Contacts of the helix formed by residues 44 - 62 (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 ASN 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ASP 3.4 1.8 + - - -
43B VAL* 1.3 73.6 - - - +
45B LEU* 1.3 57.8 + - - +
46B GLU* 3.1 47.4 + - - +
47B VAL* 3.0 15.4 + - + +
48B ALA* 2.8 31.0 + - - +
224B GLN* 3.3 36.6 + - - +
227B LEU* 4.0 17.1 - - + +
258B SER* 3.0 30.9 + - - +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B MET* 3.7 21.8 - - + -
43B VAL 3.3 3.1 + - - -
44B ASN* 1.3 75.5 - - - +
46B GLU* 1.3 80.8 + - + +
48B ALA* 3.5 4.8 + - - +
49B ARG* 3.0 47.6 + - - +
224B GLN* 2.9 18.9 + - - +
37E MET* 3.7 38.6 - - + +
40E LEU* 3.8 24.7 - - + -
41E ALA* 3.9 16.6 - - + +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASN* 3.1 21.6 + - - +
45B LEU* 1.3 88.5 - - + +
47B VAL* 1.3 64.9 + - + +
49B ARG* 3.4 8.0 + - - +
50B ASP* 3.1 22.7 + - - +
227B LEU* 5.0 13.8 - - + +
231B ARG* 5.2 5.4 + - - -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.9 15.7 - - + -
44B ASN* 3.0 16.6 + - + +
46B GLU* 1.3 77.0 - - + +
48B ALA* 1.3 58.0 + - - +
50B ASP* 3.4 7.5 - - - +
51B PHE* 2.9 27.6 + - + +
227B LEU* 3.6 24.2 - - + -
257B LEU* 4.0 23.1 - - + +
258B SER* 4.2 4.3 - - - -
261B HIS* 3.5 44.9 - - + +
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Residues in contact with ALA 48 (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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35B ARG* 4.1 14.6 - - + +
38B LEU* 4.0 24.9 - - + -
39B MET* 4.7 2.9 - - + +
43B VAL* 3.8 16.1 - - + +
44B ASN 2.8 16.2 + - - +
45B LEU* 3.6 9.9 - - - +
47B VAL* 1.3 75.5 - - - +
49B ARG* 1.3 70.1 + - - +
51B PHE* 3.3 2.4 + - - +
52B VAL* 3.2 26.2 + - - +
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 3.3 39.1 - - - +
39B MET* 3.0 37.6 - - - +
45B LEU* 3.0 34.9 + - - +
46B GLU* 3.4 11.9 - - - +
48B ALA* 1.3 77.0 - - - +
50B ASP* 1.3 63.2 - - - +
52B VAL* 3.4 3.5 + - - +
53B GLU* 3.1 30.8 + - + +
36E GLU* 6.0 0.4 + - - -
37E MET* 5.0 14.8 - - - +
40E LEU* 5.9 2.2 - - - +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU 3.1 10.8 + - - +
47B VAL* 3.4 12.8 - - - +
49B ARG* 1.3 80.4 - - - +
51B PHE* 1.3 66.5 + - - +
53B GLU* 3.3 13.1 + - - +
54B ARG* 2.9 35.3 + - - +
261B HIS* 3.9 23.8 + - + +
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 5.2 0.4 - - + -
38B LEU* 3.6 25.8 - - + -
47B VAL* 2.9 18.4 + - + +
48B ALA* 3.3 6.0 + - - +
50B ASP* 1.3 79.3 + - - +
52B VAL* 1.3 65.3 + - + +
54B ARG* 3.1 7.3 + - - +
55B VAL* 2.8 42.8 + - + +
78B VAL* 3.3 41.5 - - + -
81B ALA* 3.5 20.9 - - + -
82B LEU* 3.4 34.1 - - + -
85B ALA* 4.6 7.2 - - + -
257B LEU* 4.6 14.6 - - + -
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Residues in contact with VAL 52 (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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31B LEU* 3.3 43.1 - - + +
34B ILE* 3.9 17.5 - - + -
35B ARG* 3.8 40.2 - - + +
38B LEU* 4.2 2.0 - - + -
48B ALA 3.2 11.2 + - - +
49B ARG 3.4 10.3 - - - +
51B PHE* 1.3 81.6 - - + +
53B GLU* 1.3 59.6 + - - +
55B VAL* 3.2 8.2 + - + +
56B ARG 2.7 29.3 + - - -
78B VAL* 6.0 0.2 - - + -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.4 0.2 - - - -
49B ARG* 3.1 22.7 + - + +
50B ASP* 3.5 15.8 + - - +
52B VAL* 1.3 79.6 - - + +
54B ARG* 1.3 57.1 + - - +
56B ARG* 3.2 29.3 + - - +
57B GLU* 3.1 37.3 + - + +
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Residues in contact with ARG 54 (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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50B ASP* 2.9 24.5 + - - +
