Contacts of the helix formed by residues 44 - 61 (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 ASN 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ASP 3.4 3.2 + - - -
43A VAL* 1.3 73.9 - - - +
45A LEU* 1.3 75.1 + - - +
46A GLU* 3.0 22.5 + - - +
47A VAL* 3.2 5.9 + - + -
48A ALA* 2.9 25.8 + - - +
223A GLY 5.8 0.2 - - - +
224A GLN* 2.8 46.3 + - - +
227A LEU* 3.4 31.1 - - + +
228A SER 5.4 0.2 - - - +
258A SER* 3.0 26.7 + - - +
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Residues in contact with LEU 45 (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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35A ARG* 4.8 6.8 + - - +
39A MET* 3.8 27.3 - - + +
43A VAL 3.5 0.4 + - - -
44A ASN* 1.3 83.7 + - - +
46A GLU* 1.3 80.3 + - + +
48A ALA* 3.7 2.1 + - - +
49A ARG* 3.1 26.2 + - - +
224A GLN* 3.1 19.2 + - - +
37D MET* 3.8 54.5 - - + +
40D LEU* 3.9 18.6 - - + -
41D ALA* 4.3 15.0 - - + +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN* 3.0 14.5 + - - +
45A LEU* 1.3 85.4 - - + +
47A VAL* 1.3 60.0 + - - +
49A ARG* 3.3 23.8 + - - +
50A ASP* 3.0 35.4 + - - +
227A LEU* 4.5 17.8 - - + +
231A ARG* 4.9 7.6 + - - -
261A HIS* 5.7 0.4 - - - -
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Residues in contact with VAL 47 (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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43A VAL* 3.7 16.4 - - + -
44A ASN* 3.2 12.2 + - + +
46A GLU* 1.3 75.8 - - - +
48A ALA* 1.3 53.7 + - - +
50A ASP* 3.3 3.4 + - - +
51A PHE* 2.8 32.7 + - + +
227A LEU* 3.5 28.9 - - + -
257A LEU* 3.9 17.9 - - + -
258A SER* 3.9 16.8 - - - -
261A HIS* 3.7 44.9 - - + +
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Residues in contact with ALA 48 (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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35A ARG* 4.2 17.3 - - + +
38A LEU* 4.1 23.9 - - + +
39A MET* 4.7 5.2 - - - +
43A VAL* 3.8 17.0 - - + +
44A ASN 2.9 16.8 + - - +
45A LEU* 3.9 7.6 - - - +
47A VAL* 1.3 73.8 - - - +
49A ARG* 1.3 66.7 + - - +
51A PHE* 3.4 1.3 + - - +
52A VAL* 3.3 29.6 + - - +
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Residues in contact with ARG 49 (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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35A ARG* 3.5 48.5 - - - +
45A LEU 3.1 13.7 + - - +
46A GLU* 3.3 30.4 + - - +
48A ALA* 1.3 75.0 - - - +
50A ASP* 1.3 69.1 + - - +
52A VAL* 3.3 8.1 - - + +
53A GLU* 3.3 20.8 + - - +
33D GLU* 5.8 1.2 + - - -
37D MET* 3.0 32.4 - - - +
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Residues in contact with ASP 50 (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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46A GLU* 3.0 18.6 + - - +
47A VAL 3.7 7.0 - - - +
49A ARG* 1.3 80.1 + - - +
51A PHE* 1.3 65.7 + - - +
53A GLU* 3.2 9.0 + - - +
54A ARG* 3.0 22.3 + - - +
261A HIS* 3.5 31.8 + - + -
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Residues in contact with PHE 51 (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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34A ILE* 4.9 2.0 - - + -
38A LEU* 3.5 31.4 - - + -
47A VAL* 2.8 22.8 + - + +
48A ALA* 3.8 4.7 - - - +
49A ARG 3.3 0.2 - - - -
50A ASP* 1.3 74.3 - - - +
52A VAL* 1.3 59.2 + - + +
54A ARG* 3.3 14.0 + - - +
55A VAL* 3.1 40.3 + - + +
78A VAL* 3.9 18.2 - - + -
81A ALA* 3.5 23.6 - - + -
82A LEU* 3.4 47.8 - - + -
85A ALA* 4.5 9.0 - - + -
257A LEU* 4.4 17.7 - - + -
261A HIS* 5.4 1.3 - - - +
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Residues in contact with VAL 52 (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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31A LEU* 3.6 41.9 - - + +
34A ILE* 4.3 11.0 - - + -
35A ARG* 3.7 30.7 - - - +
38A LEU* 4.4 8.3 - - + -
48A ALA 3.3 13.0 + - - +
49A ARG* 3.3 15.9 - - + +
51A PHE* 1.3 75.9 - - + +
53A GLU* 1.3 65.0 + - - +
55A VAL* 3.4 8.5 + - + +
