Contacts of the helix formed by residues 61 - 78 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 2.9 32.0 + - - +
32D ALA* 3.9 2.0 - - - +
33D GLY* 3.3 17.4 - - - +
36D GLU* 3.5 19.3 - - - +
56H GLN 4.0 0.7 - - - +
57H HIS* 3.2 18.2 - - + -
58H ILE* 2.8 39.3 + - + +
60H SER* 1.3 79.4 - - - +
62H LYS* 1.3 64.6 + - - +
63H LYS 3.3 0.2 - - - -
64H ALA* 3.1 3.9 + - - +
65H ILE* 2.8 34.7 + - + +
4J GAL 3.1 24.4 + - - -
5J SIA 4.3 2.9 + - - -
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Residues in contact with LYS 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LYS* 4.9 14.1 + - - +
53H PRO* 4.2 25.4 - - + +
54H GLY* 4.3 10.5 + - - +
57H HIS* 3.9 31.2 - - + -
58H ILE 4.2 5.2 - - - +
59H ASP* 3.1 29.3 + - - +
61H GLN* 1.3 77.6 - - - +
63H LYS* 1.3 64.3 + - + +
65H ILE* 3.4 7.6 + - + +
66H GLU* 3.3 24.9 + - - +
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Residues in contact with LYS 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D GLU* 4.5 34.3 - - + +
63G LYS* 6.2 1.1 - - - +
59H ASP 4.6 0.8 + - - -
60H SER 4.2 5.2 + - - +
61H GLN 3.3 0.4 - - - -
62H LYS* 1.3 79.1 - - + +
64H ALA* 1.3 57.4 + - - +
66H GLU* 3.3 9.0 + - - +
67H ARG* 2.9 27.6 + - - +
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Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLU* 4.9 0.7 - - - +
30D SER 4.2 3.8 - - - +
31D LEU* 3.8 27.3 - - - +
36D GLU* 4.1 25.4 - - + -
69D LYS* 6.4 0.2 - - - +
60H SER 4.2 2.5 + - - +
61H GLN 3.1 9.6 + - - +
63H LYS* 1.3 77.2 - - - +
65H ILE* 1.3 59.7 + - - +
67H ARG* 3.3 11.6 + - - +
68H MET* 2.9 28.6 + - - +
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Residues in contact with ILE 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 4.1 24.2 - - + -
50H VAL* 3.9 15.4 - - + +
51H GLU 4.3 7.6 - - - +
53H PRO* 4.3 11.7 - - + -
57H HIS* 3.7 45.1 - - + +
61H GLN* 2.8 25.5 + - + +
62H LYS* 3.7 14.8 - - + +
64H ALA* 1.3 76.8 - - - +
66H GLU* 1.3 75.6 + - - +
68H MET* 3.2 3.5 + - - +
69H LYS* 3.2 33.6 + - - +
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Residues in contact with GLU 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LYS* 4.2 41.1 - - + +
64G ALA* 6.0 0.2 - - - -
67G ARG* 3.0 44.6 + - - +
53H PRO* 4.5 7.4 - - - +
62H LYS 3.3 12.8 + - - +
63H LYS* 3.3 9.8 + - - +
64H ALA 3.3 0.4 - - - -
65H ILE* 1.3 84.2 - - - +
67H ARG* 1.3 62.9 + - - +
69H LYS* 2.8 29.7 + - - +
70H ASP* 3.1 15.6 + - - +
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Residues in contact with ARG 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D TYR* 4.8 0.2 - - - -
29D GLU* 3.4 30.2 + - - +
66D GLU* 2.9 54.4 + - - +
69D LYS* 3.6 26.7 + - - +
70D ASP* 2.6 38.5 + - - +
73D ARG* 3.8 12.5 - - - +
63H LYS 2.9 16.6 + - - +
64H ALA* 3.6 10.6 - - - +
66H GLU* 1.3 77.1 - - - +
68H MET* 1.3 57.2 + - - +
70H ASP* 3.1 12.4 + - - +
71H THR* 2.8 30.7 + - - -
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Residues in contact with MET 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLU* 3.4 40.1 + - + +
30D SER 4.6 0.7 - - - -
31D LEU* 3.7 28.3 - - + +
50H VAL* 3.9 17.9 - - + -
64H ALA 2.9 16.2 + - - +
65H ILE 3.2 5.3 + - - +
67H ARG* 1.3 76.9 - - - +
69H LYS* 1.3 57.6 + - - +
71H THR* 3.1 2.9 + - - -
72H LEU* 2.9 42.5 + - + +
96H ILE* 4.1 15.9 - - + -
97H ALA 4.2 2.9 - - - +
98H ALA* 4.1 15.3 - - - -
99H ILE* 3.7 23.1 - - + -
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Residues in contact with LYS 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ALA* 6.3 0.8 - - - +
67G ARG* 3.5 29.7 + - - +
27H TYR* 3.7 11.5 + - - +
29H GLU* 6.1 0.4 - - + -
36H GLU* 4.2 17.6 + - - +
37H MET* 4.6 4.2 - - - +
38H ALA* 3.9 28.3 - - + +
50H VAL* 3.9 20.8 - - + +
51H GLU 5.3 0.8 + - - -
53H PRO* 4.8 4.8 - - - +
65H ILE* 3.2 26.5 + - - +
66H GLU* 2.8 38.3 + - - +
67H ARG 3.2 0.2 - - - -
68H MET* 1.3 77.8 - - - +
70H ASP* 1.3 60.8 + - - +
72H LEU* 3.4 6.3 + - - +
73H ARG* 3.1 24.6 + - - +
