Contacts of the helix formed by residues 67 - 82 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 5.0 0.9 + - - +
56A LEU* 3.5 4.8 - - - +
66A LEU* 1.3 80.4 - - - +
68A THR* 1.3 62.2 + - - +
69A ARG* 3.5 9.3 + - - +
70A LEU* 3.0 25.6 + - - +
71A PHE* 3.1 18.4 + - - +
313A ASP* 3.6 16.6 - - - -
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.7 18.9 - - + +
67A SER* 1.3 69.7 - - - +
69A ARG* 1.3 60.9 + - - +
71A PHE* 3.7 5.3 - - + +
72A ALA* 2.9 29.1 + - - +
247A GLY 5.6 1.3 - - - +
250A ILE* 4.2 17.5 - - + -
309A ALA* 3.9 17.5 - - + -
312A LYS* 3.6 38.9 + - + +
313A ASP* 2.7 32.1 + - - -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU 4.3 0.4 + - - -
4A TRP* 2.5 59.5 + - - +
6A GLU 2.6 24.4 + - - -
8A GLY 4.6 0.2 - - - +
11A GLU* 2.5 28.2 + - - +
67A SER* 3.6 10.3 - - - +
68A THR* 1.3 80.1 - - - +
70A LEU* 1.3 60.6 + - - +
72A ALA* 3.3 4.2 + - - +
73A ARG* 3.0 40.5 + - - +
306A LEU* 4.0 22.8 + - + +
309A ALA* 3.7 18.0 - - + +
310A GLU* 3.9 13.1 + - - +
313A ASP* 3.5 4.9 + - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 4.7 3.4 - - + +
11A GLU* 4.1 29.2 - - + +
14A VAL* 4.0 21.8 - - + -
15A LEU* 3.9 33.7 - - + -
66A LEU* 3.8 37.2 - - + -
67A SER* 3.0 20.0 + - - +
69A ARG* 1.3 73.7 - - - +
71A PHE* 1.3 65.8 + - - +
73A ARG* 3.2 2.4 + - + +
74A MET* 3.0 34.2 + - + +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 4.5 0.4 - - + -
55A ALA* 3.3 22.9 - - + -
56A LEU* 3.5 39.0 - - + -
66A LEU* 4.7 0.6 - - - +
67A SER 3.1 7.7 + - - +
68A THR* 3.7 9.6 - - + +
70A LEU* 1.3 75.5 - - - +
72A ALA* 1.3 62.7 + - + +
74A MET* 3.1 17.4 + - + +
75A VAL* 2.9 49.3 + - + +
89A VAL* 4.1 7.2 - - + -
90A ALA* 4.1 10.1 - - - -
93A ASN* 3.5 41.3 - - + -
94A SER* 3.9 16.6 - - - -
247A GLY 5.8 0.9 - - - -
250A ILE* 6.6 0.2 - - + -
251A GLY* 4.8 9.9 - - - -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR 2.9 18.9 + - - +
69A ARG* 3.5 4.0 - - - +
71A PHE* 1.3 82.5 - - + +
73A ARG* 1.3 61.4 + - - +
75A VAL* 3.1 5.5 + - - +
76A GLU* 3.0 18.2 + - - +
250A ILE* 4.4 15.3 - - + +
251A GLY* 5.5 1.1 - - - -
254A ALA* 3.2 19.5 - - + +
305A TYR* 3.5 28.9 - - + -
309A ALA* 5.0 0.7 - - + -
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE 3.0 27.3 + - - -
6A GLU 3.5 4.4 + - - -
7A GLU* 3.7 34.0 + - - +
11A GLU* 3.6 24.0 + - - -
15A LEU* 3.7 21.3 - - + +
19A ARG* 5.5 1.7 + - - +
69A ARG* 3.0 39.0 + - - +
70A LEU* 3.7 7.9 - - - +
72A ALA* 1.3 74.8 - - - +
74A MET* 1.3 58.2 + - - +
76A GLU* 3.2 5.6 + - - +
77A ALA* 2.9 27.4 + - - +
302A ARG* 4.3 20.2 - - - +
305A TYR* 3.7 15.7 + - - +
306A LEU* 3.5 18.2 - - + +
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.1 17.3 - - + -
15A LEU* 3.8 20.6 - - + -
18A PHE* 3.7 23.0 - - + -
50A PHE* 5.4 4.9 - - - +
52A VAL* 3.5 30.7 - - + -
55A ALA* 3.8 8.7 - - + -
66A LEU* 3.4 34.1 - - + -
70A LEU* 3.0 16.5 + - + +
71A PHE* 3.4 21.5 - - + +
73A ARG* 1.3 74.1 - - - +
75A VAL* 1.3 65.5 + - - +
77A ALA* 3.2 3.4 + - - +
