Contacts of the helix formed by residues 9 - 22 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6S GLY 2.7 14.1 + - - -
8S ALA* 1.3 79.8 - - - +
10S PHE* 1.3 57.1 + - - -
11S ILE 3.7 1.1 - - - -
13S SER* 2.7 34.6 + - - -
31S ASP* 3.2 3.4 + - - -
38S LYS* 4.9 0.2 - - - -
41S ASN* 4.2 0.2 - - - -
177S HIS* 3.8 9.0 - - - -
400S NAP 3.4 24.9 - - - -
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Residues in contact with PHE 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S GLY* 1.3 69.7 - - - -
11S ILE* 1.3 68.5 + - + +
13S SER* 3.0 9.2 + - - -
14S ASN* 2.8 28.4 + - - -
170S VAL* 3.6 33.0 - - + -
171S TYR* 3.5 5.8 - - - -
172S GLY 3.2 33.7 - - - -
173S PRO 3.1 22.0 - - - -
174S ARG 3.1 25.1 - - - +
175S GLU* 3.6 16.6 - - + -
177S HIS* 3.5 1.6 - - + -
178S LYS* 4.0 8.3 - - + -
214S VAL* 3.6 12.3 - - + -
400S NAP 2.9 41.1 + - - +
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Residues in contact with ILE 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S PHE* 1.3 87.0 - - + +
12S GLY* 1.3 62.1 + - - +
14S ASN* 3.1 5.4 + - - +
15S ILE* 3.0 28.0 + - + +
75S GLU* 3.5 22.0 - - - +
167S TYR* 3.5 36.6 - - + +
170S VAL* 4.1 23.1 - - + -
214S VAL* 4.5 8.7 - - + -
217S VAL* 4.0 14.4 - - + -
400S NAP 2.7 46.6 + - + +
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Residues in contact with GLY 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S VAL* 3.7 15.4 - - - +
6S GLY 3.5 19.0 + - - -
7S GLY* 3.8 6.7 - - - -
9S GLY 4.3 0.2 - - - -
10S PHE 3.3 0.6 - - - -
11S ILE* 1.3 78.8 - - - +
13S SER* 1.3 62.3 + - - +
15S ILE* 3.0 6.4 + - - +
16S VAL* 2.9 24.1 + - - +
75S GLU* 4.0 14.6 - - - +
400S NAP 4.3 1.0 + - - -
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Residues in contact with SER 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S GLY 3.3 17.9 + - - -
9S GLY 2.7 24.7 + - - -
10S PHE 3.0 8.8 + - - -
12S GLY* 1.3 75.2 - - - +
14S ASN* 1.3 56.2 + - - +
16S VAL* 3.2 8.4 + - - +
17S LYS* 2.9 24.4 + - - +
41S ASN* 3.6 29.5 - - - +
42S LEU* 4.9 0.2 - - - -
45S LEU* 3.4 8.1 - - - +
174S ARG* 3.3 21.7 - - - +
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Residues in contact with ASN 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S PHE* 2.8 22.6 + - - -
11S ILE 3.1 9.0 + - - +
13S SER* 1.3 79.3 + - - +
15S ILE* 1.3 60.3 + - - +
17S LYS* 3.4 12.5 + - - +
18S ALA* 3.0 28.2 + - - +
173S PRO* 2.9 29.8 + - - +
174S ARG* 3.8 15.1 + - - +
214S VAL* 3.5 37.5 - - + +
215S GLY* 5.3 1.4 + - - -
218S ALA* 3.9 12.2 - - + +
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Residues in contact with ILE 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S VAL* 4.4 5.8 - - + -
11S ILE* 3.0 20.1 + - + +
12S GLY* 3.0 7.8 + - - +
14S ASN* 1.3 75.4 - - - +
16S VAL* 1.3 66.4 + - - +
18S ALA* 3.2 6.9 + - - +
19S LEU* 2.9 37.4 + - + +
73S PHE* 4.0 26.7 - - + -
75S GLU* 3.6 32.1 - - + +
218S ALA* 4.6 8.7 - - - +
221S ASN* 3.5 38.8 - - + +
222S LEU* 4.5 7.6 - - + -
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Residues in contact with VAL 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S VAL* 4.2 16.8 - - + -
7S GLY 4.2 8.3 - - - +
12S GLY 2.9 18.9 + - - +
13S SER 3.3 7.6 - - - +
15S ILE* 1.3 75.5 - - - +
17S LYS* 1.3 57.3 + - - +
19S LEU* 3.1 11.1 + - - +
20S ASN* 2.8 30.8 + - - +
27S ILE* 4.0 10.5 - - + -
29S VAL* 4.1 23.6 - - + -
42S LEU* 4.7 1.6 - - + -
45S LEU* 3.7 21.5 - - + -
47S ILE* 3.8 25.4 - - + -
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Residues in contact with LYS 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S SER 2.9 13.1 + - - +
14S ASN* 3.7 16.4 - - - +
15S ILE 3.3 0.2 - - - -
16S VAL* 1.3 76.5 - - - +
18S ALA* 1.3 58.7 + - - +
20S ASN* 3.1 7.6 + - + +
21S ASP* 2.9 60.9 + - - +
45S LEU* 3.9 28.0 - - + +
174S ARG* 4.1 20.2 - - - +
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Residues in contact with ALA 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ASN 3.0 18.0 + - - +
15S ILE* 3.5 5.8 - - - +
16S VAL 3.2 0.2 - - - -
17S LYS* 1.3 77.7 - - - +
19S LEU* 1.3 61.9 + - - +
21S ASP* 3.2 12.7 + - - +
22S LYS* 3.1 18.4 + - - +
218S ALA* 4.0 19.7 - - + +
219S ASP* 5.3 5.2 - - - +
222S LEU* 3.8 27.3 - - + +
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Residues in contact with LEU 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2S ILE* 3.9 45.1 - - + -
4S VAL* 4.2 7.6 - - + -
15S ILE* 2.9 32.4 + - + +
16S VAL 3.1 6.0 + - - +
18S ALA* 1.3 71.8 - - - +
20S ASN* 1.3 67.0 + - - +
22S LYS* 3.0 10.6 + - + +
23S GLY 3.3 0.2 + - - -
24S ILE* 2.9 40.4 + - + +
27S ILE* 3.9 22.9 - - + -
73S PHE* 4.4 3.8 - - + -
222S LEU* 3.9 26.5 - - + -
225S LEU* 5.0 3.6 - - + -
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Residues in contact with ASN 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S VAL* 2.8 16.9 + - - +
17S LYS* 3.3 11.7 - - + +
19S LEU* 1.3 76.7 - - - +
21S ASP* 1.3 56.8 + - - +
23S GLY* 2.7 26.7 + - - -
24S ILE 2.9 19.2 + - - +
25S THR* 3.8 7.9 - - + +
27S ILE* 3.8 4.4 - - - +
45S LEU* 3.6 15.6 - - + +
46S ASN* 2.8 55.7 + - - +
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Residues in contact with ASP 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S LYS* 2.9 51.1 + - - +
18S ALA* 3.2 12.5 + - - +
20S ASN* 1.3 80.4 - - - +
22S LYS* 1.3 62.0 + - + +
23S GLY 3.2 0.9 + - - -
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Residues in contact with LYS 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S ALA 3.1 10.4 + - - +
19S LEU* 3.0 11.7 + - + +
21S ASP* 1.3 77.1 - - + +
23S GLY* 1.3 60.3 + - - +
24S ILE* 3.3 16.9 + - + +
222S LEU* 3.8 24.0 - - + -
226S GLU* 3.1 30.1 + - - +
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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