Contacts of the helix formed by residues 69 - 86 (chain A) in PDB entry 2CNW
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 THR 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 3.0 7.2 + - - -
68A LEU* 1.3 86.7 - - + +
70A PRO* 1.3 61.2 - - - +
71A ALA 3.4 2.2 - - - -
72A GLU* 3.3 35.5 + - - +
73A VAL* 3.1 27.5 + - - +
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Residues in contact with PRO 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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16A LEU 5.2 3.6 - - - +
20A GLY 3.4 18.8 - - - +
22A ILE* 3.5 49.1 - - + +
64A VAL* 3.7 20.4 - - + +
67A SER* 3.6 11.7 - - - +
68A LEU 3.4 1.3 - - - +
69A THR* 1.3 88.3 - - - +
71A ALA* 1.3 62.7 - - + +
73A VAL* 3.5 6.7 - - + +
74A ILE* 2.8 36.7 + - - +
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Residues in contact with ALA 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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13A ILE* 3.5 27.2 - - + +
16A LEU* 3.7 38.8 - - + +
17A ARG* 4.2 7.9 - - + +
22A ILE* 5.4 0.2 - - - +
69A THR 3.4 0.8 - - - -
70A PRO* 1.3 78.8 - - - +
72A GLU* 1.3 60.9 + - + +
74A ILE* 3.5 10.2 + - - +
75A LEU* 3.1 30.8 + - - +
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Residues in contact with GLU 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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17A ARG* 5.9 7.9 - - + -
69A THR* 3.3 39.3 + - - +
70A PRO 3.3 0.2 - - - -
71A ALA* 1.3 76.1 - - + +
73A VAL* 1.3 63.8 + - + +
75A LEU* 4.1 0.9 - - - +
76A ALA* 3.1 26.5 + - - +
58C GLU 5.8 0.4 - - - +
61C GLY* 3.8 30.3 - - - +
62C LYS* 3.4 39.0 + - + +
63C GLN* 6.0 0.4 - - - +
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Residues in contact with VAL 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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59A ALA* 4.8 3.1 - - - +
62A LYS* 4.3 23.1 - - + +
64A VAL* 3.9 22.0 - - + -
67A SER* 3.7 19.3 - - - +
69A THR* 3.1 17.6 + - - +
70A PRO* 3.3 9.8 + - + +
72A GLU* 1.3 74.0 - - + +
74A ILE* 1.3 60.6 + - - +
76A ALA* 3.7 4.4 - - - +
77A THR* 2.7 40.4 + - - +
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Residues in contact with ILE 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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13A ILE* 4.3 6.3 - - + -
16A LEU* 4.8 2.7 - - + -
22A ILE* 3.9 21.5 - - + -
27A LEU* 3.9 24.9 - - + -
30A THR* 3.9 35.7 - - + +
31A LEU* 5.0 7.2 - - + -
34A ILE* 4.1 15.5 - - + -
55A VAL* 4.8 2.6 - - + +
59A ALA* 5.0 5.6 - - + -
64A VAL* 3.9 12.6 - - + -
70A PRO 2.8 24.7 + - - +
71A ALA* 3.9 8.1 - - - +
73A VAL* 1.3 73.1 - - - +
75A LEU* 1.3 58.8 + - - +
77A THR* 3.2 8.5 + - - -
78A VAL* 3.0 33.0 + - + +
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Residues in contact with LEU 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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5A LEU* 3.7 35.7 - - + -
9A LEU* 5.9 2.7 - - + -
13A ILE* 3.9 27.8 - - + -
71A ALA 3.1 18.4 + - - +
72A GLU 4.1 2.5 - - - +
74A ILE* 1.3 74.7 - - - +
76A ALA* 1.3 65.1 + - - +
78A VAL* 3.3 12.6 + - + +
79A TYR* 3.0 50.2 + - + -
292A LEU* 5.5 2.2 - - + -
60C LEU 3.8 9.0 - - - +
61C GLY* 3.6 23.8 - - - +
63C GLN* 3.8 7.2 - - + -
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Residues in contact with ALA 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 GLU 3.1 19.5 + - - +
73A VAL* 3.7 5.6 - - - +
75A LEU* 1.3 77.4 - - - +
77A THR* 1.3 56.7 + - - +
79A TYR* 3.3 7.4 + - - +
80A GLU* 2.9 47.1 + - - +
57C GLU 4.5 15.2 - - - +
58C GLU* 4.9 14.1 - - + -
61C GLY* 4.5 3.9 - - - -
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Residues in contact with THR 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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55A VAL* 4.1 20.1 - - + +
58A GLU* 3.7 37.9 - - + +
59A ALA* 4.2 7.8 - - - +
62A LYS* 3.7 17.2 + - - +
73A VAL* 2.7 30.1 + - - +
74A ILE* 3.2 7.8 + - - -
76A ALA* 1.3 73.1 - - - +
78A VAL* 1.3 61.0 + - - +
80A GLU* 4.0 8.2 + - - +
81A ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 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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13A ILE* 6.0 0.4 - - + -
34A ILE* 3.7 41.5 - - + -
51A PHE* 3.9 13.1 - - + -
55A VAL* 4.2 16.2 - - + -
