Contacts of the helix formed by residues 67 - 76 (chain D) in PDB entry 2G4C
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 GLU 67 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ALA* 1.3 68.0 + - + +
69D LEU* 3.2 10.4 + - - +
70D LEU* 3.1 26.6 - - - +
71D GLU* 2.8 31.2 + - - +
83D LYS* 5.9 0.5 - - - -
294D PRO* 6.1 1.0 - - - +
295D TRP* 5.9 0.2 - - - -
351D TYR* 3.7 27.5 + - - -
354D PHE* 5.0 3.6 - - - -
355D GLN* 5.3 8.7 + - - +
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Residues in contact with ALA 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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67D GLU* 1.3 82.3 + - + +
69D LEU* 1.3 59.7 + - - +
71D GLU* 4.1 4.9 - - - +
72D ILE* 3.0 33.4 + - - +
354D PHE* 3.6 21.1 - - + -
370D LYS* 4.2 18.0 + - - +
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Residues in contact with LEU 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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67D GLU* 3.2 8.9 + - - +
68D ALA* 1.3 79.7 - - - +
70D LEU* 1.3 59.5 + - - +
72D ILE* 3.3 3.5 + - - +
73D CYS* 2.8 51.0 + - - -
350D LEU* 3.7 11.0 - - + +
351D TYR* 3.3 62.8 - - + +
354D PHE* 3.2 45.2 - - + -
372D LEU* 4.3 15.0 - - + -
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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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67D GLU* 3.1 24.4 + - - +
68D ALA 3.5 0.2 - - - -
69D LEU* 1.3 77.4 - - - +
71D GLU* 1.3 69.6 + - - +
73D CYS* 3.2 11.7 + - + +
74D GLN* 3.0 29.2 + - + +
79D LEU* 5.2 2.9 - - + -
83D LYS* 5.0 13.7 - - + -
86D LEU* 3.6 44.9 - - + +
87D SER* 6.0 0.9 - - - -
91D LEU* 4.0 13.7 - - + -
351D TYR* 5.2 12.3 + - + +
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Residues in contact with GLU 71 (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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67D GLU 2.8 19.1 + - - +
68D ALA* 4.2 5.6 - - - +
70D LEU* 1.3 76.6 - - - +
72D ILE* 1.3 53.9 + - + +
74D GLN* 2.8 24.1 + - - +
75D ARG* 2.6 83.8 + - - +
83D LYS* 3.2 31.6 + - - +
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Residues in contact with ILE 72 (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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68D ALA 3.0 23.3 + - - +
69D LEU* 3.3 5.1 + - - +
71D GLU* 1.3 74.4 - - + +
73D CYS* 1.3 54.3 + - - +
74D GLN 2.8 10.1 + - - -
75D ARG* 3.0 12.2 + - - +
76D ARG* 2.6 34.4 + - + +
354D PHE* 3.4 29.6 - - + -
370D LYS* 3.9 24.0 - - + -
372D LEU* 3.7 26.2 - - + -
434D GLU* 3.1 44.0 - - + +
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Residues in contact with CYS 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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69D LEU* 2.8 42.3 + - - +
70D LEU* 3.4 10.1 - - + +
72D ILE* 1.3 72.2 - - - +
74D GLN* 1.3 57.1 + - - +
78D PHE* 2.6 43.2 + - - -
79D LEU* 2.8 33.7 + - + -
350D LEU* 3.4 35.4 - - - -
372D LEU* 5.1 1.1 - - - -
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Residues in contact with GLN 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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70D LEU* 3.0 15.8 + - + +
71D GLU* 2.8 19.3 + - - +
72D ILE 2.8 1.4 + - - -
73D CYS* 1.3 76.5 - - - +
75D ARG* 1.3 69.1 + - - +
77D HIS* 2.9 19.8 + - - -
79D LEU* 3.8 18.3 - - + +
81D GLY 4.2 19.3 + - - +
82D SER* 5.5 0.4 - - - +
83D LYS* 3.7 37.8 + - - +
86D LEU* 6.4 1.6 - - + -
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Residues in contact with ARG 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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198B ASP* 4.8 2.6 - - - +
71D GLU* 2.6 49.0 + - - +
72D ILE* 3.9 11.2 - - - +
74D GLN* 1.3 75.5 - - + +
76D ARG* 1.3 81.9 + - + +
77D HIS* 3.4 19.1 + - - -
370D LYS* 5.4 8.1 - - - +
434D GLU* 3.3 30.1 + - - -
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Residues in contact with ARG 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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72D ILE* 2.6 23.1 + - + +
73D CYS 4.2 0.4 - - - -
75D ARG* 1.3 107.9 + - + +
77D HIS* 1.3 70.1 + - - +
78D PHE* 3.5 6.5 + - + -
102D LEU* 3.0 21.7 - - - +
431D LYS* 3.0 50.4 + - - +
434D GLU* 3.3 58.6 + - + +
435D MET* 3.5 25.0 - - + +
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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