Contacts of the helix formed by residues 61 - 78 (chain G) in PDB entry 3CHB
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 GLN 61 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G GLN 4.0 0.5 - - - +
57G HIS* 3.2 18.1 - - + -
58G ILE* 2.9 40.4 + - + +
60G SER* 1.3 77.5 - - - +
62G LYS* 1.3 59.5 + - - +
63G LYS 3.4 0.4 - - - -
64G ALA* 3.1 4.1 + - - +
65G ILE* 2.9 41.7 + - + +
31H LEU* 2.8 33.2 + - - +
32H ALA* 3.8 2.0 - - - +
33H GLY* 3.3 18.8 - - - +
36H GLU* 3.5 18.6 - - - +
4I GAL 3.1 24.7 + - - -
5I SIA 4.3 2.8 + - - -
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Residues in contact with LYS 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LYS* 6.1 2.9 - - - +
53G PRO* 5.5 12.3 - - + -
57G HIS* 5.7 5.6 - - + -
58G ILE 4.4 4.0 - - - +
59G ASP* 3.1 45.1 + - + +
61G GLN* 1.3 78.0 - - - +
63G LYS* 1.3 64.5 + - + +
65G ILE* 3.4 11.4 + - + +
66G GLU* 3.3 25.7 + - - +
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Residues in contact with LYS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ASP 4.6 1.2 + - - -
60G SER 4.5 4.1 + - - +
61G GLN 3.4 0.4 - - - -
62G LYS* 1.3 79.0 - - + +
64G ALA* 1.3 57.0 + - - +
66G GLU* 3.3 8.6 + - - +
67G ARG* 2.9 27.4 + - - +
62H LYS* 4.9 15.8 + - - +
63H LYS* 6.2 1.0 - - - +
66H GLU* 4.2 39.2 - - + +
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Residues in contact with ALA 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G SER 4.5 1.7 + - - +
61G GLN* 3.1 10.5 + - - +
63G LYS* 1.3 76.3 - - - +
65G ILE* 1.3 60.6 + - - +
67G ARG* 3.4 12.4 + - - +
68G MET* 2.9 29.1 + - - +
29H GLU* 4.9 0.3 - - - +
30H SER 4.1 7.6 - - - +
31H LEU* 3.7 29.2 - - + +
36H GLU* 4.1 18.6 - - + -
69H LYS* 6.3 0.7 - - - +
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Residues in contact with ILE 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G VAL* 3.8 19.0 - - + +
51G GLU 4.2 4.0 - - - +
53G PRO* 4.2 19.3 - - + -
57G HIS* 3.7 45.5 - - + +
61G GLN* 2.9 25.3 + - + +
62G LYS* 3.7 9.2 - - + +
63G LYS 3.3 0.2 - - - -
64G ALA* 1.3 77.8 - - - +
66G GLU* 1.3 74.8 + - - +
68G MET* 3.3 3.5 + - - +
69G LYS* 3.2 28.9 + - - +
31H LEU* 4.1 24.0 - - + -
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Residues in contact with GLU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LYS* 3.4 44.0 + - + +
64F ALA* 6.0 0.2 - - - -
67F ARG* 2.9 44.6 + - - +
53G PRO* 4.3 5.7 - - - +
62G LYS 3.3 13.9 + - - +
63G LYS* 3.3 10.0 + - - +
64G ALA 3.3 0.2 - - - -
65G ILE* 1.3 82.2 - - - +
67G ARG* 1.3 63.0 + - - +
69G LYS* 2.8 28.0 + - - +
70G ASP* 3.1 15.8 + - - +
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Residues in contact with ARG 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LYS 2.9 16.0 + - - +
64G ALA* 3.7 10.9 - - - +
66G GLU* 1.3 77.0 - - - +
68G MET* 1.4 55.4 + - - +
70G ASP* 3.1 13.5 + - - +
71G THR* 2.8 30.3 + - - -
27H TYR* 4.6 0.2 - - - -
29H GLU* 3.3 30.9 + - - +
66H GLU* 3.0 53.3 + - - +
69H LYS* 3.5 28.1 - - - +
70H ASP* 2.5 38.9 + - - +
73H ARG* 3.8 12.1 - - - +
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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
----------------------------------------------------------
50G VAL* 3.9 17.9 - - + -
64G ALA 2.9 16.1 + - - +
65G ILE 3.6 5.6 - - - +
66G GLU 3.3 0.4 - - - -
67G ARG* 1.4 75.6 - - - +
69G LYS* 1.3 58.8 + - - +
71G THR* 3.2 2.7 + - - -
72G LEU* 2.9 43.2 + - + +
96G ILE* 4.0 24.7 - - + -
97G ALA 4.2 6.7 - - - +
98G ALA* 4.0 7.0 - - - -
99G ILE* 3.7 24.7 - - + -
29H GLU* 3.5 39.4 + - + +
30H SER 4.7 0.2 - - - -
31H LEU* 3.7 23.8 - - + +
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Residues in contact with LYS 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F ALA* 6.3 0.4 - - - +
67F ARG* 3.5 29.7 + - - +
27G TYR* 3.7 11.8 + - - +
29G GLU* 6.1 0.4 - - + -
36G GLU* 4.2 19.2 + - - +
37G MET* 4.6 4.7 - - - +
38G ALA* 3.9 28.7 - - + +
50G VAL* 3.9 19.5 - - + +
51G GLU 5.3 0.4 + - - -
53G PRO* 4.8 4.2 - - - +
65G ILE* 3.2 26.4 + - - +
66G GLU* 2.8 37.5 + - - +
67G ARG 3.3 0.2 - - - -
68G MET* 1.3 76.2 - - - +
70G ASP* 1.3 63.0 + - - +
