Contacts of the helix formed by residues 82 - 95 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D VAL* 3.6 19.3 - - + -
30D ALA* 3.6 12.0 - - - +
33D ARG* 2.7 37.5 + - - +
78D ILE 2.8 15.7 + - - +
79D ALA 3.8 1.7 + - - -
81D TYR* 1.3 81.3 - - - +
83D GLY* 1.3 66.8 + - - +
84D ALA* 3.2 13.0 + - - +
85D LEU* 2.8 38.2 + - + +
86D ALA* 3.2 16.3 + - - +
357D ARG* 4.9 3.6 - - - +
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Residues in contact with GLY 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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79D ALA 4.1 4.1 + - - -
82D ASP* 1.3 70.4 - - - +
84D ALA* 1.3 66.1 + - - +
86D ALA* 3.0 9.4 + - - +
87D LEU 3.0 18.7 + - - -
210D LEU* 3.3 21.7 - - - +
255D MET* 3.6 2.9 - - - +
259D LEU* 4.3 20.2 - - - +
357D ARG* 5.7 0.2 - - - +
361D ASP* 3.8 14.3 + - - -
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Residues in contact with ALA 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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33D ARG* 6.3 0.2 - - + -
82D ASP* 3.2 9.1 + - - +
83D GLY* 1.3 74.5 - - - +
85D LEU* 1.3 57.8 + - - +
87D LEU* 3.2 6.0 + - - +
88D THR* 2.9 31.1 + - - -
210D LEU* 3.4 22.8 - - - +
211D THR 4.8 0.2 - - - +
212D ALA* 4.1 15.0 - - + +
213D SER* 3.6 31.5 - - - +
361D ASP* 4.5 1.8 + - - -
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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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26D VAL* 3.8 24.9 - - + -
33D ARG* 4.7 0.2 - - - +
40D PRO* 4.1 22.4 - - + -
43D LEU* 3.6 35.4 - - + -
44D VAL* 4.6 11.2 - - + -
47D LEU* 3.6 24.9 - - + -
53D PHE* 5.4 0.2 - - + -
78D ILE* 3.9 11.2 - - + -
82D ASP* 2.8 26.0 + - - +
84D ALA* 1.3 70.5 - - - +
86D ALA* 1.3 60.6 + - - +
88D THR* 3.3 14.3 + - + +
89D VAL* 3.0 33.6 + - + +
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Residues in contact with ALA 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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75D VAL* 4.1 10.2 - - + +
78D ILE* 3.6 8.9 - - + +
79D ALA* 3.5 43.1 - - + +
82D ASP 3.2 5.1 + - - -
83D GLY 3.0 9.3 + - - +
85D LEU* 1.3 77.5 - - - +
87D LEU* 1.3 56.8 + - - +
89D VAL* 3.3 3.9 + - - +
90D ALA* 2.8 33.2 + - - +
255D MET* 3.9 11.7 - - + -
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Residues in contact with LEU 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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83D GLY 3.0 11.4 + - - +
84D ALA* 3.6 9.6 - - - +
86D ALA* 1.3 76.0 - - - +
88D THR* 1.3 52.5 + - - +
90D ALA* 4.3 2.0 - - - -
91D SER* 2.7 45.8 + - - -
160D THR* 4.4 21.8 - - + +
207D LYS* 5.7 0.2 - - - +
210D LEU* 3.9 9.4 - - + -
213D SER* 4.0 18.6 - - - +
215D THR* 5.4 2.9 - - - +
252D ILE* 4.2 17.5 - - + -
255D MET* 4.1 23.5 - - + -
364D LEU* 3.9 28.5 - - + -
369D GLU* 5.5 1.6 - - - +
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Residues in contact with THR 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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39D PHE* 4.1 30.8 - - + -
40D PRO* 6.1 0.3 - - - +
44D VAL* 4.8 3.8 - - + -
53D PHE* 4.3 18.8 - - + -
84D ALA 2.9 16.7 + - - -
85D LEU* 3.4 16.5 - - + +
87D LEU* 1.3 78.3 - - - +
89D VAL* 1.3 62.7 + - - +
91D SER* 3.3 1.4 + - - -
92D HIS* 3.2 26.9 + - - +
122D LEU* 4.8 1.1 - - + -
160D THR* 4.8 0.2 - - - -
161D GLN* 3.3 26.6 + - + +
212D ALA 5.2 0.2 + - - -
213D SER* 4.3 9.6 - - - -
