Contacts of the helix formed by residues 72 - 79 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D GLN 4.1 1.0 + - - -
69D TRP 3.3 5.7 + - - +
71D GLN* 1.3 81.8 - - - +
73D LEU* 1.3 62.9 + - - +
74D GLU* 3.7 10.2 + - - +
75D LYS* 3.1 31.9 + - - +
76D LEU 3.2 16.1 + - - -
166D TYR* 5.6 0.2 - - - -
170D GLU* 6.0 1.1 - - - -
174D TYR* 3.0 17.3 + - - -
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D SER* 1.3 72.2 - - - +
74D GLU* 1.3 59.3 + - - +
76D LEU* 3.2 6.1 + - + +
77D LEU* 2.9 43.8 + - + +
86D PHE* 4.0 20.6 - - + -
166D TYR* 3.4 37.4 + - + +
169D MET* 4.0 7.2 - - + -
170D GLU* 3.4 49.4 + - + +
174D TYR* 3.5 32.9 - - + -
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Residues in contact with GLU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D SER* 3.2 10.0 - - - +
73D LEU* 1.3 76.8 - - - +
75D LYS* 1.3 59.6 + - + +
77D LEU* 3.5 3.7 + - - +
78D ALA* 2.8 29.7 + - + +
166D TYR* 2.9 22.6 + - + +
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Residues in contact with LYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D GLU* 4.9 1.4 - - - +
68D GLN* 3.6 29.8 - - + +
69D TRP* 3.7 12.3 + - + -
71D GLN* 4.8 6.5 - - + -
72D SER* 3.1 23.3 + - - +
74D GLU* 1.3 78.2 - - + +
76D LEU* 1.3 64.7 + - - +
78D ALA* 3.4 18.9 + - - +
79D ASN* 4.3 3.1 + - - -
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TRP* 3.4 47.9 - - + +
72D SER 3.2 13.4 + - - +
73D LEU* 3.2 11.4 + - + +
75D LYS* 1.3 79.7 - - - +
77D LEU* 1.3 62.1 + - + +
78D ALA 3.6 0.5 + - - -
79D ASN* 3.8 4.9 + - - -
82D GLY* 3.5 33.7 - - - +
83D GLN 3.8 0.2 + - - -
86D PHE* 3.9 20.9 - - + -
174D TYR* 3.8 18.4 - - + -
177D PHE* 3.3 36.1 - - + -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D LEU* 2.9 36.9 + - + +
74D GLU* 3.6 4.0 - - - +
76D LEU* 1.3 76.5 - - + +
78D ALA* 1.3 59.6 + - - +
79D ASN 3.2 3.1 - - - -
83D GLN* 2.9 39.7 + - + -
86D PHE* 3.9 15.3 - - + -
99D ILE* 3.8 26.0 - - + -
102D TRP* 3.8 49.3 - - + -
166D TYR* 4.2 5.4 - - + -
169D MET* 4.1 17.3 - - + -
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D GLU* 2.8 18.4 + - + +
75D LYS* 3.5 14.8 - - + +
76D LEU 3.3 1.0 - - - -
77D LEU* 1.3 79.4 - - - +
79D ASN* 1.3 62.1 + - + +
83D GLN* 4.0 3.8 + - - -
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Residues in contact with ASN 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU* 5.3 2.6 - - - +
65D GLU* 3.2 27.4 - - - +
69D TRP* 3.7 20.2 - - - +
75D LYS 4.3 3.0 + - - +
76D LEU 3.8 5.2 + - - +
78D ALA* 1.3 80.0 - - + +
80D GLN* 1.3 65.7 + - - +
81D THR* 4.5 6.5 - - - +
82D GLY 3.5 15.5 - - - +
83D GLN* 3.1 27.7 + - - +
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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