Contacts of the helix formed by residues 8 - 19 (chain A) in PDB entry 2JRF
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 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A THR* 4.9 6.0 - - - +
6A ASP 3.8 0.8 - - - -
7A ILE* 1.3 78.6 - - - +
9A GLY* 1.3 58.6 + - - +
10A LEU 3.3 0.9 - - - -
11A GLU* 2.9 25.4 + - - +
12A GLU* 2.8 28.7 + - - +
15A ARG* 4.2 3.3 + - - +
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Residues in contact with GLY 9 (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 ILE* 2.7 13.8 + - - -
8A ALA* 1.3 74.6 - - - +
10A LEU* 1.3 60.4 + - - +
12A GLU* 3.1 9.2 + - - +
13A SER* 3.0 25.1 + - - -
104A ALA* 3.5 16.6 - - - -
105A GLY* 3.6 6.3 + - - -
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Residues in contact with LEU 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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7A ILE* 3.6 30.7 - - + +
8A ALA 3.3 0.2 - - - -
9A GLY* 1.3 73.7 - - - +
11A GLU* 1.3 58.9 + - - +
13A SER* 3.3 4.0 + - - -
14A PHE* 2.9 27.2 + - - +
72A TYR* 4.9 12.3 - - + +
75A PHE* 4.1 15.0 - - + -
76A LYS* 5.5 1.8 - - + -
79A LEU* 3.5 28.0 - - + -
96A PHE* 5.0 3.1 - - + -
100A CYS* 3.3 36.6 - - + +
103A VAL* 4.2 26.7 - - + -
104A ALA* 3.4 12.8 - - + +
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Residues in contact with GLU 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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4A SER 4.0 14.2 - - - +
5A THR* 4.1 7.1 - - - +
6A ASP 3.7 9.2 + - - -
7A ILE* 3.5 10.5 + - + +
8A ALA* 2.9 34.4 + - - +
10A LEU* 1.3 77.2 - - + +
12A GLU* 1.3 61.4 + - - +
14A PHE* 3.4 10.3 - - - +
15A ARG* 3.1 42.6 + - - +
72A TYR* 3.5 36.0 + - + +
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Residues in contact with GLU 12 (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 ALA 2.8 12.3 + - - +
9A GLY* 3.1 13.7 + - - +
11A GLU* 1.3 74.8 - - - +
13A SER* 1.3 60.5 + - - +
15A ARG* 2.9 45.5 + - - +
16A LYS* 2.9 46.7 + - - +
105A GLY* 5.5 5.8 - - - +
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Residues in contact with SER 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 GLY 3.0 7.2 + - - -
10A LEU 3.3 6.7 + - - -
12A GLU* 1.3 72.9 - - - +
14A PHE* 1.3 65.6 + - - +
16A LYS* 3.2 10.5 - - - +
17A PHE* 3.2 34.1 + - - -
38A LEU* 5.3 1.1 - - - -
103A VAL* 3.4 24.2 + - - -
104A ALA* 4.3 0.7 - - - -
105A GLY 2.7 32.7 + - - -
106A LYS 3.0 18.3 + - - -
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Residues in contact with PHE 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 LEU 2.9 13.3 + - - +
11A GLU* 3.4 15.5 - - - +
12A GLU 3.2 0.2 - - - -
13A SER* 1.3 75.4 - - - +
15A ARG* 1.3 54.5 + - + +
17A PHE 3.2 2.3 + - - -
18A ALA* 2.7 39.1 + - + +
27A GLY* 3.3 34.5 - - - -
28A GLN 4.2 5.4 - - - -
29A GLU* 3.5 30.7 - - - -
30A MET* 3.4 29.9 - - + +
38A LEU* 5.0 3.4 - - - -
70A ILE 4.6 0.7 - - - -
72A TYR* 4.2 21.3 - + + -
75A PHE* 3.5 50.0 - + + -
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Residues in contact with ARG 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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8A ALA* 4.2 4.8 + - - +
11A GLU* 3.1 25.8 + - - +
12A GLU* 2.9 58.7 + - - +
14A PHE* 1.3 80.9 - - + +
16A LYS* 1.3 63.0 + - + +
18A ALA* 3.9 7.4 - - - -
19A ILE* 2.8 38.3 + - + +
26A SER 3.7 23.3 - - - +
27A GLY* 4.4 7.2 - - - +
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Residues in contact with LYS 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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12A GLU* 2.9 37.1 + - + +
13A SER* 3.2 10.3 - - - +
15A ARG* 1.3 77.2 - - + +
17A PHE* 1.3 59.8 + - + +
19A ILE* 4.2 10.5 - - + +
20A HIS* 3.9 11.1 + - - +
105A GLY 5.3 5.4 - - - +
106A LYS 3.6 19.3 - - - +
107A GLU* 4.1 20.0 + - + +
108A PRO* 3.6 29.8 - - + +
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Residues in contact with PHE 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 SER* 3.2 27.1 + - - -
15A ARG 3.2 0.4 - - - -
16A LYS* 1.3 82.0 - - + +
18A ALA* 1.3 60.6 + - - +
20A HIS* 3.2 7.2 - + + +
30A MET* 3.5 23.8 - - + -
34A ASN* 2.7 53.6 + - + +
37A LYS* 3.9 10.3 - - + -
38A LEU* 3.5 43.1 - - + -
41A ASP* 3.8 15.0 - - + -
42A CYS* 5.2 5.6 - - - -
106A LYS* 4.5 5.4 - - + -
107A GLU* 3.9 9.0 - - - -
108A PRO* 3.6 42.2 - - + -
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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
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14A PHE* 2.7 26.8 + - + +
15A ARG* 3.0 3.8 + - - +
17A PHE* 1.3 71.0 - - - +
19A ILE* 1.3 59.3 + - - +
20A HIS* 3.0 11.9 + - - +
22A ASP 4.7 2.1 + - - +
25A ALA* 4.9 4.0 - - + +
27A GLY* 3.8 24.9 - - - -
29A GLU* 3.4 34.7 - - - +
30A MET* 3.9 6.4 - - + +
31A ASN* 5.8 0.3 + - - -
34A ASN* 4.4 3.4 + - - +
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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 ARG* 2.8 33.2 + - + +
16A LYS* 4.2 10.1 - - + +
18A ALA* 1.3 70.3 - - + +
20A HIS* 1.3 53.9 + - - +
21A GLY 2.7 17.5 + - - -
22A ASP 3.3 30.1 + - - +
23A PRO* 4.0 19.3 - - + +
25A ALA* 5.0 0.7 - - - -
26A SER* 3.6 36.8 - - - +
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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