51B PHE* 3.4 10.1 - - - +
53B GLU* 1.3 73.4 - - - +
55B VAL* 1.3 65.4 + - + +
56B ARG 3.2 0.4 - - - -
57B GLU* 3.6 9.1 + - + +
58B GLU* 3.1 25.1 + - + +
81B ALA* 6.5 1.3 - - - -
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.3 14.6 - - + -
51B PHE* 2.8 43.0 + - + +
52B VAL* 3.2 10.5 + - + +
54B ARG* 1.3 73.6 - - - +
56B ARG* 1.3 63.3 - - - +
58B GLU* 4.0 4.7 - - - +
59B ALA* 3.1 25.4 + - + +
74B ILE* 4.7 3.4 - - + +
77B THR* 4.0 20.7 - - + +
78B VAL* 3.9 22.4 - - + -
81B ALA* 3.9 20.2 - - + -
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Residues in contact with ARG 56 (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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24B GLU* 5.7 4.0 - - - +
27B LEU* 4.8 11.0 - - + -
31B LEU* 3.4 21.5 - - + -
52B VAL 2.7 17.7 + - - +
53B GLU* 3.2 27.4 + - - +
55B VAL* 1.3 72.7 - - - +
57B GLU* 1.3 90.9 + - - +
59B ALA* 3.8 2.8 - - - +
60B LEU* 3.2 46.2 + - + +
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Residues in contact with GLU 57 (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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53B GLU* 3.1 21.6 + - + +
54B ARG* 3.9 9.0 - - + +
55B VAL 3.5 0.2 - - - -
56B ARG* 1.3 106.8 + - - +
58B GLU* 1.3 63.6 + - - +
60B LEU* 3.6 8.6 + - - +
61B GLY* 3.2 19.1 + - - -
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Residues in contact with GLU 58 (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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54B ARG* 3.1 16.2 + - + +
55B VAL* 4.0 4.3 - - - +
57B GLU* 1.3 78.2 - - - +
59B ALA* 1.3 63.9 + - - +
61B GLY* 3.2 4.9 + - - -
62B LYS* 3.0 50.4 + - + +
77B THR* 4.1 19.5 - - + -
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Residues in contact with ALA 59 (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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27B LEU* 5.4 7.6 - - + -
55B VAL* 3.1 18.9 + - + +
56B ARG* 3.4 4.0 + - - +
58B GLU* 1.3 79.6 - - - +
60B LEU* 1.3 60.8 + - + +
62B LYS* 2.9 23.1 + - - +
64B VAL* 3.2 40.4 + - + +
73B VAL* 5.0 4.0 - - + +
74B ILE* 5.9 3.4 - - - -
77B THR* 4.7 16.2 - - + +
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Residues in contact with LEU 60 (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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24B GLU* 4.2 17.5 - - - +
27B LEU* 3.9 14.1 - - + -
56B ARG* 3.2 36.4 + - + +
57B GLU* 3.9 7.2 - - - +
59B ALA* 1.3 77.5 - - - +
61B GLY* 1.3 57.9 + - - +
63B GLN* 3.1 23.2 + - - +
64B VAL* 3.8 13.9 - - + -
65B LEU* 3.7 43.3 - - + +
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Residues in contact with GLY 61 (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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57B GLU 3.2 8.3 + - - -
58B GLU* 3.2 8.3 + - - -
60B LEU* 1.3 78.8 - - - +
62B LYS* 1.3 59.9 + - - +
63B GLN* 2.6 23.6 + - - +
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Residues in contact with LYS 62 (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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58B GLU* 3.0 34.6 + - + +
59B ALA* 2.9 13.8 + - - +
61B GLY* 1.3 78.3 - - - +
63B GLN* 1.3 71.2 + - - +
64B VAL* 3.3 1.6 + - - -
73B VAL* 5.5 6.4 - - + +
81D ARG* 6.3 1.1 - - - +
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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