Contacts of the helix formed by residues 69 - 86 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B GLY* 6.4 1.8 - - - -
67B SER* 3.0 9.2 + - - -
68B LEU* 1.3 87.9 - - + +
70B PRO* 1.3 64.3 - - - +
71B ALA* 3.4 2.7 - - - -
72B GLU* 3.0 24.9 + - - +
73B VAL* 3.4 19.9 + - - +
94D LYS* 2.7 39.1 + - - +
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Residues in contact with PRO 70 (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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16B LEU* 4.8 12.3 - - + +
19B ARG* 4.8 1.3 - - + +
20B GLY 3.7 19.1 - - - +
22B ILE* 3.7 37.9 - - + +
64B VAL* 4.4 14.1 - - + +
67B SER* 3.9 12.8 - - - +
68B LEU 3.6 7.4 - - - +
69B THR* 1.3 86.7 - - - +
71B ALA* 1.3 64.7 - - + +
73B VAL* 3.1 6.8 + - + +
74B ILE* 2.9 41.8 + - + +
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Residues in contact with ALA 71 (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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13B ILE* 3.9 26.5 - - + +
16B LEU* 3.5 48.7 - - + +
17B ARG* 4.4 4.3 - - + +
18B GLY 5.6 0.2 - - - +
69B THR* 5.1 0.7 - - - -
70B PRO* 1.3 78.2 - - + +
72B GLU* 1.3 65.5 + - + +
74B ILE* 4.6 1.6 - - - -
75B LEU* 3.5 22.7 + - - +
90D PHE* 4.4 3.9 - - + -
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Residues in contact with GLU 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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69B THR* 3.0 37.0 + - - +
71B ALA* 1.3 79.4 - - + +
73B VAL* 1.3 64.4 + - + +
75B LEU* 3.9 1.7 - - - +
76B ALA* 3.1 24.8 + - - +
85D LEU* 3.8 26.0 - - + +
90D PHE* 3.7 47.0 - - + +
93D GLN 4.1 14.0 + - - -
94D LYS* 3.2 18.6 + - - -
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Residues in contact with VAL 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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59B ALA* 5.0 6.1 - - + +
62B LYS* 5.5 7.2 - - + +
64B VAL* 3.7 28.0 - - + -
67B SER* 3.9 16.6 - - - +
69B THR* 3.4 17.2 + - - +
70B PRO 3.1 8.3 + - - +
72B GLU* 1.3 76.1 - - + +
74B ILE* 1.3 58.9 + - - +
76B ALA* 3.4 1.7 + - - +
77B THR* 2.5 42.0 + - - +
81D ARG* 4.0 21.4 + - - +
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Residues in contact with ILE 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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13B ILE* 4.8 3.4 - - + -
16B LEU* 3.9 26.9 - - + -
22B ILE* 5.2 4.3 - - + -
26B ASP 6.2 0.2 - - - -
27B LEU* 3.8 28.0 - - + -
30B THR* 4.4 10.1 - - + -
31B LEU* 4.1 15.0 - - + -
34B ILE* 3.7 29.6 - - + -
55B VAL* 4.7 2.4 - - + +
59B ALA* 5.9 4.0 - - + -
64B VAL* 4.5 9.9 - - + -
70B PRO* 2.9 31.3 + - + +
71B ALA* 4.4 2.5 - - - +
73B VAL* 1.3 73.6 - - - +
75B LEU* 1.3 59.0 + - - +
77B THR* 3.4 5.7 + - - -
78B VAL* 2.9 34.2 + - + +
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Residues in contact with LEU 75 (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 LEU* 4.0 32.1 - - + -
9B LEU* 4.8 10.3 - - + -
13B ILE* 3.8 29.1 - - + +
34B ILE* 6.2 0.9 - - + -
71B ALA 3.5 14.8 + - - +
72B GLU 3.5 2.6 + - - +
73B VAL 3.3 0.4 - - - -
74B ILE* 1.3 75.9 - - - +
76B ALA* 1.3 60.5 + - - +
78B VAL* 3.4 12.4 + - + +
79B TYR* 2.9 29.8 + - - +
292B LEU* 5.3 6.0 - - + +
88D LEU* 3.8 29.4 - - + +
90D PHE* 3.9 26.0 - - + -
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Residues in contact with ALA 76 (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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72B GLU 3.1 17.8 + - - +
73B VAL 3.8 0.4 - - - +
75B LEU* 1.3 73.1 - - - +
77B THR* 1.3 57.3 + - - +
79B TYR* 3.2 1.6 + - - +
80B GLU* 2.8 42.8 + - - +
81D ARG* 3.4 35.4 - - - +
84D THR* 3.8 20.2 - - + -
85D LEU* 4.2 8.1 - - + -
88D LEU* 4.2 2.9 - - + +
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Residues in contact with THR 77 (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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55B VAL* 4.0 26.5 - - + +
58B GLU* 4.1 27.4 - - + -
59B ALA* 4.6 7.7 - - + +
73B VAL* 2.5 32.3 + - - +
74B ILE* 3.6 5.2 - - - -
76B ALA* 1.3 76.3 - - - +
78B VAL* 1.3 56.2 + - - +
80B GLU* 3.9 4.5 - - - +
81B ALA* 2.9 34.0 + - + +
81D ARG* 3.4 18.0 + - - +
