Contacts of the helix formed by residues 9 - 22 (chain R) in PDB entry 2X86
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 9 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6R GLY 2.7 13.6 + - - -
8R ALA* 1.3 80.9 - - - +
10R PHE* 1.3 58.4 + - - -
11R ILE 3.7 1.6 - - - -
13R SER* 2.7 34.4 + - - -
31R ASP* 3.2 4.3 + - - -
38R LYS* 4.9 0.2 - - - -
41R ASN* 4.2 0.7 - - - -
177R HIS* 3.8 10.1 - - - -
400R NAP 3.5 22.2 - - - -
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Residues in contact with PHE 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R GLY* 1.3 70.8 - - - -
11R ILE* 1.3 66.4 + - + +
13R SER* 3.0 9.5 + - - -
14R ASN* 2.8 28.0 + - - -
170R VAL* 3.6 32.3 - - + -
171R TYR* 3.5 5.4 - - - -
172R GLY 3.2 34.1 - - - -
173R PRO 3.1 22.0 - - - -
174R ARG 3.1 25.4 - - - +
175R GLU* 3.6 16.6 - - + -
177R HIS* 3.5 2.4 - - + -
178R LYS* 4.0 9.4 - - + -
214R VAL* 3.6 11.7 - - + -
400R NAP 2.8 42.7 + - - +
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Residues in contact with ILE 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R PHE* 1.3 87.0 - - + +
12R GLY* 1.3 62.5 + - - +
14R ASN* 3.1 9.6 + - + +
15R ILE* 3.0 28.6 + - + +
75R GLU* 3.5 21.3 - - - +
167R TYR* 3.5 37.5 - - + +
170R VAL* 4.1 22.0 - - + -
214R VAL* 4.5 4.7 - - + -
217R VAL* 4.1 14.8 - - + -
400R NAP 2.8 45.5 + - + +
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Residues in contact with GLY 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R VAL* 3.7 14.8 - - - +
6R GLY 3.5 18.9 + - - -
7R GLY* 3.8 7.4 - - - -
10R PHE 3.3 0.6 - - - -
11R ILE* 1.3 79.0 - - - +
13R SER* 1.3 62.0 + - - +
15R ILE* 3.0 6.5 + - - +
16R VAL* 2.9 24.1 + - - +
75R GLU* 4.0 15.0 - - - +
400R NAP 4.2 1.0 + - - -
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Residues in contact with SER 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R GLY 3.3 17.7 + - - -
9R GLY 2.7 24.8 + - - -
10R PHE 3.0 8.3 + - - -
12R GLY* 1.3 75.7 - - - +
14R ASN* 1.3 56.4 + - - +
16R VAL* 3.2 8.2 + - - +
17R LYS* 2.9 25.3 + - - +
41R ASN* 3.6 29.2 - - - +
42R LEU* 4.9 0.2 - - - -
45R LEU* 3.4 8.3 - - - +
174R ARG* 3.3 21.2 - - - +
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Residues in contact with ASN 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R PHE* 2.8 22.6 + - - -
11R ILE 3.1 8.8 + - - +
13R SER* 1.3 80.8 + - - +
15R ILE* 1.3 59.2 + - - +
17R LYS* 3.4 12.3 + - - +
18R ALA* 3.0 28.1 + - - +
173R PRO* 2.9 29.5 + - - +
174R ARG* 3.8 15.3 + - - +
214R VAL* 3.5 37.0 - - + +
215R GLY* 5.2 1.7 + - - -
218R ALA* 3.9 12.9 - - + +
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Residues in contact with ILE 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4R VAL* 4.4 5.6 - - + -
11R ILE* 3.0 20.7 + - + +
12R GLY* 3.4 7.6 - - - +
14R ASN* 1.3 75.8 - - - +
16R VAL* 1.3 65.1 + - - +
18R ALA* 3.2 6.6 + - - +
19R LEU* 2.9 35.8 + - + +
73R PHE* 4.0 28.9 - - + -
75R GLU* 3.6 32.3 - - + +
218R ALA* 4.7 9.2 - - - +
221R ASN* 3.5 39.3 - - + +
222R LEU* 4.4 7.6 - - + -
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Residues in contact with VAL 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R VAL* 4.2 17.0 - - + -
7R GLY 4.1 13.7 - - - +
12R GLY 2.9 18.3 + - - +
13R SER 3.3 7.4 - - - +
15R ILE* 1.3 76.0 - - - +
17R LYS* 1.3 57.0 + - - +
19R LEU* 3.1 11.8 + - - +
20R ASN* 2.8 30.4 + - - +
27R ILE* 4.0 11.4 - - + -
29R VAL* 4.2 17.5 - - + -
42R LEU* 4.7 1.1 - - + -
45R LEU* 3.7 21.5 - - + -
47R ILE* 3.8 25.6 - - + -
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Residues in contact with LYS 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R SER 2.9 13.9 + - - +
14R ASN* 3.7 15.3 - - - +
15R ILE 3.3 0.2 - - - -
16R VAL* 1.3 75.5 - - - +
18R ALA* 1.3 59.6 + - - +
20R ASN* 3.1 6.9 + - + +
21R ASP* 2.9 60.6 + - - +
45R LEU* 3.9 27.8 - - + +
174R ARG* 4.0 19.3 - - - +
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Residues in contact with ALA 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ASN 3.0 17.7 + - - +
15R ILE* 3.5 5.8 - - - +
16R VAL 3.2 0.2 - - - -
17R LYS* 1.3 78.2 - - - +
19R LEU* 1.3 61.3 + - - +
21R ASP* 3.2 12.6 + - - +
22R LYS* 3.1 18.5 + - - +
218R ALA* 4.0 19.3 - - + +
219R ASP* 5.3 4.9 - - - +
222R LEU* 3.8 27.9 - - + +
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Residues in contact with LEU 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2R ILE* 3.8 46.0 - - + -
4R VAL* 4.2 7.2 - - + -
15R ILE* 2.9 32.6 + - + +
16R VAL 3.4 5.6 - - - +
18R ALA* 1.3 71.8 - - - +
20R ASN* 1.3 67.5 + - - +
22R LYS* 3.0 10.5 + - + +
24R ILE* 2.9 40.2 + - + +
27R ILE* 3.9 21.3 - - + -
73R PHE* 4.4 3.8 - - + -
222R LEU* 3.9 26.2 - - + -
225R LEU* 4.9 4.0 - - + -
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Residues in contact with ASN 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R VAL* 2.8 17.3 + - - +
17R LYS* 3.3 12.1 - - + +
19R LEU* 1.3 75.2 - - - +
21R ASP* 1.3 57.4 + - - +
23R GLY* 2.7 25.8 + - - -
24R ILE 2.9 19.0 + - - -
25R THR* 3.8 8.7 - - + +
27R ILE* 3.8 4.2 - - - +
45R LEU* 3.6 15.9 - - + +
46R ASN* 2.8 54.3 + - - +
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Residues in contact with ASP 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R LYS* 2.9 51.6 + - - +
18R ALA* 3.2 13.1 + - - +
20R ASN* 1.3 77.8 - - - +
22R LYS* 1.3 61.3 + - + +
23R GLY 3.2 0.9 + - - -
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Residues in contact with LYS 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R ALA 3.1 9.9 + - - +
19R LEU* 3.0 11.3 + - + +
21R ASP* 1.3 79.5 - - + +
23R GLY* 1.3 59.3 + - - +
24R ILE* 3.3 15.4 + - + +
222R LEU* 3.8 24.0 - - + -
226R GLU* 3.1 30.4 + - - +
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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