72G LEU* 3.4 6.2 + - - +
73G ARG* 3.1 23.9 + - - +
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Residues in contact with ASP 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ARG* 2.7 33.1 + - - +
70F ASP* 5.7 0.5 - - - +
66G GLU* 3.1 18.0 + - - +
67G ARG* 3.1 15.1 + - - +
69G LYS* 1.3 77.1 - - - +
71G THR* 1.3 61.9 + - - +
73G ARG* 3.3 23.5 + - - +
74G ILE* 3.1 24.9 + - - +
70H ASP* 5.6 0.9 - - - +
73H ARG* 3.7 21.5 + - - +
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Residues in contact with THR 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ARG 2.8 8.9 + - - -
68G MET* 3.2 10.1 + - - -
70G ASP* 1.3 74.0 - - - +
72G LEU* 1.4 58.6 + - - +
74G ILE* 3.5 6.3 - - + +
75G ALA* 2.8 29.3 + - + +
99G ILE* 4.3 22.9 - - + -
101G MET* 4.2 20.2 - - + -
27H TYR* 5.0 1.3 - - + -
29H GLU* 2.8 32.0 + - - +
73H ARG* 3.0 29.3 + - - +
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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
----------------------------------------------------------
24G ILE* 3.7 8.2 - - + +
27G TYR* 4.0 16.1 - - + -
38G ALA* 5.0 6.1 - - + -
40G ILE* 4.1 31.2 - - + -
50G VAL* 3.6 32.3 - - + -
68G MET* 2.9 25.7 + - + +
69G LYS* 4.0 2.7 - - - +
71G THR* 1.4 76.2 - - - +
73G ARG* 1.3 58.8 + - - +
75G ALA* 3.7 3.7 - - - +
76G TYR* 2.9 30.1 + - - +
85G LEU* 5.2 0.2 - - + -
96G ILE* 3.7 17.5 - - + -
99G ILE* 3.7 28.7 - - + -
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Residues in contact with ARG 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ARG* 3.7 29.9 + - - +
70F ASP* 3.7 23.7 + - - +
71F THR* 3.0 43.7 + - + +
74F ILE* 4.2 11.6 - - - +
101F MET* 5.0 2.5 - - + -
27G TYR* 3.7 25.7 - - + +
29G GLU* 4.4 2.0 + - - -
69G LYS 3.1 17.4 + - - +
70G ASP* 3.7 28.9 + - - +
72G LEU* 1.3 75.5 - - - +
74G ILE* 1.3 59.6 + - - +
76G TYR* 3.3 3.8 + - - +
77G LEU* 3.0 41.4 + - + +
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Residues in contact with ILE 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ILE* 5.2 10.1 - - + -
70G ASP 3.1 16.6 + - - +
71G THR* 3.5 15.3 - - + +
73G ARG* 1.3 75.6 - - + +
75G ALA* 1.3 68.3 + - - +
77G LEU* 4.4 14.6 - - + +
78G THR* 2.8 44.6 + - + -
73H ARG* 4.1 13.0 - - - +
77H LEU* 3.6 28.5 - - + -
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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
----------------------------------------------------------
24G ILE* 4.0 15.6 + - + -
71G THR* 2.8 19.8 + - + +
72G LEU* 3.7 4.9 - - - +
74G ILE* 1.3 78.4 - - - +
76G TYR* 1.3 63.3 + - - +
78G THR* 3.8 5.2 - - - -
79G GLU* 3.0 19.1 + - - -
80G ALA* 3.0 21.8 + - + +
82G VAL* 5.1 2.5 - - + -
99G ILE* 5.5 2.2 - - + -
101G MET* 4.0 24.9 - - + -
77H LEU* 5.1 1.6 - - - -
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Residues in contact with TYR 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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80F ALA* 5.3 3.8 - - + -
81F LYS 4.8 0.9 + - - -
101F MET* 3.5 26.8 - - + +
102F ALA* 3.2 31.7 + - - -
103F ASN* 3.6 8.4 + - - -
24G ILE* 3.5 42.1 - - + +
25G PHE 3.6 20.4 - - - -
26G SER* 4.0 2.9 - - - -
27G TYR* 3.7 22.0 - + + -
72G LEU 2.9 18.5 + - - +
73G ARG 3.5 4.0 - - - +
74G ILE 3.3 0.2 - - - -
75G ALA* 1.3 77.4 - - - +
77G LEU* 1.3 84.3 + - + +
79G GLU* 3.2 17.7 + - - +
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Residues in contact with LEU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ILE* 3.6 42.2 - - + -
75F ALA* 5.0 1.1 - - - -
78F THR* 4.0 18.3 - - + +
80F ALA* 3.7 30.5 - - + -
101F MET* 4.3 9.2 - - + -
73G ARG* 3.0 32.5 + - + +
74G ILE* 4.0 13.0 - - + +
76G TYR* 1.3 92.2 - - + +
78G THR* 1.3 59.7 + - + +
79G GLU* 3.4 4.7 + - - +
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Residues in contact with THR 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ILE* 2.8 43.2 + - + +
75G ALA* 3.4 5.9 + - - -
77G LEU* 1.3 77.5 - - + +
79G GLU* 1.3 69.2 + - - +
80G ALA* 3.2 14.9 + - - +
77H LEU* 4.0 17.8 - - + +
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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