8 + - - +
72G LEU* 3.2 3.7 + - - +
73G MET* 3.1 19.9 + - - +
98G VAL* 3.9 16.4 - - + -
102G ILE* 3.6 19.5 - - + +
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Residues in contact with GLU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ASP 2.9 18.2 + - - +
67G GLU* 3.6 8.6 - - - +
69G ALA* 1.3 77.8 - - - +
71G HIS* 1.3 52.3 + - - +
73G MET* 3.4 1.9 + - - +
74G THR* 2.6 44.3 + - - +
102G ILE* 3.5 25.4 - - + +
105G LYS* 2.8 44.6 + - - +
106G LYS* 4.2 22.4 + - + -
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Residues in contact with HIS 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G GLU* 3.1 14.5 + - + +
68G MET* 3.0 21.6 + - - +
70G GLU* 1.3 78.8 - - - +
72G LEU* 1.3 61.8 + - - +
74G THR* 3.5 6.2 + - - -
75G LEU* 3.0 63.2 + - + +
327G ALA* 3.7 20.9 - - + +
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G LEU* 4.2 13.2 - - + -
60G PHE* 5.1 5.4 - - + -
64G ILE* 4.0 20.2 - - + -
68G MET* 2.8 29.6 + - + +
69G ALA* 3.8 4.3 - - - +
71G HIS* 1.3 76.1 - - - +
73G MET* 1.3 60.2 + - - +
75G LEU* 3.3 1.5 + - + -
76G ALA* 2.8 30.7 + - - +
324G ALA* 3.4 33.4 - - + +
326G ASN 3.6 7.0 - - - +
327G ALA* 3.6 38.1 - - + +
330G LEU* 3.4 22.1 - - + +
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Residues in contact with MET 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G LEU* 4.2 5.6 - - + +
60G PHE* 4.2 17.9 - - + -
69G ALA 3.1 13.4 + - - +
70G GLU 3.9 3.8 - - - +
72G LEU* 1.3 76.5 - - - +
74G THR* 1.3 54.5 + - - +
76G ALA* 3.2 1.7 + - - +
77G TYR* 2.8 36.9 + - - +
84G PHE* 3.3 55.5 - - + -
99G LEU* 3.4 25.8 - - + -
102G ILE* 3.8 28.3 - - + -
103G ILE* 4.2 13.7 - - + -
108G TRP* 3.8 20.9 - - + -
113G LEU* 4.6 1.6 - - + -
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Residues in contact with THR 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G GLU* 2.6 24.7 + - - +
71G HIS* 3.8 8.8 - - - -
72G LEU 3.3 0.2 - - - -
73G MET* 1.3 77.5 - - - +
75G LEU* 1.3 58.2 + - + +
77G TYR* 3.8 0.5 - - - +
78G ASP* 2.8 54.7 + - - +
106G LYS* 3.7 36.5 + - - +
108G TRP* 3.9 11.4 - - + -
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Residues in contact with LEU 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G HIS* 3.0 59.2 + - + +
72G LEU* 3.6 6.3 - - + +
74G THR* 1.3 77.7 - - + +
76G ALA* 1.3 62.9 + - - +
78G ASP* 3.5 5.8 + - + +
79G ASN* 2.7 36.3 + - - +
327G ALA* 3.8 17.0 - - + -
330G LEU* 3.9 2.0 - - + -
331G MET* 3.4 32.3 - - + -
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Residues in contact with ALA 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G LEU* 4.2 10.1 - - + -
72G LEU 2.8 18.3 + - - +
73G MET 3.6 3.1 - - - +
75G LEU* 1.3 76.5 - - - +
77G TYR* 1.3 63.2 + - - +
79G ASN* 3.0 9.0 + - - -
81G ILE* 3.0 46.8 + - + +
84G PHE* 3.8 20.4 - - + -
330G LEU* 4.0 8.7 - - + +
334G ILE* 4.7 3.1 - - - -
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Residues in contact with TYR 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G MET 2.8 20.6 + - - +
74G THR 3.8 2.2 - - - +
76G ALA* 1.3 71.8 - - - +
78G ASP* 1.3 70.2 + - - +
80G GLY* 3.0 19.8 + - - -
81G ILE 3.6 15.1 + - - +
82G ASN* 5.6 0.7 - - - -
84G PHE* 4.2 3.3 - + + -
108G TRP* 3.6 53.3 - + + +
109G ARG* 4.7 6.9 + - - -
112G SER* 2.8 37.5 + - - -
113G LEU* 3.7 26.9 - - + -
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Residues in contact with ASP 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G THR* 2.8 44.0 + - - +
75G LEU* 4.0 7.2 - - + +
77G TYR* 1.3 85.3 - - - +
79G ASN* 1.3 64.9 + - - +
80G GLY 3.2 1.9 + - - -
108G TRP* 5.1 2.6 + - - -
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Residues in contact with ASN 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G PHE* 3.8 13.9 - - - -
75G LEU* 2.7 34.6 + - - +
76G ALA 3.0 6.1 + - - +
78G ASP* 1.3 82.3 - - - +
80G GLY* 1.3 59.7 + - - +
81G ILE* 3.4 4.9 + - + +
331G MET* 4.0 24.0 - - - +
334G ILE* 4.3 24.9 - - + +
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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