Contacts of the helix formed by residues 62 - 69 (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 62 (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* 1.3 76.5 - - - +
63C ALA* 1.3 64.1 + - - +
64C ALA* 3.6 11.2 + - - +
65C GLU* 3.1 23.9 + - - +
66C VAL* 3.2 25.8 + - - +
190C LEU* 4.0 7.2 - - - -
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Residues in contact with ALA 63 (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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62C SER* 1.3 70.3 - - - +
64C ALA* 1.3 57.4 + - - +
66C VAL* 3.2 3.2 + - - +
67C MET* 2.7 47.6 + - + +
187C LEU* 4.3 11.4 - - + +
190C LEU* 4.2 17.5 + - + +
191C GLN* 4.3 24.0 - - + -
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Residues in contact with ALA 64 (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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62C SER* 3.3 10.2 + - - +
63C ALA* 1.3 77.0 - - - +
65C GLU* 1.3 60.8 + - - +
67C MET* 4.2 7.5 - - - +
68C GLN* 3.2 30.7 + - + +
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Residues in contact with GLU 65 (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* 3.4 29.8 - - + -
62C SER* 3.1 22.8 + - - +
64C ALA* 1.3 77.2 - - - +
66C VAL* 1.3 61.7 + - - +
68C GLN* 3.1 18.8 + - - +
69C TRP* 2.9 45.3 + - + +
75C LYS 4.4 3.8 - - - +
79C ASN* 4.4 16.7 - - - +
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Residues in contact with VAL 66 (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* 4.3 12.6 - - + -
62C SER 3.2 15.8 + - - +
63C ALA* 3.2 4.5 + - - +
65C GLU* 1.3 73.0 - - - +
67C MET* 1.3 59.0 + - - +
69C TRP* 3.2 31.1 + - + +
183C TYR* 2.5 46.3 + - + -
186C LEU* 3.3 36.1 - - + -
187C LEU* 4.0 23.1 - - + -
190C LEU* 4.8 4.3 - - + -
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Residues in contact with MET 67 (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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63C ALA* 2.7 29.9 + - + +
64C ALA* 4.2 6.1 - - - +
66C VAL* 1.3 72.4 - - - +
68C GLN* 1.3 60.7 + - + +
70C SER* 2.9 31.2 + - - -
71C GLN* 5.0 0.5 - - - +
183C TYR* 3.6 4.5 - - - -
187C LEU* 3.6 24.0 - - + +
191C GLN* 3.0 37.9 - - + +
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Residues in contact with GLN 68 (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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64C ALA* 3.2 18.5 + - + +
65C GLU* 3.1 15.5 + - - +
67C MET* 1.3 77.3 - - + +
69C TRP* 1.3 57.8 + - + +
70C SER 3.1 0.2 - - - -
71C GLN* 2.9 42.0 + - + +
75C LYS* 3.9 17.2 - - + +
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Residues in contact with TRP 69 (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* 4.5 4.7 - - + -
65C GLU* 2.9 43.5 + - + -
66C VAL* 3.2 35.9 - - + +
67C MET 3.1 1.0 + - - -
68C GLN* 1.3 77.7 - - + +
70C SER* 1.3 48.5 + - - +
71C GLN 3.3 0.2 - - - -
72C SER 3.3 12.2 - - - +
75C LYS* 3.9 8.7 + - + -
76C LEU* 3.6 37.3 + - + +
79C ASN* 4.4 5.5 + - - +
81C THR* 4.3 7.0 - - + -
82C GLY* 3.2 34.9 - - - -
85C VAL* 4.2 23.1 - - + -
174C TYR* 2.7 31.7 + - - -
177C PHE* 4.8 1.1 - + - -
178C LEU* 4.3 2.9 - - + -
183C TYR* 3.9 15.9 - + + -
186C LEU* 3.7 25.1 - - + -
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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