Contacts of the helix formed by residues 57 - 68 (chain B) in PDB entry 5G04
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 MET 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B PRO* 2.9 56.5 + - + +
46B LEU 4.7 1.1 - - - +
47B VAL* 3.8 35.6 - - + +
55B PHE 3.4 2.4 + - - -
56B HIS* 1.3 70.5 - - - +
58B HIS* 1.3 62.2 + - + +
60B ILE* 3.2 4.2 - - - +
61B LEU* 2.9 53.5 + - + +
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Residues in contact with HIS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B CYS* 3.6 17.3 - - - -
36B ASP* 3.7 11.7 - - + +
37B CYS* 4.9 10.4 - - + -
39B VAL* 5.9 0.2 - - + -
43B ASP 3.8 21.8 - - - -
44B CYS* 3.8 12.2 - - - -
45B PRO* 4.6 5.6 - - + +
56B HIS* 3.3 0.6 - - - +
57B MET* 1.3 83.7 - - + +
59B CYS* 1.3 60.5 + - - +
61B LEU* 3.5 17.1 - - + +
62B LYS* 3.2 31.5 + - - +
1087B ZN 3.0 28.0 - - - -
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Residues in contact with CYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.4 28.3 - - + +
26B CYS* 3.6 17.3 - - - -
34B CYS* 3.9 20.4 - - - -
35B PRO* 4.2 2.9 - - - -
36B ASP* 4.9 0.2 - - - -
56B HIS 3.0 6.2 + - - +
58B HIS* 1.3 77.0 - - - +
60B ILE* 1.3 65.0 - - - +
62B LYS* 3.3 20.3 + - - +
63B TRP* 3.2 16.6 + - - +
1085B ZN 2.7 34.8 - - - -
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.5 14.3 - - + +
47B VAL* 3.4 26.9 - - + -
55B PHE* 3.8 31.2 - - + -
56B HIS 3.0 6.8 + - - +
57B MET* 3.2 11.0 - - - +
59B CYS* 1.3 75.1 - - - +
61B LEU* 1.3 60.8 + - + +
63B TRP* 3.2 10.1 + - + +
64B LEU* 2.8 43.7 + - + +
74B PRO* 3.9 19.5 - - + -
80B TRP* 4.0 26.0 - - + -
82B PHE* 4.2 13.5 - - + -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B MET* 2.9 44.5 + - + +
58B HIS* 3.5 17.9 - - + +
60B ILE* 1.3 85.0 - - + +
62B LYS* 1.3 56.5 + - + +
64B LEU* 3.9 6.4 - - + +
65B HIS* 2.9 31.8 + - - +
82B PHE* 4.7 14.1 - - + -
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 5.7 3.4 - - + -
36B ASP* 2.4 37.8 + - - -
58B HIS* 3.2 25.4 + - - +
59B CYS* 3.3 17.7 + - - +
61B LEU* 1.3 74.1 - - - +
63B TRP* 1.3 61.5 + - - +
65B HIS* 3.8 6.1 + - - +
66B ALA* 2.9 33.7 + - - +
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Residues in contact with TRP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 4.0 16.4 - - + -
59B CYS 3.2 8.5 + - - +
60B ILE* 3.2 10.2 + - + +
62B LYS* 1.3 76.3 - - - +
64B LEU* 1.4 72.8 + - + +
66B ALA* 3.8 4.1 - - - +
67B GLN* 2.9 49.1 + - + +
72B HIS* 2.9 30.5 + - + +
73B CYS 4.8 0.7 - - - -
74B PRO* 3.6 45.9 - - + +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ILE* 2.8 32.2 + - + +
61B LEU* 3.9 8.7 - - + +
63B TRP* 1.4 84.1 - - + +
65B HIS* 1.3 65.2 + - - +
68B GLN* 3.1 34.5 + - + +
71B GLN* 4.1 23.6 - - + +
72B HIS 5.0 0.4 - - - +
80B TRP* 3.8 32.3 - - + +
82B PHE* 3.9 31.0 - - + -
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Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU 2.9 20.3 + - - +
62B LYS* 3.8 6.1 + - - +
64B LEU* 1.3 76.1 - - - +
66B ALA* 1.3 64.6 + - - +
68B GLN 3.8 9.4 - - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LYS 2.9 19.2 + - - +
63B TRP* 3.9 3.6 - - - +
65B HIS* 1.3 81.2 + - - +
67B GLN* 1.4 59.6 + - + +
68B GLN 3.6 0.2 - - - -
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TRP* 2.9 39.6 + - + +
66B ALA* 1.4 73.6 - - + +
68B GLN* 1.3 59.3 + - + +
69B VAL* 3.9 7.9 - - - +
70B GLN* 3.4 17.5 + - - +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.1 29.4 + - + +
65B HIS* 3.8 9.5 - - - +
66B ALA 3.6 0.4 - - - -
67B GLN* 1.3 78.1 - - - +
69B VAL* 1.3 66.1 + - - +
70B GLN 3.2 19.5 - - - +
71B GLN* 4.1 13.0 - - + -
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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