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Residues in contact with VAL 89 (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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47D LEU* 4.2 8.3 - - + -
52D VAL* 3.4 35.4 - - + +
53D PHE* 3.8 22.7 - - + -
71D PHE* 3.9 12.8 - - + -
75D VAL* 4.5 5.2 - - + -
78D ILE* 3.9 20.6 - - + -
85D LEU 3.0 19.8 + - - +
86D ALA* 3.8 2.9 - - - +
88D THR* 1.3 77.2 - - - +
90D ALA* 1.3 63.0 + - - +
92D HIS* 3.9 0.3 - - - +
93D ASN* 2.8 42.8 + - - +
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Residues in contact with ALA 90 (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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71D PHE* 4.2 11.4 - - - -
75D VAL* 4.3 17.0 - - + -
86D ALA 2.8 23.7 + - - +
87D LEU* 4.0 5.4 - - - +
89D VAL* 1.3 73.7 - - - +
91D SER* 1.3 57.9 + - - +
93D ASN* 3.9 0.2 - - - +
94D SER* 2.8 37.1 + - - +
248D GLY 5.9 0.2 - - - +
251D GLY* 4.7 9.9 - - - +
252D ILE* 4.6 18.4 - - + -
255D MET* 5.5 1.3 - - - -
369D GLU* 5.6 1.1 - - - -
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Residues in contact with SER 91 (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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87D LEU* 2.7 31.2 + - - +
88D THR 3.3 1.2 + - - -
90D ALA* 1.3 71.0 - - - +
92D HIS* 1.3 61.7 + - - +
94D SER* 4.8 0.4 - - - -
95D LEU* 2.8 55.2 + - - +
96D ALA 3.8 1.2 + - - -
123D GLY 5.3 0.7 - - - -
160D THR* 3.2 21.7 - - - +
161D GLN* 2.7 26.2 + - - -
369D GLU* 5.0 4.5 - - - -
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Residues in contact with HIS 92 (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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53D PHE* 2.9 55.6 + + + +
88D THR* 3.2 17.6 + - + +
89D VAL 3.9 2.0 - - - +
91D SER* 1.3 81.6 + - - +
93D ASN* 1.3 61.2 + - - +
96D ALA* 4.0 1.6 + - - +
97D THR* 2.8 38.9 + - - -
116D LEU* 3.0 21.5 + - + -
121D ALA 3.4 25.4 - - - -
122D LEU* 3.6 9.1 - - + +
123D GLY* 3.0 30.3 + - - +
161D GLN* 4.0 11.9 - - + +
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Residues in contact with ASN 93 (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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52D VAL 2.8 23.0 + - - -
53D PHE* 3.4 16.6 - - - +
54D GLY* 3.8 1.7 - - - -
55D ALA* 3.2 25.8 + - - +
56D LEU* 4.3 12.6 + - + +
57D VAL* 5.7 0.3 - - - +
71D PHE* 3.4 26.1 - - + -
89D VAL* 2.8 31.6 + - - +
92D HIS* 1.3 80.9 - - - +
94D SER* 1.3 58.3 + - - +
97D THR* 3.5 10.6 - - - +
98D GLY* 2.8 29.6 + - - -
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Residues in contact with SER 94 (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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56D LEU* 5.6 5.4 - - - +
71D PHE* 4.0 15.7 - - - -
90D ALA* 2.8 26.5 + - - -
91D SER* 4.8 0.2 - - - -
93D ASN* 1.3 74.8 - - - +
95D LEU* 1.3 65.7 + - - +
98D GLY* 3.6 10.2 - - - -
244D VAL* 3.6 16.5 - - - +
247D GLY* 4.1 6.3 + - - -
248D GLY* 3.5 34.0 + - - +
251D GLY* 4.6 3.6 - - - -
369D GLU* 5.2 1.1 - - - -
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Residues in contact with LEU 95 (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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91D SER* 2.8 37.3 + - - +
93D ASN 3.5 0.2 - - - -
94D SER* 1.3 78.8 - - - +
96D ALA* 1.3 61.4 + - - +
99D HIS* 2.8 35.0 + - - +
125D TRP* 3.5 49.8 - - + +
160D THR* 5.9 2.9 - - - +
244D VAL* 3.9 20.3 - - + +
245D LEU* 4.7 2.5 - - + -
248D GLY* 4.5 2.2 - - - -
369D GLU* 3.9 37.0 - - + +
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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