Contacts of the helix formed by residues 69 - 88 (chain G) in PDB entry 2H61
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 ASP 69 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G PHE* 3.7 7.2 - - - -
25G HIS 4.2 6.1 - - - +
26G LYS* 4.1 23.1 - - + +
63G ASP* 4.1 13.5 - - - +
65G ASP* 5.7 0.4 - - - +
67G GLU 4.0 1.0 - - - -
68G CYS* 1.3 75.4 - - - +
70G PHE* 1.3 65.1 + - - +
71G GLN* 3.2 14.6 + - - +
72G GLU* 2.8 45.4 + - - +
73G PHE* 3.0 18.2 + - - +
814G CA 4.3 0.4 - - - -
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Residues in contact with PHE 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU 3.7 20.4 - - - -
11G ILE* 3.7 25.6 - - + -
14G PHE* 3.5 37.8 - + + -
25G HIS 4.5 1.4 + - - -
69G ASP* 1.3 73.8 - - - +
71G GLN* 1.3 68.6 + - - +
73G PHE* 3.1 10.7 + + - +
74G MET* 2.9 51.5 + - + +
81H THR* 3.7 25.1 - - + -
82H THR* 3.9 10.5 - - + -
85H HIS* 3.6 43.1 - + + +
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Residues in contact with GLN 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ASP* 3.2 15.3 + - - +
70G PHE* 1.3 80.7 - - - +
72G GLU* 1.3 66.2 + - + +
74G MET* 3.4 4.2 + - - +
75G ALA* 3.3 17.3 + - - +
82H THR* 3.9 37.7 - - + +
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Residues in contact with GLU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G LEU* 3.5 23.9 - - - +
61G ASP* 4.0 0.7 - - - -
62G ASN* 2.7 34.7 + - + +
63G ASP* 3.0 12.1 + - - +
67G GLU 3.0 4.5 - - - +
68G CYS* 3.2 11.0 - - - -
69G ASP* 2.8 39.2 + - - +
71G GLN* 1.3 82.4 - - + +
73G PHE* 1.3 60.1 + - - +
75G ALA* 3.3 17.0 + - - +
76G PHE* 3.3 11.6 + - - +
814G CA 2.5 30.8 - - - -
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Residues in contact with PHE 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 3.8 24.0 - - - -
13G VAL* 5.3 0.9 - - + -
14G PHE* 3.6 28.9 - + + -
27G LEU* 3.9 14.1 - - + -
32G LEU* 5.2 1.8 - - + -
35G LEU* 3.7 37.9 - - + -
68G CYS* 3.4 10.7 - - - -
69G ASP 3.0 13.1 + - - +
70G PHE* 3.1 17.9 + + - +
72G GLU* 1.3 74.3 - - - +
74G MET* 1.3 65.1 + - - +
76G PHE* 3.0 20.9 + + - +
77G VAL* 2.8 52.0 + - + +
3H LEU* 4.4 14.6 - - + -
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Residues in contact with MET 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 3.6 33.7 - - + -
70G PHE* 2.9 50.4 + - + +
71G GLN 3.6 9.2 - - - +
72G GLU 3.3 0.2 - - - -
73G PHE* 1.3 79.7 - - - +
75G ALA* 1.3 58.3 + - - +
77G VAL* 3.4 15.3 + - + +
78G ALA* 2.9 28.1 + - - +
74H MET* 5.2 2.7 - - + -
77H VAL* 4.3 4.9 - - + -
78H ALA* 3.8 38.4 - - + +
81H THR* 4.0 10.3 - - - +
82H THR* 3.7 12.6 - - - +
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Residues in contact with ALA 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G LEU* 4.9 6.1 - - + +
62G ASN* 5.6 7.4 - - - +
71G GLN 3.3 8.0 + - - +
72G GLU* 3.3 12.5 + - - +
73G PHE 3.1 0.6 - - - -
74G MET* 1.3 77.5 - - - +
76G PHE* 1.3 59.5 + - - +
78G ALA* 3.4 7.5 + - - +
79G MET* 3.0 29.3 + - - +
78H ALA* 4.9 3.3 - - - +
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Residues in contact with PHE 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 4.8 4.3 - - + -
35G LEU* 4.9 2.2 - - + -
36G ILE* 3.7 30.3 - - + -
40G LEU* 3.6 23.8 - - + -
44G LEU* 4.0 11.9 - - + -
56G VAL* 4.1 16.4 - - + -
60G LEU* 3.6 39.6 - - + +
72G GLU 3.3 3.0 + - - -
73G PHE* 3.0 28.9 + + - +
75G ALA* 1.3 75.2 - - - +
77G VAL* 1.3 67.3 + - + +
79G MET* 3.2 23.0 + - + +
80G VAL* 3.0 46.2 + - + +
7H MET* 6.1 0.2 - - + -
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Residues in contact with VAL 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 3.9 25.6 - - + -
40G LEU* 6.4 0.2 - - + -
73G PHE* 2.8 53.7 + - + +
74G MET* 3.6 17.9 - - + +
76G PHE* 1.3 72.8 - - + +
78G ALA* 1.3 56.6 + - - +
80G VAL* 3.2 1.1 + - - +
81G THR* 2.7 43.3 + - - +
3H LEU* 4.5 1.8 - - + -
7H MET* 3.8 28.5 - - + -
10H LEU* 4.8 1.3 - - + -
74H MET* 4.3 10.8 - - + -
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Residues in contact with ALA 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G MET 2.9 20.3 + - - +
75G ALA* 3.5 8.7 - - - +
76G PHE 3.3 0.2 - - - -
77G VAL* 1.3 73.9 - - - +
79G MET* 1.3 56.8 + - - +
81G THR* 4.0 0.3 - - - -
82G THR* 2.7 38.7 + - - +
74H MET* 3.7 40.3 - - + +
75H ALA* 4.8 1.6 - - - +
78H ALA* 5.0 2.7 - - + -
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Residues in contact with MET 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LEU* 6.5 0.4 - - + -
