Contacts of the helix formed by residues 61 - 70 (chain D) in PDB entry 2GVG
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 GLY 61 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D TYR* 1.3 81.3 - - - +
62D LEU* 1.3 65.0 + - - +
63D GLN 3.3 2.5 - - - -
64D TYR* 3.0 23.0 + - - +
65D ILE* 3.3 13.6 + - - +
121D GLU* 2.9 10.5 + - - -
155D SER* 5.2 1.3 - - - -
158D PRO* 3.9 17.1 - - - +
206D ILE* 6.1 0.2 - - - -
231D TYR* 3.3 10.1 - - - -
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Residues in contact with LEU 62 (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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59D PHE* 3.8 20.8 - - + -
60D TYR 3.7 2.4 + - - -
61D GLY* 1.3 75.5 - - - +
63D GLN* 1.3 52.6 + - - +
65D ILE* 2.8 17.1 + - + +
66D LEU* 2.8 57.2 + - + +
116D ILE* 4.3 9.4 - - + -
118D ALA* 3.9 28.5 - - + -
121D GLU* 3.1 8.4 + - - +
132D PHE* 4.5 11.7 - - + -
152D LEU* 3.7 22.9 - - + -
155D SER* 5.0 6.0 - - - -
461D VAL* 4.0 20.2 - - + -
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Residues in contact with GLN 63 (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 GLY 3.3 0.2 - - - -
62D LEU* 1.3 72.0 - - - +
64D TYR* 1.3 61.7 + - - +
66D LEU* 4.2 12.3 - - + +
67D ASN* 2.9 45.1 + - - +
121D GLU* 2.7 19.7 + - - +
230D TYR* 2.8 23.6 - - - +
231D TYR* 3.3 19.0 - - + +
467D VAL* 5.4 2.2 - - + -
469D LYS 4.4 3.1 + - - +
470D SER* 3.3 22.0 - - - +
471D TYR* 2.8 54.7 + - - +
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Residues in contact with TYR 64 (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 GLY* 3.0 13.1 + - - +
63D GLN* 1.3 80.5 - - - +
65D ILE* 1.3 74.3 + - + +
67D ASN* 4.0 0.9 - - - +
68D LYS* 3.0 50.4 + - + +
69D TYR* 4.6 6.7 - + - -
158D PRO* 6.2 0.4 - - + -
202D GLU* 2.7 34.2 + - - +
206D ILE* 3.4 35.3 - - + +
226D LEU* 3.4 35.4 - - + +
230D TYR* 3.7 33.8 - + - -
231D TYR* 3.5 14.9 + - + +
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Residues in contact with ILE 65 (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 GLY 3.3 11.0 + - - +
62D LEU* 2.8 12.0 + - + +
64D TYR* 1.3 90.7 - - + +
66D LEU* 1.3 63.6 + - - +
69D TYR* 3.0 31.1 + - + +
70D LEU* 3.5 10.9 + - + +
151D ILE* 3.7 41.5 - - + +
152D LEU* 4.3 18.8 - - + +
154D GLN* 4.3 5.6 - - + +
155D SER* 3.8 35.2 - - - +
158D PRO* 5.7 2.7 - - + -
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Residues in contact with LEU 66 (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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62D LEU* 2.8 47.5 + - + +
63D GLN* 3.8 13.2 - - + +
65D ILE* 1.3 72.5 - - - +
67D ASN* 1.3 59.9 + - - +
70D LEU* 3.0 22.5 + - + -
71D LYS* 2.8 30.7 + - - +
116D ILE* 3.8 25.8 - - + -
461D VAL* 3.7 39.5 - - + +
462D PHE* 4.0 17.4 - - + -
467D VAL* 5.0 10.3 - - + -
469D LYS 5.7 0.4 - - - +
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Residues in contact with ASN 67 (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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63D GLN* 2.9 40.8 + - - +
66D LEU* 1.3 82.9 - - - +
68D LYS* 1.3 60.6 + - - +
71D LYS* 2.8 58.0 + - - +
230D TYR* 3.7 26.2 + - + -
467D VAL* 3.7 19.4 - - - +
470D SER* 4.9 1.8 + - - -
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Residues in contact with LYS 68 (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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9D PHE* 5.1 1.6 - - - -
64D TYR* 3.0 50.2 + - + +
67D ASN* 1.3 78.2 - - - +
69D TYR* 1.3 101.1 + - + +
202D GLU* 3.6 4.0 - - - -
229D LYS* 5.6 2.0 - - - +
230D TYR* 3.5 27.2 + - + +
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Residues in contact with TYR 69 (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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9D PHE* 3.6 51.5 - + + -
11D ILE* 4.2 3.6 - - - +
64D TYR* 4.6 6.7 - + - -
65D ILE* 3.0 22.5 + - + +
68D LYS* 1.3 119.4 - - + +
70D LEU* 1.3 65.8 + - + +
71D LYS 3.7 1.3 - - - -
74D VAL* 3.6 15.8 - - - +
151D ILE* 3.5 34.3 - - + -
154D GLN* 5.7 1.6 - - - -
202D GLU* 2.5 36.7 + - - -
201E GLN* 3.5 17.7 - - + +
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Residues in contact with LEU 70 (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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11D ILE* 3.7 22.4 - - + -
65D ILE* 3.5 12.1 + - + +
66D LEU* 3.0 24.8 + - + +
69D TYR* 1.3 87.1 - - + +
71D LYS* 1.3 64.3 + - - +
72D GLY 3.9 1.9 + - - +
74D VAL* 3.7 11.0 - - - +
112D LEU* 3.9 14.0 - - + +
116D ILE* 4.3 8.5 - - + -
148D ILE* 4.3 11.0 - - + -
151D ILE* 4.0 19.3 - - + -
152D LEU* 3.9 30.5 - - + -
462D PHE* 3.3 29.5 - - + -
465D GLY* 4.6 0.7 - - - -
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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