Contacts of the helix formed by residues 13 - 26 (chain A) in PDB entry 3N2E
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 GLY 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY* 3.1 7.2 - - - +
12A SER* 1.3 80.6 - - - +
14A LYS* 1.3 66.2 + - - +
15A SER* 3.4 3.1 + - - -
16A SER* 3.4 12.7 + - - -
17A LEU* 3.1 23.4 + - - +
97A LEU* 3.7 1.9 - - - +
107A ARG* 5.6 3.1 - - - -
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Residues in contact with LYS 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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6A LEU* 3.8 15.3 - - + +
7A ILE 3.8 2.7 - - - -
8A GLY 3.0 37.3 + - - +
9A PHE 3.6 19.2 + - - -
10A MET* 4.3 3.9 - - - +
11A GLY 5.3 0.7 - - - +
12A SER* 3.6 11.2 - - - +
13A GLY* 1.3 77.1 - - - +
15A SER* 1.3 53.0 + - - +
17A LEU* 3.3 3.5 + - - +
18A ALA* 2.8 33.3 + - - +
77A SER* 3.9 14.1 - - - -
78A THR 2.8 27.8 + - - +
79A GLY* 3.9 1.4 - - - -
80A GLY 3.7 10.9 - - - +
97A LEU* 3.8 25.8 - - + -
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Residues in contact with SER 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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13A GLY 3.4 0.4 - - - -
14A LYS* 1.3 75.7 - - - +
16A SER* 1.3 66.9 + - - +
18A ALA* 2.8 13.4 + - - +
19A GLN* 3.0 23.0 + - - +
31A ASP* 3.0 27.5 + - - +
77A SER* 3.5 10.9 + - - -
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Residues in contact with SER 16 (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 GLY* 3.4 13.7 + - - -
15A SER* 1.3 78.7 - - - +
17A LEU* 1.3 62.0 + - - +
19A GLN* 3.4 13.5 + - - +
20A GLU* 3.3 26.7 + - - +
150A LEU* 3.9 19.7 - - - -
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Residues in contact with LEU 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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6A LEU* 4.2 12.8 - - + -
13A GLY 3.1 14.2 + - - +
14A LYS 3.6 3.1 - - - +
16A SER* 1.3 76.3 - - - +
18A ALA* 1.3 66.5 + - - +
20A GLU* 3.5 3.8 + - + +
21A LEU* 3.0 24.6 + - + +
97A LEU* 3.9 33.7 - - + -
144A ILE* 5.1 2.7 - - + -
150A LEU* 4.3 12.6 - - + +
153A SER* 4.1 17.5 - - - +
154A LEU* 3.8 42.6 - - + +
157A VAL* 4.4 17.0 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.8 18.8 - - + -
14A LYS 2.8 14.5 + - - +
15A SER* 2.8 9.4 + - - +
17A LEU* 1.3 76.8 - - - +
19A GLN* 1.3 56.9 + - - +
21A LEU* 3.1 4.9 + - - +
22A GLY* 2.8 25.3 + - - -
29A VAL* 3.8 14.3 - - + +
75A VAL* 3.7 16.6 - - + +
77A SER* 3.9 22.0 - - - +
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Residues in contact with GLN 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 SER* 3.0 20.1 + - - +
16A SER* 3.8 14.0 + - - +
17A LEU 3.3 0.2 - - - -
18A ALA* 1.3 73.3 - - - +
20A GLU* 1.3 67.3 + - + +
22A GLY* 3.1 2.4 + - - -
23A LEU* 3.1 21.8 + - - +
29A VAL* 4.0 24.4 - - + +
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Residues in contact with GLU 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 SER 3.3 13.4 + - - +
17A LEU* 3.6 10.8 - - + +
19A GLN* 1.3 78.1 - - + +
21A LEU* 1.3 58.6 + - - +
23A LEU* 3.2 12.0 + - - +
24A ALA* 2.9 28.4 + - - +
150A LEU* 3.7 30.9 - - + +
151A ASN* 5.6 0.6 - - - +
154A LEU* 3.9 26.9 - - + +
155C LYS* 5.6 0.9 + - - -
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Residues in contact with LEU 21 (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 LEU* 4.1 13.5 - - + -
6A LEU* 4.6 16.4 - - + -
17A LEU* 3.0 19.3 + - + +
18A ALA 3.4 4.5 - - - +
20A GLU* 1.3 77.9 - - - +
22A GLY* 1.3 61.3 + - - +
24A ALA* 3.1 2.3 + - + +
25A LEU* 3.0 48.9 + - + +
75A VAL* 3.8 22.9 - - + -
154A LEU* 3.7 23.3 - - + +
157A VAL* 3.6 40.8 - - + -
158A LEU* 4.2 8.3 - - + -
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Residues in contact with GLY 22 (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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18A ALA 2.8 10.1 + - - -
19A GLN 3.1 5.0 + - - -
21A LEU* 1.3 72.9 - - - +
23A LEU* 1.3 64.8 + - - +
26A LYS* 3.0 6.4 + - - -
27A LEU 3.0 43.3 + - - -
29A VAL* 3.7 13.5 - - - -
75A VAL* 4.1 8.9 - - - +
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Residues in contact with LEU 23 (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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19A GLN 3.1 11.6 + - - +
20A GLU* 3.4 13.0 - - - +
22A GLY* 1.3 76.4 - - - +
24A ALA* 1.3 68.1 + - - +
25A LEU 3.2 1.0 + - - -
26A LYS* 3.4 8.4 + - - +
29A VAL* 5.2 0.2 - - - +
159C GLN* 5.1 6.9 + - - +
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Residues in contact with ALA 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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20A GLU 2.9 16.9 + - - +
21A LEU* 3.1 9.3 + - - +
23A LEU* 1.3 78.3 - - - +
25A LEU* 1.3 67.5 + - + +
26A LYS 3.4 0.6 + - - -
154A LEU* 4.5 10.1 - - + -
158A LEU* 4.5 10.3 - - + -
159C GLN* 3.5 48.5 + - + +
163C LEU* 3.9 13.5 - - - +
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Residues in contact with LEU 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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4A LEU* 3.7 29.4 - - + -
21A LEU* 3.0 28.8 + - + +
24A ALA* 1.3 82.3 - - + +
26A LYS* 1.3 70.7 + - - +
27A LEU* 3.4 25.5 - - + +
158A LEU* 3.7 23.8 - - + -
161A ILE* 3.8 18.6 - - + -
168A SER* 4.9 10.3 - - - +
159C GLN 5.2 0.9 - - - +
162C ALA* 4.2 18.6 - - + -
163C LEU* 3.7 22.8 - - + +
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Residues in contact with LYS 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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22A GLY 3.0 7.2 + - - -
23A LEU* 3.4 8.2 + - - +
24A ALA 3.4 0.8 + - - -
25A LEU* 1.3 82.3 - - - +
27A LEU* 1.3 63.7 + - - +
163C LEU* 5.1 6.1 - - + -
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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
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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