Contacts of the helix formed by residues 72 - 83 (chain G) in PDB entry 4GTU
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 SER 72 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12G LEU* 3.9 38.8 - - - +
16G ILE* 3.9 5.5 - - - +
60G PRO* 4.3 16.9 - - - +
71G GLN* 1.3 77.6 + - - +
73G ASN* 1.2 73.0 + - - +
75G ILE* 2.9 23.9 + - - +
76G LEU* 2.9 17.4 + - - +
104G MET* 4.1 12.5 - - - +
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Residues in contact with ASN 73 (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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71G GLN* 3.5 0.6 + - - -
72G SER* 1.2 82.8 + - - +
74G ALA* 1.3 54.3 + - - +
76G LEU* 2.8 39.0 + - - +
77G CYS* 2.8 18.0 + - - +
100G GLU* 3.3 40.8 + - - +
101G ASN* 5.0 3.2 - - - +
104G MET* 3.2 42.2 - - - +
158G LEU* 4.1 3.5 - - - +
101H ASN* 3.2 24.6 + - - +
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Residues in contact with ALA 74 (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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69G ILE* 3.7 7.1 - - + +
70G THR 3.2 16.6 - - - +
71G GLN* 2.9 19.1 + - + +
73G ASN* 1.3 78.3 - - - +
75G ILE* 1.3 59.5 + - - +
77G CYS* 3.6 1.2 + - - -
78G TYR* 3.2 23.2 + - - +
97H ASP* 3.6 47.1 - - + +
98H ILE 3.8 0.9 - - - +
101H ASN* 3.8 5.1 - - - +
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Residues in contact with ILE 75 (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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4G LEU* 6.1 2.9 - - + -
16G ILE* 4.1 16.4 - - + -
20G LEU* 6.4 0.2 - - + -
60G PRO* 3.9 20.2 - - + +
61G TYR* 3.8 21.1 - - - +
62G LEU* 3.6 34.1 - - + +
69G ILE* 3.6 37.0 - - + +
71G GLN 2.9 21.3 + - - +
72G SER* 2.9 6.0 + - - +
74G ALA* 1.3 73.6 - - - +
76G LEU* 1.3 66.7 + - - +
78G TYR* 3.3 5.2 + - - +
79G ILE* 3.1 31.2 + - + +
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Residues in contact with LEU 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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15G ALA* 4.4 11.9 - - + -
16G ILE* 3.5 36.1 - - + +
19G LEU* 3.6 26.8 - - + +
72G SER* 2.9 13.1 + - - +
73G ASN* 2.8 33.5 + - - +
75G ILE* 1.3 73.7 - - - +
77G CYS* 1.3 64.6 + - - +
79G ILE* 3.1 5.0 + - - +
80G ALA* 2.9 23.6 + - - +
104G MET* 5.7 1.1 - - + -
154G PHE* 4.1 22.4 - - + +
157G PHE* 6.0 1.8 - - + -
158G LEU* 4.3 23.6 - - + -
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Residues in contact with CYS 77 (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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73G ASN 2.8 12.8 + - - +
74G ALA* 3.8 3.4 - - - +
76G LEU* 1.3 71.6 - - - +
78G TYR* 1.3 63.2 + - - +
80G ALA* 3.0 11.5 + - - +
81G ARG* 3.0 31.4 + - + +
86G CYS* 5.9 5.3 - - - -
100G GLU* 3.7 25.1 - - - -
154G PHE* 4.2 15.4 - - - -
97H ASP* 3.1 33.0 - - - +
100H GLU* 5.8 1.8 - - - -
101H ASN* 6.1 1.6 - - - -
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Residues in contact with TYR 78 (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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2G MET* 5.1 2.7 - - - -
62G LEU* 4.0 17.9 - - + -
64G ASP* 2.8 44.2 + - + +
67G HIS* 4.0 9.7 + + + -
69G ILE* 3.7 28.0 - - + -
74G ALA 3.2 12.7 + - - +
75G ILE* 3.4 8.7 - - - +
76G LEU 3.2 0.2 - - - -
77G CYS* 1.3 80.8 - - - +
79G ILE* 1.3 66.6 + - + +
81G ARG* 3.4 37.4 + - - +
82G LYS* 3.5 37.4 + - + +
90H GLU* 4.8 9.0 - - + -
94H ILE* 3.7 22.7 - - + -
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Residues in contact with ILE 79 (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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2G MET* 5.7 4.3 - - + -
16G ILE* 4.8 5.8 - - + +
19G LEU* 4.0 28.3 - - + -
20G LEU* 3.9 36.3 - - + -
23G THR* 4.3 4.9 - - - +
25G SER* 4.7 1.1 - - - +
62G LEU* 4.2 8.1 - - + -
75G ILE* 3.1 30.3 + - + +
76G LEU* 3.8 4.0 - - - +
78G TYR* 1.3 85.5 - - + +
80G ALA* 1.3 67.8 + - - +
82G LYS* 3.0 19.2 + - + +
83G HIS* 3.4 34.4 - - + +
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Residues in contact with ALA 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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19G LEU* 4.7 3.1 - - - +
76G LEU 2.9 12.9 + - - +
77G CYS* 3.1 14.4 - - - +
79G ILE* 1.3 78.1 - - - +
81G ARG* 1.3 49.8 + - - +
83G HIS* 2.9 3.3 + - - -
84G ASN* 2.6 33.9 + - - -
85G LEU* 3.1 25.9 + - + -
86G CYS* 4.6 6.3 - - + -
154G PHE* 3.6 31.0 - - + -
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Residues in contact with ARG 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 CYS* 3.0 19.2 + - + +
78G TYR* 3.4 36.6 - - - +
79G ILE 3.3 0.4 - - - -
80G ALA* 1.3 75.2 - - + +
82G LYS* 1.3 58.0 + - - +
83G HIS 3.2 4.2 + - - -
84G ASN* 3.4 22.6 + - - +
86G CYS* 5.3 8.2 - - + +
90H GLU* 2.8 48.2 + - - +
93H LYS* 3.3 34.5 - - + +
94H ILE* 3.6 29.7 - - - +
97H ASP* 2.6 33.5 + - - +
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Residues in contact with LYS 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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2G MET* 4.8 5.1 - - - -
64G ASP* 3.2 28.5 + - - -
78G TYR* 3.5 41.5 + - + +
79G ILE* 3.0 12.2 + - + +
81G ARG* 1.3 75.8 - - - +
83G HIS* 1.3 78.7 + - + +
90H GLU* 4.6 12.6 - - - +
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Residues in contact with HIS 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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19G LEU* 5.8 0.7 - - + -
23G THR* 3.2 37.1 + - + -
25G SER* 3.0 26.7 + - - -
79G ILE* 3.4 30.2 - - + +
80G ALA* 2.9 4.2 + - - +
82G LYS* 1.3 95.7 + - + +
84G ASN* 1.3 70.6 + - - +
85G LEU* 3.1 26.9 + - + +
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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
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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