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Residues in contact with ASP 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ARG* 3.7 21.3 + - - +
67G ARG* 2.5 34.8 + - - +
70G ASP* 5.6 0.7 - - - +
66H GLU* 3.1 13.2 + - - +
67H ARG* 3.1 13.7 + - - +
69H LYS* 1.3 77.1 - - - +
71H THR* 1.4 62.2 + - - +
73H ARG* 3.4 22.6 + - - +
74H ILE* 3.1 25.6 + - - +
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Residues in contact with THR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D TYR* 4.9 0.9 - - + -
29D GLU* 2.8 34.6 + - - +
73D ARG* 3.0 26.5 + - - +
67H ARG 2.8 8.5 + - - -
68H MET* 3.5 9.2 - - - -
70H ASP* 1.4 74.4 - - - +
72H LEU* 1.3 58.4 + - - +
74H ILE* 3.4 6.8 + - - +
75H ALA* 2.8 28.8 + - - +
99H ILE* 4.3 19.7 - - + -
101H MET* 4.0 26.2 - - + -
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Residues in contact with LEU 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ILE* 3.7 8.5 - - + +
27H TYR* 3.9 16.1 - - + -
38H ALA* 5.1 3.1 - - + -
40H ILE* 4.1 30.5 - - + -
50H VAL* 3.5 32.1 - - + +
68H MET* 2.9 27.4 + - + +
69H LYS* 3.9 4.7 - - - +
70H ASP 3.4 0.2 - - - -
71H THR* 1.3 75.8 - - - +
73H ARG* 1.3 62.6 + - - +
75H ALA* 4.4 2.9 - - - -
76H TYR* 2.9 25.6 + - - +
96H ILE* 3.8 17.7 - - + -
99H ILE* 3.7 29.4 - - + -
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Residues in contact with ARG 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G ARG* 3.7 21.4 + - - +
70G ASP* 3.7 30.9 + - - +
71G THR* 3.0 42.1 + - - +
74G ILE* 4.1 13.1 - - - +
101G MET* 4.8 3.1 - - + -
27H TYR* 3.7 25.9 - - + -
29H GLU* 4.5 2.4 + - - -
69H LYS 3.1 16.5 + - - +
70H ASP* 3.7 27.9 + - - +
72H LEU* 1.3 76.6 - - - +
74H ILE* 1.3 58.7 + - - +
76H TYR* 3.3 3.8 + - - +
77H LEU* 3.0 45.2 + - + +
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Residues in contact with ILE 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ARG* 4.1 15.0 - - - +
74D ILE* 3.9 22.7 - - + -
77D LEU* 3.7 27.4 - - + -
70H ASP 3.1 17.8 + - - +
71H THR* 3.5 11.0 - - - +
73H ARG* 1.3 76.3 - - + +
75H ALA* 1.3 67.2 + - - +
77H LEU* 4.4 8.3 - - + +
78H THR* 2.8 44.1 + - + -
101H MET* 6.4 0.2 - - + -
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Residues in contact with ALA 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 4.9 2.2 - - - -
24H ILE* 4.0 15.1 + - + -
71H THR* 2.8 20.7 + - + +
72H LEU* 3.8 4.3 - - - +
74H ILE* 1.3 77.8 - - - +
76H TYR* 1.3 61.9 + - - +
78H THR* 3.8 5.4 - - - -
79H GLU* 3.0 18.5 + - - -
80H ALA* 3.1 21.4 + - + +
82H VAL* 5.1 2.7 - - + -
99H ILE* 5.4 2.2 - - + -
101H MET* 3.9 26.2 - - + -
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Residues in contact with TYR 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ALA* 5.3 3.1 - - + -
81G LYS 4.7 2.1 + - - -
101G MET* 3.3 28.5 - - + +
102G ALA* 3.1 32.6 + - - -
103G ASN* 3.4 4.3 + - - +
24H ILE* 3.5 42.5 - - + +
25H PHE 3.6 20.2 - - - -
26H SER* 4.0 2.9 - - - -
27H TYR* 3.7 23.1 - - + -
72H LEU 2.9 17.5 + - - +
73H ARG 3.5 4.0 - - - +
74H ILE 3.3 0.2 - - - -
75H ALA* 1.3 76.7 - - - +
77H LEU* 1.3 84.1 + - + +
79H GLU* 3.2 17.5 + - - +
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Residues in contact with LEU 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ILE* 3.6 41.3 - - + -
75G ALA* 5.0 1.1 - - - +
78G THR* 4.0 17.6 - - + +
80G ALA* 3.7 30.5 - - + -
101G MET* 4.3 10.1 - - + -
73H ARG* 3.0 32.3 + - + +
74H ILE* 4.0 9.0 - - + +
76H TYR* 1.3 93.7 - - + +
78H THR* 1.3 62.4 + - + +
79H GLU* 3.7 4.9 + - - +
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Residues in contact with THR 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ILE* 6.4 0.4 - - + -
77D LEU* 3.9 18.5 - - + +
74H ILE* 2.8 41.1 + - + +
75H ALA* 3.4 5.2 + - - -
77H LEU* 1.3 79.7 - - + +
79H GLU* 1.3 68.0 + - - +
80H ALA* 3.2 14.9 + - - +
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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
------------------------------------------------------------
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