Contacts of the helix formed by residues 67 - 82 (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 SER 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLU* 4.8 1.9 + - - +
56B LEU* 3.4 5.0 - - - +
65B GLY 4.1 0.2 + - - -
66B LEU* 1.3 79.3 - - - +
68B THR* 1.3 63.1 + - - +
69B ARG* 3.6 7.6 + - - +
70B LEU* 3.0 26.5 + - - +
71B PHE* 3.1 18.0 + - - +
313B ASP* 3.9 16.8 - - - -
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.6 20.3 - - + +
67B SER* 1.3 69.3 - - - +
69B ARG* 1.3 60.6 + - - +
71B PHE* 3.7 6.4 - - + +
72B ALA* 2.9 28.6 + - - +
247B GLY 5.7 1.6 - - - +
250B ILE* 4.3 13.9 - - + -
309B ALA* 3.9 19.5 - - + -
312B LYS* 3.1 42.2 + - + +
313B ASP* 3.0 26.1 + - - -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TRP* 2.4 62.2 + - - +
6B GLU 2.7 21.6 + - - -
8B GLY* 4.6 0.8 - - - +
11B GLU* 2.6 28.3 + - - +
67B SER* 3.1 7.4 - - - +
68B THR* 1.3 81.1 - - - +
70B LEU* 1.3 59.9 + - - +
72B ALA* 3.4 4.2 + - - +
73B ARG* 3.1 37.4 + - - +
306B LEU* 3.8 23.1 - - + +
309B ALA* 3.7 15.2 - - + +
310B GLU* 3.7 14.3 + - - +
313B ASP* 3.4 10.5 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 4.7 3.4 - - + +
11B GLU* 4.0 31.4 - - + +
14B VAL* 4.1 23.6 - - + -
15B LEU* 3.9 35.0 - - + -
66B LEU* 4.1 33.9 - - + -
67B SER* 3.0 22.8 + - - +
69B ARG* 1.3 74.4 - - - +
71B PHE* 1.3 67.2 + - - +
73B ARG* 3.2 3.2 + - + -
74B MET* 2.9 24.1 + - + +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.9 2.0 - - + -
55B ALA* 3.2 26.2 - - + -
56B LEU* 3.7 27.4 - - + -
66B LEU* 4.8 1.9 - - + +
67B SER 3.1 16.6 + - - +
68B THR* 3.7 10.3 - - + +
70B LEU* 1.3 75.9 - - - +
72B ALA* 1.3 61.7 + - + +
74B MET* 3.1 13.4 + - + +
75B VAL* 2.9 50.2 + - + +
89B VAL* 4.1 7.2 - - + -
90B ALA* 4.2 8.1 - - - -
93B ASN* 3.5 41.3 - - + -
94B SER* 3.9 18.8 - - - -
247B GLY 5.8 0.9 - - - -
250B ILE* 6.5 0.4 - - + -
251B GLY* 4.7 10.5 - - - -
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Residues in contact with ALA 72 (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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68B THR* 2.9 18.6 + - + +
69B ARG* 3.6 4.5 - - - +
70B LEU 3.2 0.2 - - - -
71B PHE* 1.3 82.9 - - + +
73B ARG* 1.3 62.7 + - - +
75B VAL* 3.1 5.1 + - - +
76B GLU* 2.9 19.8 + - - +
250B ILE* 4.4 14.1 - - + +
251B GLY* 5.6 1.3 - - - -
254B ALA* 3.3 19.6 - - + +
305B TYR* 3.4 30.5 - - + -
309B ALA* 5.1 0.4 - - + -
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Residues in contact with ARG 73 (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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5B PHE 3.2 25.7 + - - -
6B GLU 3.5 5.9 + - - -
7B GLU* 3.5 35.8 + - - +
11B GLU* 3.5 20.5 + - - -
15B LEU* 3.7 22.6 - - + +
19B ARG* 5.5 3.5 + - - +
69B ARG* 3.1 36.7 + - - +
70B LEU* 3.6 8.3 - - - +
72B ALA* 1.3 75.8 - - - +
74B MET* 1.3 58.3 + - - +
76B GLU* 3.2 5.9 + - - +
77B ALA* 2.9 27.4 + - - +
302B ARG* 4.2 22.2 - - - +
305B TYR* 3.6 14.2 + - - +
306B LEU* 3.7 21.6 - - + +
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Residues in contact with MET 74 (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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14B VAL* 4.0 21.1 - - + -
15B LEU* 3.8 19.3 - - + -
18B PHE* 3.8 27.5 - - + -
50B PHE* 4.4 10.3 - - + +
52B VAL* 3.3 43.5 - - + -
55B ALA* 5.6 1.3 - - - -
66B LEU* 3.6 28.5 - - + -
70B LEU* 2.9 19.2 + - + +