56A ARG* 2.9 27.4 + - - +
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Residues in contact with GLU 53 (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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49A ARG 3.3 14.0 + - - +
50A ASP* 3.2 12.5 + - - +
52A VAL* 1.3 80.6 - - - +
54A ARG* 1.3 63.2 + - - +
56A ARG* 3.4 41.1 + - - +
57A GLU* 3.4 33.1 + - - +
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Residues in contact with ARG 54 (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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50A ASP 3.0 12.7 + - - +
51A PHE* 3.4 16.7 - - - +
52A VAL 3.3 0.2 - - - -
53A GLU* 1.3 74.6 - - - +
55A VAL* 1.3 64.1 + - - +
57A GLU* 3.4 14.9 + - - +
58A GLU* 3.2 42.7 + - + +
81A ALA* 2.6 47.5 + - - +
84A GLU* 4.0 18.4 - - - +
85A ALA* 3.8 24.1 - - - +
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Residues in contact with VAL 55 (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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31A LEU* 3.7 21.1 - - + -
34A ILE* 5.1 1.1 - - + -
51A PHE* 3.1 45.2 + - + +
52A VAL* 3.6 11.0 - - + +
53A GLU 3.3 0.2 - - - -
54A ARG* 1.3 76.3 - - - +
56A ARG* 1.3 55.7 + - - +
58A GLU* 3.3 2.2 + - - +
59A ALA* 2.9 33.1 + - + +
74A ILE* 4.8 3.8 - - + +
77A THR* 4.1 22.8 - - + +
78A VAL* 4.2 18.8 - - + -
81A ALA* 4.2 11.4 - - + -
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Residues in contact with ARG 56 (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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24A GLU* 4.4 18.4 + - - +
27A LEU* 4.5 9.5 - - + +
28A LYS* 4.6 26.0 - - - +
31A LEU* 3.8 23.1 - - + +
52A VAL 2.9 17.5 + - - +
53A GLU* 3.4 38.9 + - - +
54A ARG 3.2 0.2 - - - -
55A VAL* 1.3 75.9 - - - +
57A GLU* 1.3 64.5 + - - +
59A ALA* 3.8 3.5 - - - +
60A LEU* 3.0 47.5 + - + +
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Residues in contact with GLU 57 (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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53A GLU* 3.4 22.5 + - - +
54A ARG* 3.7 13.4 - - - +
55A VAL 3.4 0.2 - - - -
56A ARG* 1.3 80.8 - - + +
58A GLU* 1.3 54.1 + - + +
60A LEU* 3.4 6.7 + - - +
61A GLY* 2.8 31.5 + - - -
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Residues in contact with GLU 58 (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* 3.2 43.6 + - + +
57A GLU* 1.3 79.8 - - + +
59A ALA* 1.3 58.5 + - - +
61A GLY* 3.1 3.5 + - - -
62A LYS* 2.9 47.6 + - + +
77A THR* 3.7 26.3 - - + +
80A GLU* 5.3 4.3 - - - +
81A ALA* 4.1 15.0 + - - +
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Residues in contact with ALA 59 (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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27A LEU* 4.5 13.7 - - + -
55A VAL* 2.9 26.4 + - + +
56A ARG 3.8 3.6 - - - +
58A GLU* 1.3 71.3 - - - +
60A LEU* 1.3 58.4 + - - +
62A LYS* 3.0 17.0 + - - +
63A GLN 3.3 0.3 + - - -
64A VAL* 3.0 44.1 + - + +
73A VAL* 5.0 2.5 - - + -
74A ILE* 5.0 6.1 - - + -
77A THR* 4.2 14.7 - - + +
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Residues in contact with LEU 60 (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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24A GLU* 5.8 6.1 - - + +
27A LEU* 3.9 16.8 - - + -
56A ARG* 3.0 42.5 + - + +
57A GLU* 3.8 6.1 - - - +
59A ALA* 1.3 69.6 - - - +
61A GLY* 1.3 57.7 + - - +
62A LYS 3.1 4.7 - - - -
63A GLN* 2.9 22.0 + - - +
64A VAL* 3.7 21.1 - - + +
65A LEU* 3.9 26.0 - - + -
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Residues in contact with GLY 61 (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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57A GLU 2.8 19.0 + - - -
58A GLU* 3.1 7.6 + - - -
60A LEU* 1.3 72.6 - - - +
62A LYS* 1.3 60.3 + - - +
63A GLN* 3.3 10.3 + - - +
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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