Contacts of the helix formed by residues 72 - 79 (chain C) in PDB entry 2GTP
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C GLN 4.1 1.4 + - - -
69C TRP 3.3 9.9 - - - +
71C GLN* 1.3 83.6 - - - +
73C LEU* 1.3 66.4 + - - +
74C GLU* 4.0 11.8 + - - +
75C LYS* 3.4 26.7 + - - +
76C LEU 3.2 15.6 + - - -
166C TYR* 5.5 0.2 - - - -
170C GLU* 5.7 2.9 - - - -
174C TYR* 3.3 12.7 + - - -
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C SER* 1.3 71.6 - - - +
74C GLU* 1.3 60.6 + - - +
76C LEU* 3.2 7.6 + - + +
77C LEU* 2.9 48.8 + - + +
86C PHE* 3.9 21.3 - - + -
166C TYR* 3.6 31.8 + - + +
169C MET* 3.9 8.5 - - + -
170C GLU* 3.6 48.0 + - + +
174C TYR* 3.8 32.8 - - + -
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Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C SER* 3.2 9.6 + - - +
73C LEU* 1.3 77.1 - - - +
75C LYS* 1.3 59.4 + - + +
77C LEU* 3.4 3.2 + - - +
78C ALA* 2.9 30.4 + - + +
166C TYR* 2.9 24.4 + - + +
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLU* 4.4 4.3 - - - +
68C GLN* 3.9 28.7 - - + +
69C TRP* 3.9 11.4 + - + -
71C GLN* 4.8 6.1 - - + -
72C SER* 3.4 22.1 + - - +
74C GLU* 1.3 81.0 - - + +
76C LEU* 1.3 65.0 + - - +
78C ALA* 3.3 19.8 + - + +
79C ASN 4.3 1.4 + - - -
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TRP* 3.6 45.4 + - + +
72C SER 3.2 12.9 + - - +
73C LEU* 3.2 15.3 + - + +
75C LYS* 1.3 79.3 - - - +
77C LEU* 1.3 61.1 + - + +
78C ALA 3.6 0.2 + - - -
79C ASN 3.8 3.5 + - - +
82C GLY* 3.3 39.1 - - - +
83C GLN 3.8 0.3 + - - -
86C PHE* 3.8 19.1 - - + -
174C TYR* 3.8 18.4 - - + -
177C PHE* 3.4 34.5 - - + -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 2.9 47.1 + - + +
74C GLU* 3.6 3.6 - - - +
76C LEU* 1.3 74.6 - - + +
78C ALA* 1.3 65.0 + - - +
79C ASN 3.1 3.4 - - - -
83C GLN* 3.2 34.1 + - + -
86C PHE* 3.9 13.5 - - + -
99C ILE* 3.8 31.2 - - + -
102C TRP* 3.9 37.0 - - + -
166C TYR* 4.2 11.4 - - + -
169C MET* 4.4 12.3 - - + -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLU* 6.0 0.2 - - - +
74C GLU* 2.9 18.2 + - + +
75C LYS* 3.4 14.6 - - - +
76C LEU 3.3 0.8 - - - -
77C LEU* 1.3 79.0 - - - +
79C ASN* 1.3 60.1 + - + +
80C GLN 4.4 0.2 + - - -
83C GLN* 4.7 2.4 + - - -
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Residues in contact with ASN 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 4.9 3.3 - - - +
65C GLU* 4.4 20.6 - - - +
69C TRP* 4.4 3.5 - - - -
75C LYS 5.1 0.7 - - - +
76C LEU 3.8 4.9 + - - +
78C ALA* 1.3 83.0 - - + +
80C GLN* 1.3 63.9 + - - +
81C THR* 2.7 39.4 + - - +
82C GLY* 3.0 8.8 + - - +
83C GLN* 3.0 32.5 + - - +
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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