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Residues in contact with VAL 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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9B LEU* 6.0 0.9 - - + -
31B LEU* 5.2 0.2 - - + -
34B ILE* 3.9 38.8 - - + -
38B LEU* 5.9 0.2 - - + -
51B PHE* 3.3 24.5 - - + -
52B VAL* 6.0 0.2 - - + -
55B VAL* 3.9 20.4 - - + -
74B ILE* 2.9 22.7 + - + +
75B LEU* 3.6 11.7 - - + +
77B THR* 1.3 76.0 - - - +
79B TYR* 1.3 56.8 + - - +
82B LEU* 3.0 26.6 + - + +
292B LEU* 3.8 32.3 - - + -
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Residues in contact with TYR 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 LEU* 2.9 17.7 + - + +
76B ALA 3.6 3.8 - - - +
78B VAL* 1.3 76.8 - - - +
80B GLU* 1.3 60.3 + - + +
82B LEU* 3.8 2.3 - - - +
83B LYS* 3.1 33.1 + - + +
285B GLU* 3.1 48.1 + - + +
288B ALA* 4.2 5.3 - - + +
289B GLY* 3.8 23.7 + - - -
292B LEU* 3.9 23.6 - - + -
84D THR* 4.3 21.1 - - + -
87D LYS* 3.6 31.5 + - + -
88D LEU* 4.3 20.9 - - + -
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Residues in contact with GLU 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 ALA 2.8 22.4 + - - +
77B THR* 4.0 4.3 - - - +
79B TYR* 1.3 75.1 - - + +
81B ALA* 1.3 63.9 + - - +
83B LYS* 4.1 6.8 - - + +
84B GLU* 3.2 23.7 + - - +
80D GLU* 3.5 24.2 - - + +
81D ARG* 3.0 47.3 + - - -
84D THR* 2.9 32.1 + - + +
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Residues in contact with ALA 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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51B PHE* 3.5 22.7 - - + -
54B ARG* 6.5 1.3 - - - -
55B VAL* 3.9 12.1 - - + -
77B THR* 2.9 21.3 + - + +
80B GLU* 1.3 76.5 - - - +
82B LEU* 1.3 58.6 + - - +
84B GLU* 3.5 5.1 + - - +
85B ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 82 (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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38B LEU* 4.7 9.0 - - + -
51B PHE* 3.4 14.1 - - + -
78B VAL 3.0 16.7 + - - +
79B TYR 3.8 4.7 - - - +
80B GLU 3.3 0.2 - - - -
81B ALA* 1.3 75.3 - - - +
83B LYS* 1.3 65.4 + - - +
85B ALA* 3.2 3.6 + - - +
86B LEU* 2.9 37.0 + - + +
257B LEU* 3.9 29.4 - - + -
288B ALA* 3.4 39.3 - - + +
291B ILE* 4.1 17.9 - - + -
292B LEU* 3.7 25.1 - - + -
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Residues in contact with LYS 83 (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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79B TYR* 3.1 21.7 + - + +
80B GLU* 4.1 6.3 - - - +
82B LEU* 1.3 79.1 - - - +
84B GLU* 1.3 61.3 + - - +
86B LEU 3.2 1.6 + - - -
87B GLY 3.2 6.6 + - - -
88B GLY* 2.8 46.1 + - - +
89B GLU* 3.8 18.3 + - - -
284B PRO* 3.6 16.1 - - - +
285B GLU* 3.8 43.2 + - + +
288B ALA* 4.0 9.3 - - + +
80D GLU* 6.2 2.0 - - - +
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Residues in contact with GLU 84 (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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80B GLU 3.2 18.1 + - - +
81B ALA* 3.8 5.6 - - - +
83B LYS* 1.3 79.9 - - - +
85B ALA* 1.3 58.7 + - - +
87B GLY* 2.9 20.4 + - - -
88B GLY* 3.9 16.5 + - - +
260B ARG* 4.4 6.2 + - - -
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Residues in contact with ALA 85 (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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51B PHE* 4.6 8.1 - - + -
81B ALA 2.9 19.1 + - - +
82B LEU* 3.5 5.2 - - - +
84B GLU* 1.3 76.4 - - - +
86B LEU* 1.3 56.3 + - - +
87B GLY 3.2 0.2 - - - -
257B LEU* 3.4 30.7 - - + +
260B ARG* 3.0 25.0 + - - +
261B HIS* 5.3 0.9 + - - -
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Residues in contact with LEU 86 (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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82B LEU* 2.9 27.3 + - + +
83B LYS 3.6 6.3 - - - +
84B GLU 3.2 0.2 - - - -
85B ALA* 1.3 76.9 - - - +
87B GLY* 1.3 56.4 + - - +
88B GLY 3.8 0.2 - - - -
256B ALA* 4.3 5.2 - - + -
257B LEU* 4.1 32.1 - - + +
260B ARG* 3.6 12.8 - - - +
267B ILE* 4.4 8.8 + - + +
282B PHE* 3.7 12.0 - - + -
284B PRO* 3.4 41.0 - - + +
287B LEU* 3.8 30.1 - - + +
288B ALA* 3.5 22.2 - - - +
291B ILE* 4.5 4.7 - - + -
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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
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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