Contacts of the helix formed by residues 82 - 95 (chain B) in PDB entry 2CX9
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 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B VAL* 3.7 18.4 - - + -
30B ALA* 3.5 13.6 - - - +
33B ARG* 2.8 37.8 + - - +
78B ILE* 2.8 19.5 + - - +
79B ALA 3.7 2.2 + - - -
81B TYR* 1.3 76.4 - - - +
83B GLY* 1.3 66.2 + - - +
84B ALA* 3.1 17.5 + - - +
85B LEU* 2.7 36.1 + - + +
86B ALA* 3.1 17.3 + - - +
357B ARG* 5.1 3.6 - - - +
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ALA 4.0 4.3 + - - -
82B ASP* 1.3 69.8 - - - +
84B ALA* 1.3 58.9 + - - +
86B ALA* 3.1 6.9 + - - +
87B LEU* 2.9 27.7 + - - +
210B LEU* 3.4 16.6 - - - +
255B MET* 3.9 2.1 - - - +
259B LEU* 4.2 22.0 - - - +
357B ARG* 5.5 0.8 - - - +
361B ASP* 3.7 18.8 + - - -
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 6.2 0.2 - - + -
82B ASP* 3.1 9.8 + - - +
83B GLY* 1.3 76.6 - - - +
85B LEU* 1.3 57.4 + - + +
87B LEU* 3.3 4.0 + - - +
88B THR* 3.0 29.8 + - - -
210B LEU* 3.5 23.5 - - - +
212B ALA* 4.1 15.9 - - + +
213B SER* 3.8 29.9 - - - +
361B ASP* 4.3 2.4 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.0 20.0 - - + -
33B ARG* 4.5 0.7 - - - +
40B PRO* 3.7 25.6 - - + -
43B LEU* 3.7 35.2 - - + -
44B VAL* 4.5 13.7 - - + -
47B LEU* 4.0 24.5 - - + -
53B PHE* 5.7 0.2 - - + -
78B ILE* 3.8 14.6 - - + -
82B ASP* 2.7 22.6 + - - +
84B ALA* 1.3 71.1 - - + +
86B ALA* 1.3 68.0 + - - +
88B THR* 3.2 12.3 + - + +
89B VAL* 2.9 28.6 + - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 4.0 10.0 - - + +
78B ILE* 3.4 10.0 - - + +
79B ALA* 3.6 42.8 - - + +
82B ASP 3.1 4.8 + - - +
83B GLY 3.1 8.8 + - - +
85B LEU* 1.3 75.3 - - - +
87B LEU* 1.3 58.0 + - - +
89B VAL* 3.3 4.4 + - - +
90B ALA* 2.8 32.7 + - - +
255B MET* 4.1 9.9 - - + -
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLY 2.9 12.6 + - - +
84B ALA* 3.6 8.5 - - - +
86B ALA* 1.3 77.0 - - - +
88B THR* 1.3 62.6 + - - +
90B ALA* 4.4 1.1 - - - -
91B SER* 2.8 37.2 + - - +
160B THR* 4.2 16.6 - - + +
207B LYS* 6.0 1.1 - - - -
210B LEU* 3.8 24.0 - - + -
213B SER* 3.4 21.3 - - - +
215B THR* 5.6 2.2 - - - +
252B ILE* 4.4 23.1 - - + -
255B MET* 4.0 16.7 - - + -
364B LEU* 4.2 13.0 - - + -
369B GLU* 5.8 1.3 - - - +
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 4.0 32.0 - - + -
40B PRO* 6.0 0.2 - - - +
44B VAL* 4.8 3.1 - - + -
53B PHE* 4.3 20.9 - - + -
84B ALA 3.0 17.3 + - - -
85B LEU* 3.4 15.5 - - + +
87B LEU* 1.3 75.7 - - - +
89B VAL* 1.3 62.5 + - - +
91B SER* 3.2 1.7 + - - -
92B HIS* 3.1 28.3 + - + +
122B LEU* 5.0 0.7 - - + -
160B THR* 4.8 0.2 - - - -
161B GLN* 3.4 27.6 + - + +
212B ALA 5.0 0.3 + - - -
