Contacts of the helix formed by residues 82 - 95 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C VAL* 3.6 20.0 - - + -
30C ALA* 3.8 12.8 - - - +
33C ARG* 2.5 33.8 + - - +
78C ILE 2.8 18.1 + - - +
79C ALA* 3.7 2.8 + - - -
81C TYR* 1.3 75.8 - - - +
83C GLY* 1.3 64.9 + - - +
84C ALA* 3.1 13.5 + - - +
85C LEU* 2.7 38.5 + - + +
86C ALA* 3.0 18.4 + - - +
357C ARG* 5.1 3.1 - - - +
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Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ALA* 4.2 4.3 + - - -
82C ASP* 1.3 71.8 - - - +
84C ALA* 1.3 63.6 + - - +
86C ALA* 3.0 10.2 + - - +
87C LEU* 2.9 21.0 + - - +
210C LEU* 3.3 21.6 - - - +
255C MET* 4.6 2.4 - - - +
259C LEU* 4.3 18.6 - - - +
357C ARG* 5.6 0.6 - - - +
361C ASP* 3.6 15.7 + - - -
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 6.0 0.2 - - - -
40C PRO* 6.2 0.2 - - + -
82C ASP* 3.1 9.1 + - - +
83C GLY* 1.3 73.8 - - - +
85C LEU* 1.3 63.8 + - + +
87C LEU* 3.2 5.4 + - - +
88C THR* 3.1 25.7 + - - -
210C LEU* 3.4 18.7 - - - +
212C ALA* 3.9 21.3 - - + +
213C SER* 3.6 31.2 - - - +
361C ASP* 4.3 2.2 + - - +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 3.3 42.4 - - + -
33C ARG* 4.9 1.1 - - - +
40C PRO* 3.6 30.1 - - + -
43C LEU* 4.1 17.0 - - + -
44C VAL* 4.8 9.4 - - + -
47C LEU* 4.2 25.6 - - + -
53C PHE* 6.3 0.4 - - + -
78C ILE* 3.8 11.9 - - + -
82C ASP* 2.7 25.3 + - + +
84C ALA* 1.3 72.2 - - + +
86C ALA* 1.3 63.9 + - - +
88C THR* 3.0 10.4 + - - +
89C VAL* 2.9 27.0 + - + +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C VAL* 4.2 8.7 - - + +
78C ILE* 3.4 9.6 - - + +
79C ALA* 3.6 33.9 - - + +
82C ASP 3.0 14.3 + - - +
83C GLY 3.0 8.9 + - - +
85C LEU* 1.3 77.2 - - - +
87C LEU* 1.3 56.4 + - - +
89C VAL* 3.8 3.6 - - - +
90C ALA* 2.8 33.1 + - - +
255C MET* 3.8 12.6 - - + -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLY 2.9 12.5 + - - +
84C ALA 3.2 8.3 + - - +
86C ALA* 1.3 73.0 - - - +
88C THR* 1.3 64.2 + - - +
91C SER* 2.8 37.2 + - - +
160C THR* 4.3 23.1 - - + +
207C LYS* 5.9 0.4 - - - -
210C LEU* 4.1 6.7 - - + -
213C SER* 4.0 23.3 - - - +
215C THR* 5.2 4.0 - - - +
252C ILE* 4.3 12.6 - - + -
255C MET* 3.4 26.2 - - + +
364C LEU* 4.0 29.2 - - + -
369C GLU* 5.4 1.6 - - - +
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Residues in contact with THR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C PHE* 4.3 24.7 - - + -
44C VAL* 4.8 4.9 - - + -
53C PHE* 4.4 18.6 - - + -
84C ALA 3.1 14.3 + - - -
85C LEU* 3.0 14.9 + - - +
87C LEU* 1.3 77.3 - - - +
89C VAL* 1.3 63.3 + - - +
91C SER* 3.1 2.3 + - - -
92C HIS* 3.0 28.0 + - + +
122C LEU* 4.9 2.2 - - + -
160C THR* 4.7 0.4 - - - -
161C GLN* 3.0 30.5 + - + +
213C SER* 4.2 14.6 - - - -
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU* 4.2 9.4 - - + -