71B PHE* 3.4 11.0 - - + +
73B ARG* 1.3 73.6 - - - +
75B VAL* 1.3 67.3 + - - +
77B ALA* 3.1 3.3 + - - +
78B ILE* 3.0 28.7 + - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 2.9 51.8 + - + +
72B ALA* 3.1 8.3 + - - +
74B MET* 1.3 75.3 - - + +
76B GLU* 1.3 64.2 + - - +
78B ILE* 3.2 10.6 + - - +
79B ALA* 2.9 21.5 + - - +
86B ALA* 4.0 7.7 - - + +
89B VAL* 4.5 8.3 - - + -
90B ALA* 4.3 16.4 - - + -
251B GLY* 3.5 23.8 - - - +
254B ALA* 4.3 3.1 - - + -
255B MET* 3.8 19.1 - - + +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA 2.9 12.2 + - - +
73B ARG* 3.4 11.3 + - - +
75B VAL* 1.3 77.5 - - - +
77B ALA* 1.3 62.4 + - - +
79B ALA* 3.3 1.0 + - - -
80B TYR* 3.1 21.9 + - + +
254B ALA 3.4 17.0 + - - +
257B VAL* 3.6 8.2 - - - +
258B GLY* 3.4 25.5 - - - +
261B GLN* 4.8 4.3 - - - +
302B ARG* 2.8 40.4 + - - -
305B TYR* 2.7 31.2 + - - +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 4.9 2.5 - - + -
18B PHE* 4.3 7.4 - - + -
19B ARG* 4.5 22.0 - - + +
22B LEU* 3.5 24.8 - - + +
73B ARG 2.9 13.8 + - - +
74B MET* 3.1 12.3 + - - +
76B GLU* 1.3 77.2 - - - +
78B ILE* 1.3 63.4 + - - +
80B TYR* 3.3 19.6 - - - +
81B TYR* 3.5 6.2 - - + -
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Residues in contact with ILE 78 (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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18B PHE* 3.7 26.7 - - + -
22B LEU* 4.0 17.0 - - + -
26B VAL* 5.1 1.2 - - + +
47B LEU* 4.7 6.3 - - + -
52B VAL* 4.2 5.8 - - + -
74B MET 3.0 17.5 + - - +
75B VAL* 3.6 6.7 - - - +
77B ALA* 1.3 77.2 - - - +
79B ALA* 1.3 51.4 + - - +
81B TYR* 2.9 8.5 + - - +
82B ASP* 2.8 31.5 + - + +
85B LEU* 3.8 18.6 - - + -
86B ALA* 3.4 26.9 - - + +
89B VAL* 3.7 36.6 - - + -
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Residues in contact with ALA 79 (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 2.9 17.6 + - - +
76B GLU 3.3 5.4 + - - +
78B ILE* 1.3 73.1 - - - +
80B TYR* 1.3 66.1 + - - +
81B TYR 3.2 0.9 + - - -
82B ASP 3.7 10.0 + - - -
83B GLY 4.0 0.2 + - - -
86B ALA* 3.6 20.8 - - + +
255B MET* 3.3 34.1 - - + +
258B GLY* 4.0 4.3 - - - -
259B LEU* 3.4 26.9 - - + +
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Residues in contact with TYR 80 (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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76B GLU* 3.1 13.2 + - + +
77B ALA* 3.3 15.9 - - - +
78B ILE 3.1 0.4 - - - -
79B ALA* 1.3 76.9 - - - +
81B TYR* 1.3 94.1 + + + +
258B GLY* 3.5 21.3 + - - -
261B GLN* 3.7 12.8 - - + -
262B ALA* 3.3 40.8 - - + +
265B ASP* 2.4 39.6 + - - +
358B TYR* 4.5 9.0 + - - -
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Residues in contact with TYR 81 (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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19B ARG* 4.7 6.9 - - + +
22B LEU* 3.7 28.7 - - + -
23B LYS* 2.9 42.0 - - + +
26B VAL* 4.0 17.0 - - + -
27B ALA* 3.5 27.8 - - + -
30B ALA* 3.2 23.6 - - - +
77B ALA* 3.5 16.2 - - - -
78B ILE 2.9 4.8 + - - +
79B ALA 4.1 0.4 - - - -
80B TYR* 1.3 113.0 - + + +
82B ASP* 1.3 58.4 + - - +
259B LEU* 6.3 0.2 - - - -
357B ARG* 3.4 11.8 + - - +
358B TYR* 5.9 0.2 - - - -
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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
------------------------------------------------------------
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