Contacts of the helix formed by residues 6 - 22 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D GLN* 5.6 13.5 - - + +
4D GLN* 2.8 42.7 + - - +
5D TYR* 1.3 78.5 + - - +
7D PRO* 1.4 66.3 - - - +
8D GLU* 4.0 20.0 - - - +
9D GLU* 3.6 41.9 + - + +
10D ILE* 3.2 32.3 + - + +
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Residues in contact with PRO 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 3.7 33.6 - - + +
6D ARG* 1.4 81.9 - - + +
8D GLU* 1.3 74.6 + - - +
9D GLU 3.2 2.2 - - - -
10D ILE* 4.3 2.9 - - + +
11D GLU* 2.8 58.7 + - + +
634D VAL 5.6 0.9 - - - +
635D GLU 6.1 0.4 - - - +
636D ARG 5.4 2.0 - - - +
637D TYR 3.5 24.0 - - - +
638D GLY* 4.0 7.4 - - - -
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Residues in contact with GLU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ARG* 4.0 15.0 - - + +
7D PRO* 1.3 95.6 - - - +
9D GLU* 1.3 67.4 + - + +
12D SER* 3.3 20.5 + - - +
635D GLU 5.1 11.0 - - - +
636D ARG 5.4 2.8 - - - +
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Residues in contact with GLU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLN* 5.4 7.8 - - - +
6D ARG* 3.6 45.2 + - + +
7D PRO 3.2 0.2 - - - -
8D GLU* 1.3 84.4 - - + +
10D ILE* 1.3 66.6 + - + +
12D SER* 3.8 9.8 + - - -
13D LYS* 4.0 11.4 - - - +
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Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 4.1 8.1 - - + -
6D ARG* 3.2 33.8 + - + +
7D PRO* 3.2 4.2 + - + +
9D GLU* 1.3 79.3 - - + +
11D GLU* 1.3 67.7 + - + +
13D LYS* 3.4 8.7 + - - +
14D VAL* 3.3 25.2 + - + +
674D TRP* 3.8 33.9 - - + -
767D HIS 4.3 10.3 - - - +
768D ILE* 5.2 2.5 - - - +
771D THR* 3.1 31.9 - - + +
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 3.5 16.8 + - + +
7D PRO* 2.8 36.9 + - + +
10D ILE* 1.3 75.0 - - + +
12D SER* 1.3 57.0 + - - +
14D VAL 3.3 1.3 + - - +
15D GLN* 3.0 42.0 + - - +
114D MET 4.9 0.2 - - - +
634D VAL* 5.2 2.6 - - - +
638D GLY* 4.1 1.0 - - - -
639D ALA* 3.1 34.4 + - - +
640D ASP* 3.2 25.3 + - - -
767D HIS* 3.7 32.5 - - + -
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Residues in contact with SER 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PRO 4.3 1.4 + - - -
8D GLU 3.3 19.6 + - - -
9D GLU* 3.8 5.2 + - - -
11D GLU* 1.3 77.0 - - - +
13D LYS* 1.3 58.3 + - - +
15D GLN* 3.9 13.9 - - - +
16D LEU* 3.2 28.1 + - - +
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Residues in contact with LYS 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLU 4.0 9.6 - - - +
10D ILE* 3.4 11.6 + - - +
11D GLU 3.2 0.2 - - - -
12D SER* 1.3 79.8 + - - +
14D VAL* 1.3 61.4 + - + +
16D LEU* 3.3 10.2 + - + +
17D HIS* 2.9 28.5 + - + +
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Residues in contact with VAL 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 3.3 15.8 + - + +
11D GLU 3.8 6.5 - - - +
13D LYS* 1.3 76.5 - - + +
15D GLN* 1.3 63.8 - - - +
17D HIS* 3.4 7.7 + - - +
18D TRP* 3.2 58.0 + - + +
767D HIS* 4.1 25.1 - - + +
770D PHE* 3.7 34.1 - - + -
771D THR* 4.2 7.6 - - - +
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Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU* 3.0 29.8 + - - +
12D SER* 3.9 10.8 - - - +
14D VAL* 1.3 77.2 - - - +
16D LEU* 1.3 61.4 + - - +
18D TRP* 3.4 12.5 + - + +
19D ASP* 3.0 31.3 + - - +
113D LYS* 3.2 24.0 - - + +
114D MET* 2.7 40.4 + - - +
116D GLY* 4.6 2.9 - - - -
767D HIS* 3.4 24.3 + - - +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER 3.2 17.1 + - - +
13D LYS* 3.3 10.1 + - + +
15D GLN* 1.3 75.7 - - - +
17D HIS* 1.3 64.1 + - - +
19D ASP* 3.5 9.3 + - + +
20D GLU* 3.3 49.7 + - + +
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Residues in contact with HIS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LYS* 2.9 14.7 + - + +
14D VAL* 3.5 12.6 - - - +
15D GLN 3.3 0.2 - - - -
16D LEU* 1.3 76.7 - - - +
18D TRP* 1.3 68.5 + + - +
20D GLU* 4.1 3.3 - - - +
21D LYS* 3.0 73.9 + - + +
23D THR* 4.8 2.7 - - - -
770D PHE* 3.8 23.8 - + + -
781D ASP* 3.4 26.6 + - - -
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Residues in contact with TRP 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL* 3.2 37.5 + - + +
15D GLN* 3.4 14.1 + - + +
17D HIS* 1.3 88.7 - + - +
19D ASP* 1.3 61.8 + - - +
22D ARG* 3.0 23.4 + - - -
23D THR* 3.3 31.6 + - + +
24D PHE* 4.0 19.5 - + + -
64D ARG* 3.3 30.1 - - - -
116D GLY* 3.8 12.8 - - - -
117D PHE 5.9 0.2 - - - -
118D GLY* 5.8 1.3 - - - -
766D PRO* 3.9 22.7 - - + -
767D HIS* 3.8 26.2 - + - -
770D PHE* 4.4 8.1 - - + -
783D ASP* 2.7 27.9 + - - -
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Residues in contact with ASP 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLN* 3.0 19.7 + - - +
16D LEU* 3.8 12.9 - - + +
17D HIS 3.3 0.4 - - - -
18D TRP* 1.3 82.2 - - - +
20D GLU* 1.3 63.3 + - + +
22D ARG* 3.7 17.7 + - - +
113D LYS* 3.6 35.3 + - - +
121D TRP* 5.4 5.2 - - - -
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.3 42.3 + - + +
17D HIS* 4.2 3.4 - - - +
19D ASP* 1.3 77.8 - - + +
21D LYS* 1.3 67.8 + - + +
22D ARG* 3.5 10.7 + - - +
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Residues in contact with LYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D HIS* 3.0 52.3 + - + +
20D GLU* 1.3 79.0 - - + +
22D ARG* 1.3 71.6 + - - +
23D THR* 4.2 10.9 - - - +
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D TRP 3.0 11.1 + - - -
19D ASP 3.8 14.6 + - - +
20D GLU 3.3 7.5 + - - +
21D LYS* 1.3 82.2 - - - +
23D THR* 1.3 64.9 + - - +
24D PHE 3.5 2.4 + - - -
25D GLU* 3.2 60.9 + - + +
122D SER* 5.6 1.2 - - - -
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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