Contacts of the helix formed by residues 23 - 41 (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 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ILE* 1.3 83.1 - - - +
24A GLU* 1.3 64.2 + - - +
25A GLU* 3.4 11.5 + - - +
26A ASP* 3.0 33.7 + - - +
27A LEU* 3.2 16.6 + - - +
65A LEU* 4.6 3.4 - - - +
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Residues in contact with GLU 24 (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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23A THR* 1.3 72.3 - - - +
25A GLU* 1.3 64.3 - - - +
27A LEU* 3.2 14.2 + - + +
28A LYS* 3.0 24.5 + - + +
56A ARG* 4.4 18.1 + - - +
60A LEU* 5.8 6.1 - - + +
65A LEU* 4.2 32.0 - - + +
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Residues in contact with GLU 25 (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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23A THR* 3.2 10.9 + - - +
24A GLU* 1.3 78.9 - - - +
26A ASP* 1.3 55.5 + - - +
28A LYS* 3.4 6.8 + - + +
29A ALA* 2.9 32.2 + - + +
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Residues in contact with ASP 26 (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 ARG* 4.1 16.6 + - - -
16A LEU* 3.7 23.7 - - + +
22A ILE* 3.9 17.5 - - + +
23A THR* 3.0 40.0 + - - +
25A GLU* 1.3 76.1 - - - +
27A LEU* 1.3 52.6 + - - +
29A ALA* 3.6 7.3 + - - +
30A THR* 2.7 37.5 + - - -
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Residues in contact with LEU 27 (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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22A ILE* 4.3 7.5 - - + +
23A THR 3.2 11.0 + - - +
24A GLU* 3.2 20.3 + - + +
26A ASP* 1.3 73.4 - - - +
28A LYS* 1.3 55.5 + - - +
30A THR* 3.0 7.9 + - - -
31A LEU* 2.8 60.8 + - + +
56A ARG* 4.5 11.7 - - + +
59A ALA* 4.5 8.3 - - + -
60A LEU* 3.9 31.0 - - + -
64A VAL* 4.2 14.8 - - + -
65A LEU* 5.0 3.4 - - + -
74A ILE* 3.9 27.6 - - + -
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Residues in contact with LYS 28 (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* 3.0 16.9 + - + +
25A GLU* 3.9 7.6 - - + +
27A LEU* 1.3 77.0 - - - +
29A ALA* 1.3 56.5 + - - +
31A LEU* 3.8 8.9 - - + +
32A ARG* 2.9 41.9 + - + +
56A ARG* 4.6 27.4 - - - +
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Residues in contact with ALA 29 (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 ARG* 5.6 8.1 - - - +
25A GLU* 2.9 19.9 + - + +
26A ASP* 3.7 9.9 - - - +
28A LYS* 1.3 76.4 - - - +
30A THR* 1.3 61.9 + - - +
32A ARG* 3.5 33.4 + - - +
33A GLU* 3.3 24.6 + - - +
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Residues in contact with THR 30 (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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12A ALA* 4.5 9.7 + - + +
13A ILE* 3.9 18.6 - - + -
15A ARG* 5.1 2.3 + - - -
16A LEU* 3.2 23.1 - - + +
26A ASP 2.7 19.9 + - - -
27A LEU* 3.0 10.5 + - - -
29A ALA* 1.3 72.5 - - - +
31A LEU* 1.3 59.3 + - - +
32A ARG 3.1 2.0 - - - -
33A GLU* 2.9 23.3 + - - +
34A ILE* 3.0 21.9 + - + +
74A ILE* 3.9 32.9 - - + +
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Residues in contact with LEU 31 (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* 2.8 48.4 + - + +
28A LYS* 3.9 8.1 - - + +
30A THR* 1.3 72.7 - - - +
32A ARG* 1.3 55.6 - - - +
34A ILE* 3.7 17.7 - - + -
35A ARG* 3.1 27.4 + - - +
52A VAL* 3.6 28.3 - - + +
55A VAL* 3.7 30.3 - - + -
56A ARG* 3.8 33.7 - - + +
74A ILE* 5.0 3.1 - - + -
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Residues in contact with ARG 32 (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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25A GLU 5.5 0.2 + - - -
28A LYS* 2.9 26.9 + - + +
29A ALA* 3.5 41.9 + - - +
30A THR 3.1 0.2 - - - -
31A LEU* 1.3 78.5 - - - +
33A GLU* 1.3 66.3 + - - +
35A ARG* 3.4 12.7 - - + +
36A ARG* 3.1 40.5 + - + +
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Residues in contact with GLU 33 (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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8A ARG* 3.3 33.7 + - + +