213B SER* 4.4 8.8 + - - -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.2 9.9 - - + -
52B VAL* 3.5 26.7 - - + +
53B PHE* 4.0 29.2 - - + -
71B PHE* 4.1 10.3 - - + -
75B VAL* 4.5 4.7 - - + -
78B ILE* 3.7 25.4 - - + -
85B LEU* 2.9 19.9 + - + +
86B ALA 3.7 3.1 - - - +
88B THR* 1.3 75.1 - - - +
90B ALA* 1.3 66.1 + - - +
93B ASN* 2.8 42.6 + - - +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 4.2 11.2 - - - -
75B VAL* 4.3 19.3 - - + -
86B ALA 2.8 21.6 + - - +
87B LEU* 3.9 4.9 - - - +
89B VAL* 1.3 75.2 - - - +
91B SER* 1.3 57.7 + - - +
93B ASN* 4.0 0.2 - - - +
94B SER* 2.9 36.3 + - - +
251B GLY* 4.6 17.3 - - - +
252B ILE* 4.6 11.9 - - + -
255B MET* 5.4 1.6 - - - -
369B GLU* 5.8 1.1 - - - -
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 2.8 29.4 + - - +
88B THR 3.2 1.9 + - - -
90B ALA* 1.3 70.6 - - - +
92B HIS* 1.3 67.0 + - - +
95B LEU* 2.9 49.0 + - - +
96B ALA 4.0 0.5 + - - -
123B GLY 5.2 0.4 - - - -
160B THR* 3.2 25.6 - - - +
161B GLN* 2.6 27.1 + - - -
252B ILE* 5.9 0.6 - - - +
369B GLU* 5.3 2.7 - - - -
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Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 2.9 43.1 + + + -
88B THR 3.1 16.4 + - - +
89B VAL 3.9 2.5 - - - +
91B SER* 1.3 82.9 + - - +
93B ASN* 1.3 61.3 + - - +
96B ALA* 4.0 2.1 + - - +
97B THR* 2.8 39.0 + - - -
116B LEU* 2.9 36.6 + - + -
121B ALA 3.4 20.4 - - - -
122B LEU* 3.5 10.5 - - + +
123B GLY 3.0 29.8 + - - -
161B GLN* 3.9 11.4 - - + +
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL 2.8 22.6 + - - -
53B PHE* 3.4 11.8 - - - +
54B GLY* 3.4 8.0 + - - -
55B ALA* 3.1 26.3 + - - +
56B LEU* 4.4 10.4 + - + +
57B VAL* 5.7 0.2 - - - +
71B PHE* 3.5 23.6 - - + -
89B VAL* 2.8 33.6 + - - +
92B HIS* 1.3 83.2 - - - +
94B SER* 1.3 59.1 + - - +
97B THR* 3.5 10.5 - - - +
98B GLY* 2.8 27.5 + - - -
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Residues in contact with SER 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 5.7 4.1 - - - +
71B PHE* 3.9 18.5 - - - -
90B ALA* 2.9 22.6 + - - +
93B ASN* 1.3 74.1 - - - +
95B LEU* 1.3 63.2 + - - +
98B GLY* 3.6 10.4 - - - -
244B VAL* 3.3 20.4 - - - +
247B GLY 4.0 5.7 + - - -
248B GLY* 3.6 33.4 + - - -
251B GLY* 4.9 2.6 - - - -
369B GLU* 4.9 1.3 - - - -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B SER* 2.9 37.9 + - - +
94B SER* 1.3 78.2 - - - +
96B ALA* 1.3 59.0 + - - +
99B HIS* 2.7 38.6 + - - +
125B TRP* 3.3 49.8 - - + +
160B THR* 5.4 4.9 - - - +
244B VAL* 3.9 20.4 - - + +
245B LEU* 4.7 4.9 - - + -
248B GLY* 4.8 0.7 - - - -
369B GLU* 3.7 33.4 - - - +
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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