Contacts of the helix formed by residues 72 - 83 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E ASN* 5.5 0.2 + - - -
12F LEU* 4.2 28.2 - - - +
16F ILE* 4.5 6.4 - - - +
60F PRO* 4.6 10.1 - - - +
71F GLN* 1.3 78.2 + - - +
73F ASN* 1.3 63.4 + - - -
75F ILE* 3.0 17.4 + - - +
76F LEU* 2.8 37.4 + - - +
104F MET* 4.0 23.2 - - - +
158F LEU* 6.5 0.2 - - - -
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Residues in contact with ASN 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ASN* 5.8 1.0 - - - +
101E ASN* 2.8 30.0 + - - +
71F GLN 3.3 0.6 - - - -
72F SER* 1.3 80.9 + - - +
74F ALA* 1.3 52.9 + - - +
76F LEU* 2.8 41.1 + - - +
77F CYS* 2.9 18.9 + - - +
100F GLU* 3.6 34.3 + - - +
101F ASN* 4.6 5.3 - - - +
104F MET* 3.7 36.9 - - - +
154F PHE* 6.3 0.4 - - + -
158F LEU* 4.3 4.2 - - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ILE* 5.6 1.2 - - - +
97E ASP* 4.0 32.9 - - + +
98E ILE* 4.1 11.4 - - + +
101E ASN* 4.2 4.0 - - - +
69F ILE* 3.7 13.4 - - + +
70F THR 3.2 21.5 - - - +
71F GLN* 2.9 11.5 + - + +
73F ASN* 1.3 75.3 - - - +
75F ILE* 1.3 62.0 + - - +
77F CYS* 3.7 2.5 + - - +
78F TYR* 3.2 21.8 + - - +
81F ARG* 4.5 0.9 + - - -
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Residues in contact with ILE 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 5.1 2.2 - - + -
16F ILE* 3.7 29.8 - - + -
20F LEU* 5.9 0.2 - - + -
60F PRO* 3.6 39.7 - - + +
61F TYR* 3.8 9.2 - - - +
62F LEU* 3.5 42.6 - - + -
69F ILE* 4.0 2.2 - - + +
70F THR 3.8 9.0 - - - +
71F GLN 3.0 17.2 + - - +
72F SER* 3.2 11.0 - - - +
74F ALA* 1.3 74.1 - - - +
76F LEU* 1.3 65.5 + - - +
78F TYR* 3.1 19.2 + - - +
79F ILE* 3.3 8.3 + - + +
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ALA* 4.4 7.6 - - + -
16F ILE* 4.0 24.7 - - + +
19F LEU* 3.4 33.2 - - + +
72F SER* 2.8 18.0 + - - +
73F ASN* 2.8 35.6 + - - +
75F ILE* 1.3 78.5 - - - +
77F CYS* 1.3 63.8 + - - +
79F ILE* 3.3 6.1 + - - +
80F ALA* 3.2 23.0 + - - +
154F PHE* 4.3 18.4 - - + +
157F PHE* 5.8 0.7 - - + -
158F LEU* 3.7 30.3 - - + -
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Residues in contact with CYS 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASP* 3.4 14.1 - - - +
73F ASN 2.9 20.4 + - - +
74F ALA* 4.1 1.1 - - - +
76F LEU* 1.3 72.3 - - - +
78F TYR* 1.3 57.3 + - - +
80F ALA* 3.2 6.6 + - - +
81F ARG* 2.8 54.6 + - - +
86F CYS* 4.4 6.9 - - - -
100F GLU* 4.6 11.7 - - - -
154F PHE* 3.7 31.2 - - - -
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Residues in contact with TYR 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E GLU* 4.0 20.4 - - - -
94E ILE* 3.6 37.7 - - + -
62F LEU* 3.9 20.9 - - + -
64F ASP* 3.2 27.9 + - + -
67F HIS* 3.0 25.2 + + + -
69F ILE* 4.5 11.4 - - + -
74F ALA 3.2 11.9 + - - +
75F ILE* 3.1 12.4 + - - +
77F CYS* 1.3 77.8 - - - +
79F ILE* 1.3 67.8 + - + +
81F ARG* 3.0 30.6 - - - +
82F LYS* 2.9 42.7 + - + +
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Residues in contact with ILE 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F MET* 3.8 31.0 - - + -
16F ILE* 5.9 0.9 - - + -
19F LEU* 3.3 46.2 - - + +
20F LEU* 3.7 20.9 - - + -
23F THR* 4.9 2.0 - - + +
25F SER* 4.8 11.9 - - - +
62F LEU* 4.3 4.0 - - + -
64F ASP* 5.0 2.0 - - - +
75F ILE* 3.3 8.4 + - + +
76F LEU* 3.3 4.0 + - - +
78F TYR* 1.3 94.7 - - + +
80F ALA* 1.3 67.9 + - - +
81F ARG 3.5 0.5 + - - -
82F LYS* 3.5 13.3 + - + +
83F HIS* 3.5 23.8 - - + -
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Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F LEU* 4.0 3.8 - - + -
76F LEU 3.2 13.7 + - - +
77F CYS 3.7 3.1 - - - +
79F ILE* 1.3 80.9 - - - +
81F ARG* 1.3 55.3 + - - +
82F LYS 3.3 0.2 - - - -
83F HIS 3.0 1.3 + - - +
84F ASN* 2.7 32.4 + - - -
85F LEU* 2.9 44.2 + - + +
86F CYS* 4.1 3.5 + - - -
154F PHE* 3.9 20.0 - - + -
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E GLU* 3.1 30.7 + - - +
93E LYS* 3.3 41.8 + - - +
94E ILE* 5.1 3.0 - - - +
97E ASP* 2.9 40.0 + - - -
74F ALA 4.5 1.0 + - - -
77F CYS* 2.8 42.6 + - - +
78F TYR* 3.0 24.0 - - - +
80F ALA* 1.3 76.7 - - - +
82F LYS* 1.3 58.9 + - - +
83F HIS 2.9 6.4 + - - -
84F ASN* 3.2 16.2 + - - +
86F CYS* 4.6 10.3 - - - -
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Residues in contact with LYS 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E GLU* 4.3 14.8 - - - +
64F ASP* 3.8 13.4 + - - +
67F HIS* 4.5 7.1 - - - -
78F TYR* 2.9 47.8 + - + +
79F ILE* 3.5 10.1 + - + +
80F ALA 3.3 0.8 - - - -
81F ARG* 1.3 77.5 - - - +
83F HIS* 1.3 79.3 + - + +
84F ASN 3.8 0.2 - - - -
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Residues in contact with HIS 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F THR* 3.2 50.6 + - + -
25F SER* 3.7 11.4 + - - -
79F ILE* 3.5 19.9 - - + +
80F ALA 3.0 3.3 + - - +
81F ARG 3.0 0.8 - - - -
82F LYS* 1.3 94.6 + - + +
84F ASN* 1.3 66.8 + - - +
85F LEU* 3.0 36.0 + - + +
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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