78A ILE* 3.0 28.5 + - - +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE* 2.9 50.5 + - + +
72A ALA* 3.1 9.2 + - - +
74A MET* 1.3 75.4 - - + +
76A GLU* 1.3 63.8 + - - +
78A ILE* 3.3 9.8 + - - +
79A ALA* 2.9 22.0 + - - +
86A ALA* 4.0 8.0 - - + +
89A VAL* 4.7 6.1 - - + -
90A ALA* 4.3 18.6 - - + +
251A GLY* 3.5 24.9 - - - +
254A ALA* 4.3 2.7 - - + -
255A MET* 3.8 18.2 - - + +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA 3.0 12.8 + - - +
73A ARG* 3.4 10.5 + - - +
74A MET 3.2 0.2 - - - -
75A VAL* 1.3 76.7 - - - +
77A ALA* 1.3 62.3 + - - +
79A ALA* 3.3 0.7 + - - -
80A TYR* 3.0 22.5 + - + +
254A ALA 3.3 17.0 + - - +
257A VAL* 3.7 7.6 - - + +
258A GLY* 3.4 27.2 - - - +
261A GLN* 4.9 4.2 - - - +
302A ARG* 3.0 39.8 + - - -
305A TYR* 2.6 31.7 + - - +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.9 1.1 - - + -
18A PHE* 4.3 5.2 - - + -
19A ARG* 4.1 28.3 - - + +
22A LEU* 3.5 25.1 - - + +
73A ARG 2.9 13.8 + - - +
74A MET* 3.2 11.6 + - - +
76A GLU* 1.3 77.2 - - - +
78A ILE* 1.3 62.6 + - - +
80A TYR* 3.3 20.0 - - - +
81A TYR* 3.5 7.2 - - - -
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.8 26.2 - - + -
22A LEU* 3.9 16.6 - - + -
26A VAL* 5.1 1.0 - - + +
47A LEU* 4.7 8.1 - - + -
52A VAL* 4.5 3.6 - - + -
74A MET 3.0 23.1 + - - +
75A VAL* 3.7 7.4 - - - +
77A ALA* 1.3 74.7 - - - +
79A ALA* 1.3 52.1 + - - +
81A TYR* 2.9 8.0 + - - +
82A ASP* 2.8 35.4 + - + +
85A LEU* 3.7 15.7 - - + -
86A ALA* 3.3 27.1 - - - +
89A VAL* 3.7 36.3 - - + -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL 2.9 17.3 + - - +
76A GLU 3.3 5.4 + - - +
78A ILE* 1.3 76.5 - - - +
80A TYR* 1.3 63.7 + - - +
81A TYR 3.1 1.0 + - - -
82A ASP 3.7 9.0 + - - -
83A GLY* 4.0 0.9 + - - -
86A ALA* 3.5 19.7 - - + +
255A MET* 3.2 33.9 - - + +
258A GLY* 3.9 4.7 - - - -
259A LEU* 3.4 26.2 - - + +
358A TYR* 6.0 0.2 - - - -
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 3.0 13.4 + - + +
77A ALA* 3.3 16.2 - - - +
78A ILE 3.1 0.2 - - - -
79A ALA* 1.3 74.8 - - - +
81A TYR* 1.3 94.5 + + + +
258A GLY* 3.6 13.7 - - - +
261A GLN* 3.8 12.1 - - + -
262A ALA* 3.3 50.4 - - + +
265A ASP* 2.5 39.7 + - - +
358A TYR* 4.6 8.1 + - - -
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 4.7 10.8 - - + +
22A LEU* 3.7 28.9 - - + -
23A LYS* 2.9 39.4 - - + +
26A VAL* 3.9 17.5 - - + -
27A ALA* 3.5 27.2 - - + -
30A ALA* 3.3 11.1 - - - +
77A ALA* 3.5 16.4 - - - -
78A ILE 2.9 4.8 + - - +
79A ALA 4.1 0.9 - - - -
80A TYR* 1.3 112.1 - + + +
82A ASP* 1.3 59.4 + - - +
259A LEU* 6.3 0.2 - - - -
357A ARG* 3.3 23.9 + - - +
358A TYR* 6.0 0.2 - - - -
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.7 18.6 - - + -
30A ALA* 3.6 12.2 - - - +
33A ARG* 2.7 36.2 + - - +
78A ILE* 2.8 18.8 + - - +
79A ALA 3.7 2.0 + - - -
81A TYR* 1.3 76.0 - - - +
83A GLY* 1.3 61.9 + - - +
84A ALA* 3.1 14.1 + - - +
85A LEU* 2.7 39.3 + - + +
86A ALA* 3.1 17.7 + - - +
212A ALA* 5.7 0.2 - - - +
357A ARG* 5.0 2.7 - - - +
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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