Contacts of the helix formed by residues 4 - 20 (chain A) in PDB entry 2CNR
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 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA 5.4 0.3 + - - -
3A ALA* 1.3 74.9 - - - +
5A GLN* 1.3 76.3 + - + +
6A GLU* 3.5 5.6 - - - -
7A GLU* 2.7 24.4 + - - -
8A ILE* 2.9 22.3 + - - +
78A LEU* 4.0 7.0 - - + -
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Residues in contact with GLN 5 (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 THR* 1.3 84.4 - - + +
6A GLU* 1.3 54.9 + - - +
8A ILE* 3.2 1.5 - - - +
9A VAL* 2.7 43.7 + - + +
29A LEU* 3.2 46.3 - - + +
74A THR* 5.2 0.4 - - + -
75A LYS* 4.3 8.8 + - - +
78A LEU* 4.0 22.8 - - + +
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Residues in contact with GLU 6 (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 THR* 5.3 3.4 - - - -
5A GLN* 1.3 80.9 - - - +
7A GLU* 1.3 72.3 + - + +
9A VAL* 3.7 8.6 - - - +
10A ALA* 2.9 30.1 + - - +
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Residues in contact with GLU 7 (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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2A ALA 5.0 1.7 - - - +
3A ALA* 3.7 17.5 - - + +
4A THR* 2.7 41.7 + - - +
5A GLN 3.3 0.2 - - - -
6A GLU* 1.3 90.5 - - + +
8A ILE* 1.3 62.6 + - - +
10A ALA* 3.3 6.4 + - - +
11A GLY 3.3 15.2 + - - -
55A PHE* 3.7 9.5 - - + -
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Residues in contact with ILE 8 (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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3A ALA* 4.1 7.6 - - + +
4A THR 2.9 15.7 + - - +
5A GLN 3.2 11.2 - - - +
7A GLU* 1.3 74.2 - - - +
9A VAL* 1.3 58.6 + - - +
11A GLY 3.2 1.7 + - - -
12A LEU* 2.7 56.8 + - + +
55A PHE* 3.6 34.0 - - + -
74A THR* 3.3 24.9 - - + -
77A ILE* 3.9 27.4 - - + -
78A LEU* 3.4 18.2 - - + -
81A GLN* 5.8 0.9 - - - +
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 2.7 32.8 + - + +
6A GLU* 3.7 8.5 - - - +
8A ILE* 1.3 74.2 - - - +
10A ALA* 1.3 55.1 + - - +
12A LEU* 3.5 6.0 - - + +
13A ALA* 2.6 38.1 + - - +
24A VAL 4.8 6.3 - - - +
27A VAL* 3.9 34.8 - - + +
29A LEU* 4.0 20.9 - - + -
70A VAL* 5.9 0.2 - - + -
74A THR* 3.7 20.0 - - + +
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Residues in contact with ALA 10 (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 GLU 2.9 18.3 + - - +
7A GLU* 3.5 7.4 - - - +
8A ILE 3.2 0.2 - - - -
9A VAL* 1.3 78.5 - - - +
11A GLY* 1.3 57.7 + - - +
13A ALA* 3.7 4.6 - - - +
14A GLU* 3.0 30.8 + - - +
24A VAL* 5.1 4.1 - - - +
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Residues in contact with GLY 11 (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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7A GLU 3.3 4.9 + - - -
8A ILE 3.2 3.6 + - - -
10A ALA* 1.3 80.1 - - - +
12A LEU* 1.3 62.1 + - - +
14A GLU* 4.4 2.5 - - - -
15A ILE* 3.5 11.8 + - - +
51A ALA* 4.3 0.6 - - - +
54A ARG* 2.9 32.1 + - - -
55A PHE* 3.5 25.6 - - - -
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 2.7 40.8 + - + +
9A VAL* 3.5 8.3 - - - +
11A GLY* 1.3 72.0 - - - +
13A ALA* 1.3 61.2 + - - +
15A ILE* 3.0 4.5 + - - +
16A VAL* 2.9 52.9 + - + +
27A VAL* 5.3 0.4 - - + -
33A PHE* 4.1 7.9 - - + -
48A VAL* 3.8 21.8 - - + -
51A ALA* 3.6 23.8 - - + +
55A PHE* 4.3 0.4 - - - -
70A VAL* 4.4 18.2 - - + +
