Contacts of the helix formed by residues 15 - 24 (chain M) in PDB entry 4N3E
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 ALA 15 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13M PRO 3.8 2.2 + - - -
14M ILE* 1.3 79.8 - - - +
16M PRO* 1.4 77.2 - - + +
17M HIS* 3.0 28.6 + - + +
18M ARG* 3.1 19.6 + - - +
19M LEU* 3.3 7.8 + - - +
110M GLY 3.8 11.9 - - - +
111M GLY 3.8 4.9 - - - -
17O HIS* 4.0 17.7 - - + +
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Residues in contact with PRO 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M ALA* 1.4 87.0 - - + +
17M HIS* 1.3 59.2 + - - +
19M LEU* 4.0 1.1 - - + +
20M PHE* 3.1 31.4 + - - +
80M PHE* 3.5 39.6 - - + -
105M LEU* 3.5 11.5 - - + +
106M GLU 4.0 7.9 - - - +
107M ALA* 3.5 24.0 - - + -
111M GLY 3.6 14.1 - - - +
112M SER* 3.4 14.8 - - - +
16O PRO* 6.2 2.2 - - + -
17O HIS* 6.1 0.2 - - - +
107O ALA* 4.5 2.9 - - + -
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Residues in contact with HIS 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M ALA* 3.0 27.2 + - + +
16M PRO* 1.3 81.3 - - - +
18M ARG* 1.3 67.9 + - + +
20M PHE* 4.0 3.0 - - - +
21M LYS* 3.2 26.7 + - - +
80M PHE* 4.2 6.3 - - + -
158M PHE 3.6 17.3 + - - +
159M ALA* 2.8 31.7 + - - -
15O ALA* 3.7 25.7 - - + +
16O PRO* 5.9 0.8 - - - +
17O HIS* 4.2 5.4 - + - -
109O GLY 3.7 23.9 + - - +
110O GLY* 3.8 20.2 - - - -
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Residues in contact with ARG 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M ILE* 3.7 22.7 - - + +
15M ALA* 3.1 15.8 + - - +
17M HIS* 1.3 90.0 - - + +
19M LEU* 1.3 62.1 + - - +
20M PHE 3.2 0.2 - - - -
21M LYS* 3.5 0.9 + - - +
22M ALA* 3.0 32.7 + - - +
151M LEU* 2.7 56.9 + - + +
152M ALA* 4.7 0.6 - - - +
154M ASN 3.1 17.6 + - - -
155M PRO* 3.6 22.4 + - - +
157M VAL 2.9 25.1 + - - -
158M PHE* 3.5 29.8 - - + +
159M ALA* 4.9 1.6 - - - +
159O ALA* 5.7 2.6 + - - -
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Residues in contact with LEU 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M SER* 3.9 12.1 - - - +
14M ILE* 3.7 31.4 - - + +
15M ALA 3.3 7.2 + - - +
18M ARG* 1.3 80.4 - - - +
20M PHE* 1.3 58.7 + - - +
22M ALA* 4.8 0.9 - - - -
23M LEU* 3.1 53.6 + - + +
105M LEU* 3.9 13.9 - - + +
112M SER* 4.0 10.1 - - - +
144M TYR* 4.5 8.3 - - + -
147M VAL* 5.0 2.5 - - + -
148M GLU 5.2 1.8 - - - +
151M LEU* 4.2 10.5 - - + -
202M 2AN 3.3 44.1 - - + -
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Residues in contact with PHE 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M PRO 3.1 19.9 + - - +
17M HIS* 4.5 2.5 - - - +
19M LEU* 1.3 78.9 - - - +
21M LYS* 1.3 60.7 + - - +
24M VAL* 3.3 26.6 + - + +
25M LEU* 3.2 39.7 + - + +
75M ILE* 4.9 2.9 - - + -
77M ALA* 3.8 31.0 - - + -
80M PHE* 3.1 40.6 - + + -
81M TYR* 3.3 29.4 - - - -
82M CYS* 4.0 14.1 - - + -
103M VAL* 4.5 3.8 - - + -
105M LEU* 3.7 14.1 - - + -
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Residues in contact with LYS 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M HIS 3.2 21.1 + - - +
18M ARG 3.5 2.7 + - - +
20M PHE* 1.3 77.7 - - - +
22M ALA* 1.3 58.1 + - - +
25M LEU* 4.3 20.2 - - + +
26M GLU* 2.8 65.9 + - + +
158M PHE* 3.9 40.2 - - + +
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Residues in contact with ALA 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M ARG 3.0 20.1 + - - +
19M LEU 4.5 1.1 - - - +
21M LYS* 1.3 74.4 - - - +
23M LEU* 1.3 63.5 + - - +
24M VAL 3.5 0.4 - - - -
27M ARG* 3.6 7.7 - - - -
30M VAL* 3.5 25.5 - - - +
143M PHE* 4.5 0.9 - - - -
147M VAL* 3.7 13.2 - - + -
151M LEU* 4.1 3.4 - - + -
158M PHE* 3.5 23.5 - - + -
203M 2AN 3.7 20.4 - - + -
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Residues in contact with LEU 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M LEU* 3.1 32.7 + - + +
22M ALA* 1.3 77.5 - - - +
24M VAL* 1.3 63.4 + - - +
27M ARG* 2.7 42.1 + - - +
84M TYR* 4.6 0.9 + - - -
143M PHE* 3.6 26.2 - - + -
144M TYR* 3.8 37.5 - - + -
147M VAL* 3.8 26.5 - - + -
202M 2AN 3.5 35.9 - - + -
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Residues in contact with VAL 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M PHE* 3.3 36.8 + - + +
22M ALA 3.5 1.2 - - - -
23M LEU* 1.3 82.3 - - + +
25M LEU* 1.3 74.0 + - + +
26M GLU 3.1 2.3 + - - -
27M ARG* 3.2 16.2 + - - +
28M HIS* 5.1 0.7 + - - -
72M PHE* 4.1 20.2 - - + -
82M CYS* 3.8 32.8 - - + -
84M TYR* 4.5 10.8 - - + -
103M VAL* 4.3 12.6 - - + -
202M 2AN 4.1 19.5 - - + -
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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