59G THR* 6.0 6.5 - - + -
60G LEU* 6.2 0.9 - - + -
75G ALA 3.0 15.0 + - - +
76G PHE* 3.5 30.7 - - + +
78G ALA* 1.3 80.4 - - - +
80G VAL* 1.3 70.3 + - + +
82G THR* 3.7 4.9 - - - -
83G ALA* 3.1 25.1 + - - +
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Residues in contact with VAL 80 (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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40G LEU* 4.7 2.9 - - + -
43G PHE* 4.4 20.6 - - + -
44G LEU* 4.3 21.3 - - + -
76G PHE* 3.0 49.9 + - + +
77G VAL 3.8 2.5 - - - +
79G MET* 1.3 83.2 - - + +
81G THR* 1.3 63.8 + - - +
83G ALA* 3.2 7.1 + - - +
84G CYS* 3.0 24.3 + - - -
7H MET* 3.9 23.8 - - + -
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Residues in contact with THR 81 (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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77G VAL* 2.7 28.0 + - - +
78G ALA 4.0 2.0 - - - -
80G VAL* 1.3 71.2 - - - +
82G THR* 1.3 55.2 + - - +
84G CYS* 3.1 7.9 + - - +
85G HIS* 2.7 33.8 + - - +
7H MET* 3.5 47.8 - - + +
10H LEU* 4.5 1.5 - - + +
11H ILE* 3.9 6.0 - - + +
70H PHE* 3.7 23.1 - - + -
74H MET* 3.9 16.1 - - + +
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Residues in contact with THR 82 (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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78G ALA* 2.7 25.7 + - - +
79G MET* 3.7 5.6 - - - -
81G THR* 1.3 75.9 - - - +
83G ALA* 1.3 64.9 + - - +
85G HIS* 3.1 12.7 + - - +
86G GLU* 3.1 30.7 + - + +
70H PHE* 3.7 12.5 - - + -
71H GLN* 3.8 45.8 - - + +
74H MET* 3.7 17.8 - - - +
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Residues in contact with ALA 83 (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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79G MET* 3.1 19.5 + - - +
80G VAL* 3.5 11.4 - - - +
81G THR 3.2 0.2 - - - -
82G THR* 1.3 79.0 - - - +
84G CYS* 1.3 60.3 + - - +
86G GLU* 3.7 8.1 + - - +
87G PHE* 3.6 16.8 + - - +
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Residues in contact with CYS 84 (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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88F PHE* 6.1 0.9 - - + -
43G PHE* 3.6 50.5 - - + -
80G VAL* 3.0 24.5 + - - -
81G THR* 3.4 10.3 - - - +
83G ALA* 1.3 76.1 - - - +
85G HIS* 1.3 64.2 + - - +
87G PHE* 3.2 20.4 - - - +
88G PHE* 3.3 19.7 - - + -
7H MET* 5.8 0.7 - - + -
11H ILE* 4.1 13.0 - - + -
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Residues in contact with HIS 85 (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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81G THR 2.7 13.1 + - - +
82G THR* 3.1 5.2 + - - +
84G CYS* 1.3 72.2 - - - +
86G GLU* 1.3 63.4 + - + +
88G PHE* 2.7 29.4 + - - +
89G GLU* 3.2 46.2 + - + +
11H ILE* 3.8 17.9 - - + -
14H PHE* 4.3 10.9 - + - -
15H HIS* 3.7 26.8 + + - -
25H HIS* 5.5 2.2 - - + -
70H PHE* 3.5 58.3 - + + +
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Residues in contact with GLU 86 (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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82G THR* 3.1 29.8 + - - +
83G ALA* 4.1 7.4 - - - +
84G CYS 3.3 0.2 - - - -
85G HIS* 1.3 83.2 + - + +
87G PHE* 1.3 56.7 + - - +
89G GLU* 2.9 41.7 + - + +
71H GLN* 5.5 1.0 + - - -
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Residues in contact with PHE 87 (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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42F HIS 4.8 1.4 - - - +
84F CYS* 6.5 1.1 - - - -
87F PHE* 3.3 57.9 - + + -
88F PHE* 5.3 7.6 - + - -
83G ALA 3.6 8.8 + - - +
84G CYS* 3.2 17.0 - - - +
86G GLU* 1.3 77.2 - - - +
88G PHE* 1.3 78.8 + + - -
89G GLU 3.3 1.8 + - - +
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Residues in contact with PHE 88 (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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0E MET* 3.4 37.9 - - + -
8E VAL* 6.0 2.5 - - + -
41F SER 4.5 0.7 - - - +
42F HIS* 3.6 47.5 - - + +
43F PHE* 4.8 9.4 - + - -
88F PHE* 4.2 24.7 - + - -
43G PHE* 6.1 1.3 - + - -
84G CYS* 3.3 21.5 - - + -
85G HIS 2.7 13.0 + - - +
87G PHE* 1.3 98.2 - + - +
89G GLU* 1.3 61.9 + - - +
90G HIS 3.8 1.2 + - - -
8H VAL* 4.7 11.9 - - + -
11H ILE* 4.1 27.8 - - + -
15H HIS* 4.4 7.4 - - + +
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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
------------------------------------------------------------
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