Contacts of the helix formed by residues 79 - 93 (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 ASN 79 (chain C).
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Specific contacts
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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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Residues in contact with GLN 80 (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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78C ALA 4.4 0.6 + - - -
79C ASN* 1.3 74.1 - - - +
81C THR* 1.3 66.2 + - - +
83C GLN* 3.5 22.8 + - - +
84C ASN* 3.2 41.2 + - - +
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Residues in contact with THR 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C VAL 5.3 2.8 + - - -
61C LEU* 3.7 36.3 - - + +
69C TRP* 4.3 2.0 - - + -
79C ASN* 2.7 24.5 + - - -
80C GLN* 1.3 75.1 - - - +
82C GLY* 1.3 55.6 + - - +
84C ASN* 3.1 13.1 + - + +
85C VAL* 3.0 36.5 + - + +
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Residues in contact with GLY 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TRP* 3.2 28.4 - - - -
76C LEU* 3.3 24.5 - - - +
79C ASN* 3.0 10.9 + - - -
81C THR* 1.3 72.4 - - - +
83C GLN* 1.3 60.2 + - - +
86C PHE* 3.0 33.1 + - - +
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Residues in contact with GLN 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU 3.8 0.8 + - - -
77C LEU* 3.2 37.8 + - + +
78C ALA 4.7 2.4 + - - -
79C ASN 3.0 20.4 + - - +
80C GLN* 3.5 28.4 + - - +
82C GLY* 1.3 76.1 - - - +
84C ASN* 1.3 54.4 + - - +
87C GLY* 2.7 33.1 + - - -
99C ILE* 3.5 16.7 - - + +
102C TRP* 4.1 6.3 - - - -
103C LEU* 3.7 35.8 - - + +
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Residues in contact with ASN 84 (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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166A ASN* 5.5 6.7 - - - +
80C GLN* 3.2 38.1 + - - +
81C THR* 3.1 12.6 + - + +
83C GLN* 1.3 80.4 - - - +
85C VAL* 1.3 59.6 + - + +
87C GLY* 3.3 1.7 + - - -
88C SER* 2.9 29.8 + - - -
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TRP* 4.2 22.9 - - + -
81C THR* 3.0 25.1 + - + +
82C GLY 4.0 3.4 - - - +
83C GLN 3.3 0.2 - - - -
84C ASN* 1.3 75.0 - - + +
86C PHE* 1.3 65.1 + - - +
88C SER* 3.2 9.3 - - - -
89C PHE* 3.2 16.5 + - - +
177C PHE* 3.7 25.0 - - + -
182C ILE* 3.7 22.2 - - + +
183C TYR* 5.3 0.7 - - - -
186C LEU* 4.9 16.2 - - + -
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Residues in contact with PHE 86 (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* 3.9 18.8 - - + -
76C LEU* 3.8 15.5 - - + -
77C LEU* 3.9 10.8 - - + -
82C GLY 3.0 18.1 + - - +
83C GLN* 3.8 2.5 - - - +
85C VAL* 1.3 74.9 - - - +
87C GLY* 1.3 59.8 + - - +
89C PHE* 3.1 3.0 + + - +
90C LEU* 2.9 53.8 + - + +
99C ILE* 3.8 18.8 - - + -
169C MET* 3.8 28.9 - - + -
173C SER* 4.2 10.8 - - - -
174C TYR* 4.2 12.1 - - + -
177C PHE* 3.7 44.4 - + + -
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Residues in contact with GLY 87 (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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83C GLN 2.7 19.6 + - - -
84C ASN* 3.5 3.1 - - - -
86C PHE* 1.3 76.5 - - - +
88C SER* 1.3 55.8 + - - +
90C LEU* 3.1 5.5 + - - +
91C LYS* 2.9 31.9 + - - +
96C GLU* 4.5 2.5 - - - +
99C ILE* 4.1 21.0 - - - +
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASN 2.9 13.9 + - - -
85C VAL* 3.2 13.6 - - - -
87C GLY* 1.3 75.0 - - - +
89C PHE* 1.3 62.1 + - - +
91C LYS* 3.3 11.3 + - - +
92C SER* 3.2 20.4 + - - -
182C ILE* 4.6 13.7 - - - +
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Residues in contact with PHE 89 (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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85C VAL 3.2 1.8 + - - +
86C PHE* 3.1 9.9 + + - +
88C SER* 1.3 75.6 - - - +
90C LEU* 1.3 77.9 + - + +
92C SER* 2.8 22.6 + - - -
93C GLU* 3.1 47.5 + - + +
173C SER* 3.5 20.2 - - - -
176C ARG* 3.9 8.3 - - + -
177C PHE* 3.5 44.2 - + + -
180C SER* 3.5 31.6 - - - -
182C ILE* 3.7 21.1 - - + -
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Residues in contact with LEU 90 (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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86C PHE* 2.9 40.7 + - + +
87C GLY 3.5 6.7 - - - +
89C PHE* 1.3 82.7 - - + +
91C LYS* 1.3 57.6 + - - +
93C GLU* 3.0 4.3 + - - +
94C PHE 2.8 24.1 + - - -
95C SER* 2.9 38.1 + - - +
96C GLU* 3.7 13.0 - - + -
98C ASN* 6.0 0.4 - - + +
99C ILE* 3.6 38.4 - - + +
169C MET* 4.2 6.1 - - + -
173C SER* 3.7 28.0 - - - +
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Residues in contact with LYS 91 (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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87C GLY 2.9 13.5 + - - +
88C SER* 3.5 12.8 - - - +
89C PHE 3.1 0.2 - - - -
90C LEU* 1.3 76.1 - - - +
92C SER* 1.3 58.5 + - - +
94C PHE* 2.9 30.0 + - - -
96C GLU* 3.9 38.1 - - + +
100C GLU* 5.7 3.4 + - - -
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Residues in contact with SER 92 (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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184B ILE 4.4 2.1 - - - +
88C SER 3.2 7.1 + - - -
89C PHE* 2.8 29.4 + - - -
91C LYS* 1.3 79.7 - - - +
93C GLU* 1.3 59.9 + - - +
94C PHE* 3.4 15.9 + - - -
182C ILE* 4.0 12.3 - - - +
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Residues in contact with GLU 93 (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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182B THR 5.0 0.4 - - - +
183B GLY* 3.1 3.6 - - - -
184B ILE 2.7 40.7 + - - +
185B VAL* 3.6 16.6 - - + +
89C PHE* 3.1 43.9 + - + +
90C LEU* 3.0 8.2 + - - +
92C SER* 1.3 79.5 - - - +
94C PHE* 1.3 67.3 + - - +
95C SER* 4.2 10.0 + - - +
173C SER* 4.5 2.9 - - - -
176C ARG* 2.9 46.8 + - - +
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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