52C VAL* 3.7 33.0 - - + +
53C PHE* 3.8 21.5 - - + -
71C PHE* 4.0 12.1 - - + -
75C VAL* 4.7 4.5 - - + -
78C ILE* 3.8 23.1 - - + -
85C LEU* 2.9 18.6 + - + +
86C ALA* 3.8 2.9 - - - +
88C THR* 1.3 77.4 - - - +
90C ALA* 1.3 62.9 + - - +
92C HIS* 3.8 0.3 - - - +
93C ASN* 2.6 46.0 + - - +
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 4.2 11.9 - - - -
75C VAL* 4.3 14.8 - - + -
86C ALA 2.8 21.4 + - - +
87C LEU 4.1 0.2 - - - +
89C VAL* 1.3 74.3 - - - +
91C SER* 1.3 58.8 + - - +
93C ASN* 4.0 0.2 - - - +
94C SER* 2.8 38.9 + - - +
248C GLY 5.9 0.4 - - - +
251C GLY* 4.7 8.3 - - - -
252C ILE* 4.6 8.1 - - + -
255C MET* 3.8 19.7 - - + -
369C GLU* 5.5 1.3 - - - +
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 2.8 28.6 + - - -
88C THR 3.1 2.1 + - - -
90C ALA* 1.3 74.4 - - - +
92C HIS* 1.3 65.3 + - - +
94C SER* 4.7 0.4 - - - -
95C LEU* 2.8 54.1 + - - +
96C ALA* 3.7 1.2 + - - +
123C GLY 5.5 0.4 - - - -
160C THR* 3.3 21.8 - - - +
161C GLN* 2.9 19.0 + - - -
252C ILE* 5.8 0.2 - - - +
369C GLU* 4.8 5.1 + - - -
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Residues in contact with HIS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PHE* 3.1 45.6 + + + -
88C THR 3.0 15.3 + - - +
89C VAL 3.8 2.7 - - - +
91C SER* 1.3 82.6 + - - +
93C ASN* 1.3 61.0 + - - +
96C ALA* 3.7 1.4 + - - +
97C THR* 3.1 37.2 + - - -
116C LEU* 3.0 35.7 + - + -
121C ALA 3.4 24.7 - - - -
122C LEU* 3.8 8.8 - - + +
123C GLY* 3.1 29.4 + - - -
161C GLN* 4.0 11.0 - - - +
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Residues in contact with ASN 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL 3.0 20.4 + - - -
53C PHE* 3.2 30.3 - - - +
54C GLY* 3.4 5.2 + - - -
55C ALA* 3.4 9.9 + - - +
56C LEU* 4.5 11.7 + - + +
71C PHE* 3.5 25.3 - - + -
89C VAL* 2.6 32.8 + - - +
92C HIS* 1.3 82.0 - - - +
94C SER* 1.3 56.5 + - - +
97C THR* 3.4 10.5 + - - +
98C GLY* 2.7 34.5 + - - -
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Residues in contact with SER 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 5.7 5.0 - - - +
71C PHE* 4.0 15.7 - - - -
90C ALA* 2.8 27.7 + - - +
91C SER* 4.7 0.2 - - - -
93C ASN* 1.3 74.6 - - - +
95C LEU* 1.3 65.4 + - - +
98C GLY* 3.6 9.6 - - - -
244C VAL* 3.3 19.8 - - - +
247C GLY 4.2 6.2 + - - -
248C GLY* 3.5 34.1 + - - -
251C GLY* 4.8 3.3 - - - -
369C GLU* 5.1 1.1 - - - -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER* 2.8 36.4 + - - +
94C SER* 1.3 76.4 - - - +
96C ALA* 1.3 68.8 + - - +
99C HIS* 2.9 28.8 + - - +
125C TRP* 3.4 50.9 - - + +
160C THR* 5.7 3.8 - - - +
244C VAL* 3.8 22.8 - - + +
245C LEU* 4.5 4.9 - - + -
369C GLU* 4.0 35.2 - - + +
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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