74A ILE* 3.0 18.7 + - + +
75A LEU* 3.6 13.2 - - + +
76A ALA 3.3 0.2 - - - -
77A THR* 1.3 73.3 - - - +
79A TYR* 1.3 66.9 + - - +
80A GLU 3.1 0.3 + - - -
81A ALA 3.3 0.3 + - - -
82A LEU* 3.0 25.3 + - + +
292A LEU* 3.8 32.5 - - + -
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Residues in contact with TYR 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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4A GLN* 3.9 14.4 + - - +
5A LEU* 3.5 24.6 + - + +
75A LEU* 3.0 50.1 + - + -
76A ALA* 3.6 10.3 - - - +
78A VAL* 1.3 76.1 - - - +
80A GLU* 1.3 61.6 + - - +
82A LEU* 4.3 1.7 - - - +
83A LYS* 3.3 24.6 + - - +
285A GLU 6.0 0.2 - - - -
288A ALA* 4.5 7.3 - - + +
289A GLY* 4.2 22.6 + - - -
292A LEU* 3.7 26.0 - - + +
57C GLU* 4.2 17.7 - - + +
60C LEU* 4.3 43.7 + - + +
61C GLY 5.0 0.7 - - - -
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Residues in contact with GLU 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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58A GLU* 5.3 4.6 - - - +
62A LYS* 3.6 22.9 + - - -
76A ALA* 2.9 31.3 + - - +
77A THR* 4.0 6.7 - - - +
79A TYR* 1.3 75.0 - - + +
81A ALA* 1.3 64.9 + - - +
83A LYS* 3.6 4.1 + - - +
84A GLU* 3.2 23.7 + - - +
54C ARG* 5.9 2.3 - - - +
57C GLU* 3.5 37.9 - - + +
58C GLU* 5.0 6.9 - - - +
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Residues in contact with ALA 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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51A PHE* 3.5 18.2 - - + -
54A ARG* 2.6 46.0 + - - +
55A VAL* 4.2 7.6 - - + -
58A GLU* 4.1 13.4 + - - +
77A THR* 2.9 23.0 + - + +
80A GLU* 1.3 74.2 - - - +
82A LEU* 1.3 57.5 + - - +
84A GLU* 4.5 1.1 - - - -
85A ALA* 3.0 16.5 + - - +
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Residues in contact with LEU 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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38A LEU* 4.7 5.2 - - + -
51A PHE* 3.4 14.7 - - + -
78A VAL 3.0 16.6 + - - +
79A TYR* 4.3 0.7 - - - +
81A ALA* 1.3 73.8 - - - +
83A LYS* 1.3 66.1 + - - +
85A ALA* 3.2 1.4 + - - -
86A LEU* 3.0 42.9 + - + +
257A LEU* 3.8 30.3 - - + -
288A ALA* 3.5 37.7 - - + +
291A ILE* 4.0 20.9 - - + -
292A LEU* 3.6 24.7 - - + -
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Residues in contact with LYS 83 (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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79A TYR 3.3 17.9 + - - +
80A GLU 3.7 5.2 - - - +
82A LEU* 1.3 77.1 - - - +
84A GLU* 1.3 61.2 + - - +
86A LEU 3.1 7.8 + - - -
88A GLY* 2.9 41.0 + - - +
89A GLU* 3.1 22.1 + - - +
284A PRO* 3.4 11.8 - - - +
285A GLU* 3.6 36.8 - - + +
288A ALA* 3.9 10.5 - - + +
53C GLU* 6.4 0.4 - - - +
56C ARG* 5.8 3.4 - - - +
57C GLU* 4.0 28.5 + - - +
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Residues in contact with GLU 84 (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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54A ARG* 4.0 18.6 + - - +
80A GLU 3.2 14.9 + - - +
81A ALA* 3.7 4.9 - - - +
83A LYS* 1.3 79.4 - - - +
85A ALA* 1.3 56.6 + - - +
86A LEU 3.1 0.2 - - - -
87A GLY* 3.0 18.7 + - - -
88A GLY* 3.4 18.1 + - - +
260A ARG* 4.7 3.6 + - - -
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Residues in contact with ALA 85 (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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51A PHE* 4.5 6.3 - - + -
54A ARG* 3.8 18.8 - - - +
81A ALA 3.0 18.7 + - - +
82A LEU* 3.2 5.6 + - - +
84A GLU* 1.3 76.6 - - - +
86A LEU* 1.3 58.5 + - - +
87A GLY 3.3 1.1 - - - -
257A LEU* 3.6 26.5 - - + +
260A ARG* 3.1 28.1 + - - +
261A HIS 5.3 0.2 + - - -
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Residues in contact with LEU 86 (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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82A LEU* 3.0 37.7 + - + +
83A LYS 3.6 5.6 - - - +
84A GLU 3.1 0.6 - - - -
85A ALA* 1.3 79.1 - - - +
87A GLY* 1.3 55.3 + - - +
88A GLY 3.7 0.2 - - - -
256A ALA* 4.0 7.4 - - + +
257A LEU* 3.8 32.8 - - + +
260A ARG* 3.4 15.1 + - - +
267A ILE* 4.2 8.3 + - + +
282A PHE* 3.6 11.7 - - + -
284A PRO* 3.4 27.4 - - + +
287A LEU* 3.7 23.1 - - + -
288A ALA* 3.8 26.7 - - - +
291A ILE* 4.1 7.9 - - + -
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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