Contacts of the helix formed by residues 8 - 20 (chain N) in PDB entry 3IR0
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 8 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3M VAL* 6.2 1.4 - - - +
7M CYS* 5.2 0.2 - - - -
6N LEU 4.4 0.6 + - - -
7N CYS* 1.3 72.8 - - - +
9N SER* 1.3 63.0 + - - -
11N LEU* 3.1 19.1 + - - +
12N VAL* 3.7 3.6 + - - +
26N TYR* 4.5 5.6 + - - -
16P TYR* 3.4 32.8 - - - -
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Residues in contact with SER 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N CYS 3.6 0.6 + - - -
8N GLY* 1.3 71.4 - - - -
10N HIS* 1.3 66.6 + - - +
12N VAL* 3.2 7.2 + - - +
13N GLU* 2.9 31.8 + - - +
13P GLU* 4.3 25.0 + - - -
16P TYR* 3.5 34.6 - - - -
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Residues in contact with HIS 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N HIS 5.5 0.9 - - - +
6N LEU* 3.4 27.5 - - + +
7N CYS* 3.2 27.1 - - + +
8N GLY 3.3 1.0 - - - -
9N SER* 1.3 84.8 + - - +
11N LEU* 1.3 59.8 + - - +
13N GLU* 3.9 11.0 - - - +
14N ALA* 3.3 13.2 + - - +
31N CU 2.1 32.1 - - - -
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Residues in contact with LEU 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M ILE* 4.4 4.7 - - + +
3M VAL* 3.5 42.4 - - + +
6M CYS* 3.8 13.0 - - + -
16M LEU* 3.7 29.6 - - + -
6N LEU* 3.9 28.8 - - + +
7N CYS 4.1 1.0 + - - -
8N GLY 3.1 14.7 + - - +
10N HIS* 1.3 75.6 - - - +
12N VAL* 1.3 61.2 + - - +
14N ALA* 3.0 6.0 + - - +
15N LEU* 3.0 38.1 + - + +
26N TYR* 3.9 18.6 - - + -
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Residues in contact with VAL 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N GLY 3.7 1.0 + - - +
9N SER* 3.2 11.9 + - - +
11N LEU* 1.3 78.8 - - - +
13N GLU* 1.3 61.8 + - - +
15N LEU* 3.4 7.7 + - + -
16N TYR* 3.1 22.9 + - - +
24N PHE* 3.8 5.0 - - + -
26N TYR* 4.0 17.0 - - + -
12P VAL* 3.3 40.6 - - + +
13P GLU* 4.0 7.6 - - + +
16P TYR* 3.7 25.4 - - + -
24P PHE* 3.7 28.7 - - + -
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Residues in contact with GLU 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N SER 2.9 19.9 + - - +
10N HIS* 4.1 11.0 - - - +
11N LEU 3.3 0.2 - - - -
12N VAL* 1.3 76.9 - - + +
14N ALA* 1.3 55.9 + - - +
16N TYR* 3.4 5.3 + - - +
17N LEU* 3.0 36.2 + - + +
9P SER* 3.6 28.1 + - - +
10P HIS* 5.8 1.7 + - - -
12P VAL* 5.8 0.4 - - - -
13P GLU* 3.0 40.0 - - + +
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Residues in contact with ALA 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M LEU* 5.2 4.3 - - + -
16M LEU* 3.4 23.1 - - + -
6N LEU* 3.6 23.3 - - + -
10N HIS 3.3 8.3 + - - +
11N LEU 3.0 10.1 + - - +
13N GLU* 1.3 78.3 - - - +
15N LEU* 1.3 58.3 + - - +
17N LEU* 3.4 6.0 + - - +
18N VAL* 2.9 35.9 + - - +
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Residues in contact with LEU 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M ILE* 5.8 4.3 - - + -
16M LEU* 3.9 39.9 - - + +
19M TYR* 4.0 18.4 - - + -
11N LEU* 3.0 29.5 + - + +
12N VAL* 3.9 3.4 - - - +
13N GLU 3.3 0.2 - - - -
14N ALA* 1.3 73.0 - - - +
16N TYR* 1.3 57.7 + - - +
18N VAL* 4.4 3.8 - - - -
19N CYS* 2.7 41.5 + - - +
24N PHE* 3.5 38.4 - - + -
25N PHE 4.3 6.1 - - - +
26N TYR* 3.9 25.6 - - + -
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Residues in contact with TYR 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N VAL 3.1 18.2 + - - +
13N GLU* 3.8 6.1 - - - +
15N LEU* 1.3 74.3 - - - +
17N LEU* 1.3 74.8 + - + +
20N GLY* 2.6 48.9 + - - +
21N GLU* 4.9 2.3 + - - +
24N PHE* 3.6 8.2 - + + -
8P GLY* 3.2 33.9 - - - -
9P SER* 3.9 20.4 - - - -
12P VAL* 3.9 25.8 - - + -
26P TYR* 4.1 26.1 + + - -
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Residues in contact with LEU 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M LEU* 6.5 1.3 - - + -
13N GLU* 3.0 24.7 + - + +
14N ALA* 3.6 8.1 - - - +
16N TYR* 1.3 88.4 - - + +
18N VAL* 1.3 62.5 - - + +
19N CYS 4.9 0.3 - - - -
20N GLY* 4.5 1.4 + - - -
9P SER* 6.5 0.4 - - - -
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Residues in contact with VAL 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M LEU* 4.0 34.8 - - + +
16M LEU* 4.2 8.5 - - + -
17M GLU* 3.6 44.3 - - + +
20M CYS* 4.1 4.0 - - - -
14N ALA 2.9 21.9 + - - +
15N LEU* 4.0 5.4 - - - +
17N LEU* 1.3 81.5 - - + +
19N CYS* 1.3 58.2 + - - +
22N ARG* 3.6 14.2 + - - -
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Residues in contact with CYS 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M LEU 4.3 7.6 - - - -
19M TYR 4.4 0.2 - - - -
20M CYS* 2.0 54.3 - - + -
15N LEU* 2.7 27.1 + - - +
17N LEU 4.9 0.2 - - - -
18N VAL* 1.3 78.0 - - - +
20N GLY* 1.3 62.8 + - - +
21N GLU 3.5 0.2 + - - -
22N ARG* 3.2 24.1 + - - +
23N GLY 3.3 19.7 - - - +
24N PHE* 3.6 14.1 - - + -
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Residues in contact with GLY 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N LEU 3.9 0.2 + - - -
16N TYR* 2.6 48.6 + - - +
17N LEU 4.5 1.3 + - - -
18N VAL 3.9 0.2 - - - -
19N CYS* 1.3 72.1 - - - +
21N GLU* 1.3 57.6 + - - -
23N GLY* 3.0 19.9 + - - -
24N PHE* 4.9 0.5 - - - -
26P TYR* 3.6 12.1 - - - -
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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