9A LEU* 4.4 2.0 - - - -
12A ALA* 4.0 26.2 - - + -
29A ALA 3.3 12.2 + - - +
30A THR* 2.9 8.6 + - - +
32A ARG* 1.3 89.3 + - - +
34A ILE* 1.3 59.7 + - - +
36A ARG* 3.5 26.0 + - - -
37A ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 34 (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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9A LEU* 3.9 23.8 - - + -
13A ILE* 5.4 2.5 - - + -
30A THR* 3.0 29.1 + - + +
31A LEU* 3.7 31.0 - - + +
32A ARG 3.4 0.2 - - - -
33A GLU* 1.3 73.0 - - - +
35A ARG* 1.3 64.3 + - - +
37A ALA* 3.2 3.3 + - - +
38A LEU* 3.0 41.0 + - + +
51A PHE* 4.9 2.5 - - + -
52A VAL* 4.3 11.0 - - + -
55A VAL* 5.1 1.3 - - + -
74A ILE* 4.1 4.3 - - + -
78A VAL* 3.7 43.3 - - + -
292A LEU* 5.0 3.4 - - + -
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Residues in contact with ARG 35 (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 3.1 18.8 + - - +
32A ARG* 3.4 13.5 - - - +
33A GLU 3.3 0.2 - - - -
34A ILE* 1.3 74.6 - - - +
36A ARG* 1.3 62.6 + - + +
38A LEU* 3.1 9.0 + - - +
39A MET* 3.1 38.9 + - + +
45A LEU* 4.8 5.5 + - - +
48A ALA* 4.0 23.0 - - + +
49A ARG* 3.5 51.7 - - - +
52A VAL* 3.7 21.9 - - + +
37D MET* 4.5 13.3 - - - +
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Residues in contact with ARG 36 (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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8A ARG* 2.9 43.9 - - - +
32A ARG* 3.1 21.8 + - + +
33A GLU* 3.7 31.1 + - - +
34A ILE 3.3 0.4 - - - -
35A ARG* 1.3 79.9 - - + +
37A ALA* 1.3 57.2 + - - +
39A MET* 3.2 13.8 + - + +
40A ASP* 3.0 25.6 + - - +
46D LEU* 3.4 45.2 + - + +
50D GLU* 5.1 15.0 + - - +
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Residues in contact with ALA 37 (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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6A SER* 4.9 3.8 - - - +
8A ARG* 3.6 19.2 - - - +
9A LEU* 3.8 27.8 - - + -
33A GLU 3.0 19.4 + - - +
34A ILE 3.4 5.8 - - - +
36A ARG* 1.3 77.4 - - - +
38A LEU* 1.3 58.3 + - + +
40A ASP* 3.5 9.0 - - - +
41A ALA* 3.1 25.1 + - - +
291A ILE 4.8 3.2 - - - +
292A LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 38 (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* 3.0 22.1 + - + +
35A ARG 3.1 6.0 + - - +
37A ALA* 1.3 75.0 - - + +
39A MET* 1.3 58.4 + - - +
41A ALA* 3.1 7.6 + - - -
43A VAL* 2.8 52.0 + - + +
48A ALA* 4.1 17.5 - - + +
51A PHE* 3.5 40.8 - - + -
52A VAL* 4.4 6.5 - - + -
82A LEU* 4.7 9.2 - - + -
257A LEU* 5.2 2.2 - - + -
291A ILE* 3.9 25.1 - - + -
292A LEU* 4.3 18.8 - - + -
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Residues in contact with MET 39 (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* 3.1 25.9 + - + +
36A ARG* 3.5 27.1 - - + +
38A LEU* 1.3 75.6 - - - +
40A ASP* 1.3 58.9 + - - +
42A ASP* 3.1 20.3 + - - +
43A VAL 3.7 16.4 + - - +
45A LEU* 3.8 28.5 - - + +
48A ALA* 4.7 6.0 - - + +
224A GLN* 4.3 14.0 + - - +
40D LEU* 4.4 20.2 - - + -
46D LEU* 3.7 31.9 - - + -
234D GLN* 4.8 4.7 - - - +
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Residues in contact with ASP 40 (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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8A ARG* 2.7 36.1 + - - +
36A ARG 3.0 10.8 + - - +
37A ALA* 3.5 12.3 - - - +
38A LEU 3.3 0.2 - - - -
39A MET* 1.3 74.2 - - - +
41A ALA* 1.3 56.6 + - - +
42A ASP* 3.1 6.3 + - - +
252A ARG* 4.8 4.9 - - - +
46D LEU* 4.1 21.2 + - - +
234D GLN* 4.3 25.7 - - - +
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Residues in contact with ALA 41 (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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37A ALA 3.1 16.1 + - - +
38A LEU 3.1 7.5 + - - +
40A ASP* 1.3 75.7 - - - +
42A ASP* 1.3 63.9 + - - +
43A VAL* 3.3 2.0 - - + -
252A ARG* 3.7 24.7 - - + +
254A GLY* 3.0 27.2 + - - -
291A ILE* 3.6 35.2 - - + +
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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