73A ALA* 5.7 2.0 - - + -
74A THR* 5.1 5.4 - - + -
77A ILE* 4.0 17.7 - - + -
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Residues in contact with ALA 13 (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 VAL 2.6 22.4 + - - +
10A ALA* 3.7 4.5 - - - +
12A LEU* 1.3 72.6 - - - +
14A GLU* 1.3 63.6 + - - +
16A VAL* 3.2 4.4 + - - +
17A ASN* 3.0 24.6 + - - +
22A ILE 4.5 4.2 - - - +
24A VAL* 3.7 26.7 - - + +
27A VAL* 3.3 36.2 - - + +
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Residues in contact with GLU 14 (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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10A ALA 3.0 18.9 + - - +
11A GLY* 3.9 4.9 - - - +
13A ALA* 1.3 76.8 - - - +
15A ILE* 1.3 61.0 + - + +
17A ASN* 3.5 14.4 - - - +
18A GLU* 4.0 4.9 + - - +
24A VAL* 4.1 12.9 - - + +
54A ARG* 2.8 36.5 + - - -
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Residues in contact with ILE 15 (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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11A GLY 3.5 5.8 + - - +
12A LEU 3.0 7.4 + - - +
14A GLU* 1.3 78.3 - - + +
16A VAL* 1.3 66.5 + - + +
17A ASN 3.1 2.0 - - - -
18A GLU* 2.9 28.7 + - + +
19A ILE* 3.6 1.4 + - - +
47A VAL* 3.0 47.4 - - + +
48A VAL* 4.1 4.0 - - - -
50A ALA* 3.7 11.0 - - + +
51A ALA* 3.4 41.7 - - + +
54A ARG* 3.8 22.2 - - - +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 2.9 43.6 + - + +
13A ALA* 4.0 5.8 - - - +
15A ILE* 1.3 71.9 - - - +
17A ASN* 1.3 57.4 + - - +
18A GLU 3.0 4.9 - - - -
19A ILE* 2.9 30.1 + - + +
20A ALA* 2.9 20.4 + - + +
21A GLY 3.9 1.6 + - - +
22A ILE* 5.3 3.6 - - + +
27A VAL* 5.6 2.2 - - + -
33A PHE* 3.7 24.2 - - + -
37A LEU* 3.5 34.5 - - + -
39A VAL* 5.2 1.3 - - + -
48A VAL* 4.0 6.1 - - + -
70A VAL* 5.3 2.2 - - + -
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Residues in contact with ASN 17 (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 ALA 3.0 16.7 + - - +
14A GLU* 3.5 11.9 - - - +
15A ILE 3.1 0.2 - - - -
16A VAL* 1.3 78.6 - - - +
18A GLU* 1.3 57.8 + - - +
20A ALA 4.0 12.1 - - - +
21A GLY* 4.2 17.5 - - - -
22A ILE 3.6 21.4 + - - +
23A PRO* 4.6 5.3 - - - +
24A VAL* 5.1 7.0 - - + +
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Residues in contact with GLU 18 (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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14A GLU 4.0 3.0 + - - +
15A ILE* 2.9 21.0 + - + +
17A ASN* 1.3 81.4 - - - +
19A ILE* 1.3 59.2 + - - +
47A VAL* 4.1 22.3 - - + +
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Residues in contact with ILE 19 (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 ILE 3.8 4.0 - - - +
16A VAL* 2.9 14.4 + - + +
18A GLU* 1.3 81.0 - - - +
20A ALA* 1.3 61.4 + - + +
39A VAL* 3.3 28.3 - - + -
43A SER* 3.3 38.4 - - - +
44A MET* 4.1 1.6 - - - -
47A VAL* 3.4 35.7 - - + -
48A VAL* 3.6 25.1 - - + -
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Residues in contact with ALA 20 (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 VAL* 2.9 13.7 + - + +
17A ASN 4.0 6.7 - - - +
19A ILE* 1.3 84.2 - - + +
21A GLY* 1.3 60.2 + - - +
22A ILE 5.0 0.2 - - - +
37A LEU 3.0 27.8 - - - +
38A ASP* 4.3 14.1 - - + +
39A VAL* 5.0 1.3 - - + +
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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