Contacts of the helix formed by residues 6 - 22 (chain A) in PDB entry 5ON2
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 ARG 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLN* 3.8 37.6 + - - +
4A GLN* 3.5 45.2 + - - +
5A TYR* 1.3 77.8 - - - +
7A PRO* 1.4 66.7 - - - +
8A GLU* 3.5 17.6 + - - +
9A GLU* 3.5 40.0 + - + +
10A ILE* 3.2 29.7 + - + +
674A TRP* 5.6 0.2 - - - -
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Residues in contact with PRO 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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5A TYR* 3.5 38.3 - - + +
6A ARG* 1.4 82.3 - - - +
8A GLU* 1.3 65.2 + - - +
10A ILE* 3.0 4.3 + - + -
11A GLU* 2.8 49.2 + - + +
636A ARG 5.6 1.6 - - - +
637A TYR 3.4 26.7 - - - +
638A GLY* 4.1 14.8 - - - -
667A ASN* 5.2 1.8 - - - +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.5 18.8 - - - +
7A PRO* 1.3 91.9 - - - +
9A GLU* 1.3 68.6 + - + +
11A GLU* 5.5 1.1 - - - -
12A SER* 3.4 20.5 + - - -
635A GLU 5.8 3.4 - - - +
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Residues in contact with GLU 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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2A GLN* 5.3 4.9 - - - +
6A ARG* 3.5 42.9 + - + +
7A PRO 3.2 0.6 - - - -
8A GLU* 1.3 87.9 - - + +
10A ILE* 1.3 67.0 + - + +
12A SER* 4.3 1.6 + - - -
13A LYS* 3.7 22.7 + - - +
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Residues in contact with ILE 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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5A TYR* 3.7 31.4 - - + -
6A ARG 3.2 20.0 - - - +
7A PRO* 3.0 5.2 + - + +
9A GLU* 1.3 78.4 - - + +
11A GLU* 1.3 69.3 + - + +
12A SER 3.5 0.2 - - - -
13A LYS* 3.2 10.3 + - - +
14A VAL* 3.1 26.0 + - + +
674A TRP* 3.9 23.3 - - + -
767A HIS* 3.9 17.9 - - + +
768A ILE* 4.9 1.6 - - + +
771A THR* 3.2 29.2 - - + +
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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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5A TYR* 4.4 4.0 + - - +
7A PRO* 2.8 37.4 + - + +
8A GLU* 5.5 0.9 - - - +
10A ILE* 1.3 76.8 - - + +
12A SER* 1.3 57.4 + - - +
14A VAL* 3.4 1.1 + - - -
15A GLN* 3.0 40.5 + - - +
114A MET 4.7 2.3 - - - +
634A VAL* 5.1 2.9 - - - +
638A GLY* 3.8 6.9 - - - -
639A ALA* 3.0 41.2 + - - +
640A ASP* 3.2 22.7 + - - +
767A HIS* 3.7 28.8 - - + -
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Residues in contact with SER 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 GLU 3.4 19.1 + - - -
9A GLU* 4.3 3.1 + - - -
11A GLU* 1.3 76.3 - - - +
13A LYS* 1.3 63.7 + - - +
15A GLN* 3.7 12.7 + - - +
16A LEU* 3.3 22.9 + - - +
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Residues in contact with LYS 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 GLU 3.7 16.4 - - - +
10A ILE* 3.2 12.4 + - - +
12A SER* 1.3 81.8 + - - +
14A VAL* 1.3 65.1 + - + +
16A LEU* 3.7 10.6 + - + +
17A HIS* 3.4 18.4 + - - +
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Residues in contact with VAL 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 ILE* 3.1 31.1 + - + +
11A GLU 4.0 3.6 - - - +
13A LYS* 1.3 79.8 - - + +
15A GLN* 1.3 65.7 + - - +
17A HIS* 3.2 8.5 + - + +
18A TRP* 3.1 56.1 + - + +
767A HIS* 4.4 11.2 - - + +
770A PHE* 3.9 35.4 - - + -
771A THR* 4.3 5.6 - - - +
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Residues in contact with GLN 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 GLU* 3.0 27.7 + - - +
12A SER* 3.9 11.5 - - - +
13A LYS 3.4 0.2 - - - -
14A VAL* 1.3 76.2 - - - +
16A LEU* 1.3 59.3 + - - +
18A TRP* 3.5 15.7 + - + +
19A ASP* 3.0 31.3 + - - +
113A LYS 3.2 21.8 + - - +
114A MET* 2.7 40.1 + - - +
116A GLY* 4.0 1.5 - - - +
767A HIS* 3.1 30.4 + - + +
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Residues in contact with LEU 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 SER 3.3 15.5 + - - +
13A LYS* 3.8 9.4 - - + +
14A VAL 3.3 0.4 - - - -
15A GLN* 1.3 76.0 - - - +
17A HIS* 1.3 55.6 + - - +
19A ASP* 3.2 8.9 + - + +
20A GLU* 2.8 73.3 + - + +
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Residues in contact with HIS 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 LYS 3.4 10.6 + - - +
14A VAL* 3.2 13.1 + - - +
16A LEU* 1.3 79.4 - - - +
18A TRP* 1.3 66.3 + + - +
20A GLU* 4.6 7.0 - - - +
21A LYS* 3.0 69.3 + - + +
23A THR* 4.8 2.9 + - - -
770A PHE* 3.6 28.3 - + + -
781A ASP* 3.0 26.0 + - - -
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Residues in contact with TRP 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 VAL* 3.1 26.4 + - + -
15A GLN* 3.8 22.4 - - + +
16A LEU 3.3 0.2 - - - -
17A HIS* 1.3 83.6 - + - +
19A ASP* 1.3 63.8 + - - +
22A ARG* 3.2 17.8 + - - -
23A THR* 3.3 23.9 + - - -
24A PHE* 3.6 28.8 + + + -
64A ARG* 3.5 33.9 - - - -
116A GLY* 3.9 8.7 - - - -
117A PHE 6.1 0.2 - - - -
118A GLY* 6.0 0.2 - - - -
766A PRO* 3.9 20.6 - - + -
767A HIS* 3.5 37.9 - + - -
770A PHE* 4.1 9.0 - + - -
781A ASP* 5.9 0.2 - - - -
783A ASP* 2.8 30.0 + - - -
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Residues in contact with ASP 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 GLN* 3.0 16.4 + - - +
16A LEU* 3.2 14.8 + - + +
18A TRP* 1.3 80.8 - - - +
20A GLU* 1.3 63.0 + - + +
22A ARG* 3.5 18.0 + - - +
25A GLU* 5.3 1.7 - - - +
113A LYS* 3.0 34.2 + - - +
121A TRP* 5.2 4.1 - - - -
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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 LEU* 2.8 56.1 + - + +
17A HIS* 4.2 5.2 + - - +
19A ASP* 1.3 77.1 - - + +
21A LYS* 1.3 67.3 + - + +
22A ARG* 3.6 9.7 + - - +
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Residues in contact with LYS 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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17A HIS* 3.0 54.1 + - + +
20A GLU* 1.3 82.0 - - + +
22A ARG* 1.3 70.1 + - - +
23A THR* 4.1 10.1 - - - +
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Residues in contact with ARG 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 TRP 3.2 9.6 + - - -
19A ASP 3.5 13.3 + - - +
20A GLU 3.3 7.8 + - - +
21A LYS* 1.3 79.8 - - - +
23A THR* 1.3 65.4 + - - +
24A PHE 3.4 2.7 - - - -
25A GLU* 3.1 64.1 + - + +
122A SER* 5.7 1.4 - - - -
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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