Contacts of the helix formed by residues 54 - 67 (chain G) in PDB entry 1V8O
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 TRP 54 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G LEU* 4.7 9.0 - - + -
47G ALA* 3.5 32.5 - - + -
51G ARG* 3.6 17.1 + - + +
52G VAL* 4.2 6.1 + - - -
53G ASP* 1.3 81.7 + - - +
55G ALA* 1.3 91.7 + - + +
56G ALA 3.1 0.4 - - - -
57G ALA* 3.6 9.2 - - - +
58G SER* 2.5 39.1 + - - -
77H ASP 5.2 0.9 - - - -
80H MSE 3.6 21.5 - - + -
81H ARG* 3.6 50.3 - - + -
84H VAL* 4.0 29.8 - - + +
85H GLU* 5.5 4.0 - - + -
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Residues in contact with ALA 55 (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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52G VAL 5.4 0.4 - - - +
53G ASP 2.3 20.7 + - - +
54G TRP* 1.3 101.7 - - + +
56G ALA* 1.3 56.9 + - - +
58G SER* 2.8 17.6 + - - -
59G ARG* 3.1 25.5 + - - +
77H ASP* 4.6 0.7 - - - +
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Residues in contact with ALA 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ASP* 3.4 17.7 + - - +
55G ALA* 1.3 77.7 - - - +
57G ALA* 1.3 67.3 + - - +
58G SER 3.2 0.4 - - - -
59G ARG* 3.2 35.7 + - - +
60G HIS* 3.2 11.6 + - - +
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Residues in contact with ALA 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU* 3.9 12.9 - - + +
51G ARG* 3.5 31.9 - - - +
53G ASP* 3.9 3.9 - - + +
54G TRP* 3.2 21.6 + - - +
56G ALA* 1.3 80.4 - - - +
58G SER* 1.3 61.9 + - - +
60G HIS* 3.2 9.6 + - - +
61G LEU* 3.0 22.7 + - - +
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Residues in contact with SER 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU* 3.6 11.2 - - - +
54G TRP* 2.5 20.2 + - - -
55G ALA* 2.8 25.1 + - - -
57G ALA* 1.3 70.5 - - - +
59G ARG* 1.3 62.8 + - - +
61G LEU 3.3 0.3 + - - -
62G LYS* 2.9 21.5 + - - +
76H LEU* 3.3 25.1 - - - +
77H ASP* 3.4 16.8 + - - -
80H MSE 3.9 23.3 - - - +
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Residues in contact with ARG 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ALA* 3.1 19.1 + - - +
56G ALA* 3.2 41.7 + - - +
58G SER* 1.3 82.8 + - - +
60G HIS* 1.3 61.6 + - - +
62G LYS* 3.1 11.9 + - + +
63G LYS* 3.0 42.2 + - - +
77H ASP* 3.6 24.5 - - - +
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Residues in contact with HIS 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ALA* 3.7 23.4 + - + +
19G TYR* 5.3 8.5 - + + +
56G ALA 3.2 8.2 + - - +
57G ALA* 3.2 12.7 + - - +
59G ARG* 1.3 77.7 - - - +
61G LEU* 1.3 64.6 + - - +
63G LYS* 3.0 13.9 + - + +
64G VAL* 3.0 42.3 + - + +
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Residues in contact with LEU 61 (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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12G LEU* 3.8 23.8 - - + -
13G TYR* 4.8 11.0 - - + -
16G ALA* 5.4 5.8 - - + -
39G ALA* 3.7 26.9 - - + +
43G LEU* 4.0 22.9 - - + -
57G ALA 3.0 12.7 + - - +
58G SER 3.6 7.6 - - - +
60G HIS* 1.3 76.9 + - - +
62G LYS* 1.3 56.3 + - - +
64G VAL* 3.1 8.7 + - + +
65G MSE 2.8 53.7 + - + +
76H LEU* 3.4 25.1 - - + -
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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
----------------------------------------------------------
58G SER 2.9 13.2 + - - +
59G ARG* 3.1 12.8 + - + +
61G LEU* 1.3 76.2 - - - +
63G LYS* 1.3 64.5 + - + +
65G MSE 3.5 7.6 - - - +
66G SER* 3.1 23.6 + - - -
75H PRO* 4.0 18.0 - - + +
76H LEU* 4.3 15.3 - - + +
77H ASP* 3.5 42.0 + - + +
78H GLU* 5.6 1.0 - - - +
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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
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19G TYR* 5.2 6.2 + - + +
59G ARG* 3.0 33.9 + - - +
60G HIS* 3.0 12.7 + - + +
62G LYS* 1.3 75.3 - - + +
64G VAL* 1.3 67.0 + - + +
66G SER* 2.6 24.3 + - - +
67G SER* 3.3 8.5 + - - -
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Residues in contact with VAL 64 (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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12G LEU* 4.3 10.3 - - + -
16G ALA* 4.2 21.1 - - + +
19G TYR* 4.2 17.0 - - + -
22G TRP* 3.4 27.6 - - + -
60G HIS* 3.0 41.2 + - + +
61G LEU* 3.6 8.5 - - + +
63G LYS* 1.3 74.9 - - + +
65G MSE 1.3 59.1 + - - +
67G SER* 2.8 33.4 + - - -
68G PHE* 3.1 16.5 - - + -
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Residues in contact with MSE 65 (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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12G LEU* 3.1 43.5 - - + -
31G ILE* 3.8 24.9 - - + +
35G THR* 4.5 5.4 - - + -
36G ILE* 3.7 41.5 - - + +
39G ALA* 4.2 11.2 - - + -
61G LEU* 2.8 39.4 + - + +
62G LYS* 3.5 8.1 - - - +
64G VAL* 1.3 72.6 - - - +
66G SER* 1.3 63.9 + - - +
68G PHE* 2.9 24.1 + - + +
70G VAL* 5.8 0.5 - - - +
76H LEU* 4.5 7.9 - - + -
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Residues in contact with SER 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ARG* 4.3 4.9 + - - -
62G LYS* 3.1 11.4 + - - -
63G LYS* 2.6 24.8 + - - -
65G MSE 1.3 76.7 - - - +
67G SER* 1.3 61.0 + - - +
68G PHE 3.1 9.0 + - - +
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Residues in contact with SER 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G TYR* 3.7 19.9 + - - -
22G TRP* 3.7 22.2 - - - -
23G ILE* 5.3 1.6 - - - +
26G ARG* 3.3 47.8 + - - +
27G GLU 4.6 1.0 + - - -
63G LYS 3.3 8.5 + - - -
64G VAL* 2.8 20.1 + - - -
66G SER* 1.3 80.6 + - - +
68G PHE* 1.3 58.2 + - - +
69G LYS 4.2 0.2 + - - -
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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