Contacts of the helix formed by residues 79 - 88 (chain D) in PDB entry 2CNW
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 ASP 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D GLU* 3.2 35.1 + - - +
78D PRO* 1.3 82.7 - - + +
80D GLU* 1.3 62.0 + - - +
81D ARG* 3.1 33.9 + - - +
82D ARG* 3.4 14.1 + - + +
83D ALA* 4.3 5.7 + - - +
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Residues in contact with GLU 80 (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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80B GLU* 3.5 32.2 - - + +
83B LYS* 6.2 2.0 - - - +
79D ASP* 1.3 73.4 - - - +
81D ARG* 1.3 75.4 + - - +
82D ARG 3.3 1.1 - - - -
83D ALA* 3.0 11.9 + - + +
84D THR* 2.7 40.6 + - - +
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Residues in contact with ARG 81 (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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62B LYS* 6.3 1.2 - - - +
73B VAL* 4.0 33.7 - - - +
76B ALA* 3.4 18.9 - - - +
77B THR* 3.4 23.6 + - - +
80B GLU* 3.0 37.3 + - - -
79D ASP* 3.1 12.9 + - - +
80D GLU* 1.3 86.6 + - - +
82D ARG* 1.3 57.3 + - - +
84D THR* 3.3 1.2 + - - -
85D LEU* 3.0 44.5 + - + +
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Residues in contact with ARG 82 (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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77D GLU* 3.3 16.6 + - - +
79D ASP* 3.4 13.1 + - - +
80D GLU 3.3 0.6 - - - -
81D ARG* 1.3 78.6 - - - +
83D ALA* 1.3 58.1 + - - +
85D LEU* 3.4 9.2 + - + +
86D ARG* 2.9 64.9 + - + +
93D GLN* 5.6 2.8 - - - +
94D LYS* 2.6 34.2 + - - +
95D PRO* 4.2 12.3 + - - +
294D PRO* 5.7 4.0 - - - +
295D GLU* 6.0 0.4 - - - -
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Residues in contact with ALA 83 (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 GLY* 6.6 0.4 - - - -
77D GLU* 6.4 0.9 - - + -
79D ASP 4.3 3.5 + - - +
80D GLU* 3.0 17.4 + - + +
82D ARG* 1.3 75.9 - - - +
84D THR* 1.3 56.0 + - - +
86D ARG* 3.3 25.5 + - - +
87D LYS* 2.8 38.4 + - - +
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Residues in contact with THR 84 (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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76B ALA* 3.8 20.4 - - + +
79B TYR* 4.3 16.0 - - + -
80B GLU* 2.9 34.1 + - + +
80D GLU* 2.7 20.5 + - - +
81D ARG 3.3 8.7 + - - -
83D ALA* 1.3 72.8 - - - +
85D LEU* 1.3 56.9 + - - +
87D LYS* 3.7 8.2 - - - +
88D LEU* 2.9 49.9 + - + +
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Residues in contact with LEU 85 (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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72B GLU* 3.8 42.4 - - + +
76B ALA* 4.2 9.9 - - + -
81D ARG* 3.0 40.0 + - + +
82D ARG* 3.9 7.9 - - + +
84D THR* 1.3 73.5 - - - +
86D ARG* 1.3 63.2 + - - +
88D LEU* 3.4 4.6 + - + -
89D GLY 3.2 3.8 + - - -
90D PHE* 2.9 60.0 + - + +
93D GLN 5.5 7.9 - - - +
94D LYS* 6.0 1.3 - - - +
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Residues in contact with ARG 86 (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 VAL* 3.6 27.6 - - - +
74D GLY* 6.2 0.2 - - - -
77D GLU* 2.6 35.6 + - - +
82D ARG* 2.9 41.4 + - + +
83D ALA* 3.3 38.7 - - - +
85D LEU* 1.3 75.3 - - - +
87D LYS* 1.3 57.1 + - - +
89D GLY* 2.9 22.3 + - - -
90D PHE 4.2 6.1 + - - +
93D GLN* 6.3 2.9 - - + -
294D PRO* 4.8 3.0 - - - +
295D GLU* 3.9 31.8 + - - +
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Residues in contact with LYS 87 (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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4B GLN* 5.5 4.2 + - - -
79B TYR* 3.6 35.1 + - + +
285B GLU* 3.0 37.4 + - - +
70D GLU* 5.9 2.3 + - - -
83D ALA 2.8 22.6 + - - +
84D THR* 3.7 10.1 - - - +
86D ARG* 1.3 70.3 - - + +
88D LEU* 1.3 63.3 + - + +
89D GLY* 3.2 5.9 + - - -
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Residues in contact with LEU 88 (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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5B LEU* 5.1 10.5 - - + -
75B LEU* 3.8 39.5 - - + +
76B ALA* 4.2 12.8 - - + +
79B TYR* 4.3 24.0 - - + -
292B LEU* 6.2 0.7 - - + -
84D THR* 2.9 38.8 + - + +
85D LEU* 3.9 5.6 - - - +
86D ARG 3.2 0.4 - - - -
87D LYS* 1.3 80.3 - - + +
89D GLY* 1.3 60.4 + - - +
90D PHE* 3.4 22.3 + - + -
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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