Contacts of the helix formed by residues 9 - 22 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6O GLY 2.7 14.0 + - - -
8O ALA* 1.3 80.3 - - - +
10O PHE* 1.3 59.4 + - - -
11O ILE 3.7 0.7 - - - -
13O SER* 2.7 33.8 + - - -
31O ASP* 3.2 3.6 + - - -
41O ASN* 4.2 0.4 - - - -
177O HIS* 3.8 10.1 - - - -
400O NAP 3.5 24.0 - - - -
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Residues in contact with PHE 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O GLY* 1.3 70.2 - - - -
11O ILE* 1.3 67.6 + - + +
13O SER* 3.0 9.2 + - - -
14O ASN* 2.8 27.7 + - - -
170O VAL* 3.6 27.8 - - + -
171O TYR* 3.6 5.4 - - - -
172O GLY 3.2 34.3 - - - -
173O PRO 3.1 22.0 - - - -
174O ARG 3.1 25.4 - - - +
175O GLU* 3.6 16.8 - - + -
177O HIS* 3.5 2.0 - - + -
178O LYS* 4.0 8.3 - - + -
214O VAL* 3.6 11.9 - - + -
400O NAP 3.0 48.7 + - - +
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Residues in contact with ILE 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O PHE* 1.3 87.7 - - + +
12O GLY* 1.3 62.4 + - - +
14O ASN* 3.1 9.4 + - - +
15O ILE* 2.9 28.2 + - + +
75O GLU* 3.5 21.3 - - - +
167O TYR* 3.5 37.7 - - + +
170O VAL* 4.1 19.5 - - + -
214O VAL* 4.5 5.2 - - + -
217O VAL* 4.1 14.8 - - + -
400O NAP 2.8 48.4 + - + +
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Residues in contact with GLY 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O VAL* 3.7 15.7 - - - +
6O GLY 3.5 18.8 + - - -
7O GLY* 3.8 7.2 - - - -
9O GLY 4.3 0.2 - - - -
10O PHE 3.3 0.6 - - - -
11O ILE* 1.3 78.2 - - - +
13O SER* 1.3 61.5 + - - +
15O ILE* 3.0 6.1 + - - +
16O VAL* 2.9 24.8 + - - +
75O GLU* 4.0 15.4 - - - +
400O NAP 4.4 1.0 + - - -
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Residues in contact with SER 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O GLY 3.3 17.9 + - - -
9O GLY 2.7 24.0 + - - -
10O PHE 3.0 9.0 + - - -
12O GLY* 1.3 75.3 - - - +
14O ASN* 1.3 56.1 + - - +
16O VAL* 3.2 7.8 + - - +
17O LYS* 2.9 24.3 + - - +
41O ASN* 3.6 29.9 - - - +
45O LEU* 3.4 8.2 - - - +
174O ARG* 3.3 21.4 - - - +
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Residues in contact with ASN 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O PHE* 2.8 22.2 + - - -
11O ILE* 3.1 9.1 + - + +
13O SER* 1.3 80.1 + - - +
15O ILE* 1.3 59.2 + - - +
17O LYS* 3.4 12.2 + - - +
18O ALA* 3.0 27.7 + - - +
173O PRO* 2.9 31.7 + - - +
174O ARG* 3.8 14.8 + - - +
214O VAL* 3.5 35.0 - - + +
215O GLY* 5.6 1.4 - - - -
218O ALA* 4.0 12.9 - - + +
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Residues in contact with ILE 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O VAL* 4.4 6.1 - - + -
11O ILE* 2.9 19.2 + - + +
12O GLY* 3.0 8.2 + - - +
14O ASN* 1.3 74.7 - - - +
16O VAL* 1.3 64.7 + - - +
18O ALA* 3.2 6.6 + - - +
19O LEU* 2.9 37.5 + - + +
73O PHE* 4.0 27.8 - - + -
75O GLU* 3.6 32.1 - - + +
218O ALA* 4.7 9.6 - - + +
221O ASN* 3.5 39.0 - - + +
222O LEU* 4.5 6.5 - - + -
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Residues in contact with VAL 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O VAL* 4.2 16.6 - - + -
7O GLY 4.1 8.5 - - - +
12O GLY 2.9 18.8 + - - +
13O SER 3.3 7.9 - - - +
15O ILE* 1.3 76.2 - - - +
17O LYS* 1.3 56.7 + - - +
19O LEU* 3.1 11.5 + - - +
20O ASN* 2.8 30.6 + - - +
27O ILE* 4.0 11.0 - - + -
29O VAL* 4.1 22.2 - - + -
42O LEU* 4.7 1.8 - - + -
45O LEU* 3.7 21.8 - - + -
47O ILE* 3.8 24.7 - - + -
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Residues in contact with LYS 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O SER 2.9 13.5 + - - +
14O ASN* 3.7 16.2 - - - +
15O ILE 3.3 0.2 - - - -
16O VAL* 1.3 75.4 - - - +
18O ALA* 1.3 58.4 + - - +
20O ASN* 3.1 8.1 + - + +
21O ASP* 2.9 59.9 + - - +
45O LEU* 3.9 26.7 - - + -
174O ARG* 4.1 20.0 - - - +
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Residues in contact with ALA 18 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14O ASN 3.0 17.9 + - - +
15O ILE* 3.5 5.6 - - - +
16O VAL 3.2 0.2 - - - -
17O LYS* 1.3 77.5 - - - +
19O LEU* 1.3 60.4 + - - +
21O ASP* 3.2 12.1 + - - +
22O LYS* 3.1 18.0 + - - +
218O ALA* 4.0 19.3 - - + +
219O ASP* 5.4 4.3 - - - +
222O LEU* 3.8 28.5 - - + +
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Residues in contact with LEU 19 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2O ILE* 3.8 46.4 - - + -
4O VAL* 4.2 7.2 - - + -
15O ILE* 2.9 32.9 + - + +
16O VAL 3.4 5.8 - - - +
18O ALA* 1.3 71.4 - - - +
20O ASN* 1.3 67.0 + - - +
22O LYS* 3.0 10.7 + - + +
23O GLY 3.3 0.2 + - - -
24O ILE* 2.9 40.3 + - + +
27O ILE* 3.9 22.9 - - + -
73O PHE* 4.4 3.8 - - + -
222O LEU* 3.9 26.5 - - + -
225O LEU* 5.0 3.4 - - + -
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Residues in contact with ASN 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O VAL* 2.8 16.7 + - - +
17O LYS* 3.3 12.1 - - + +
19O LEU* 1.3 76.1 - - - +
21O ASP* 1.3 56.7 + - - +
23O GLY* 2.7 26.3 + - - -
24O ILE 2.9 19.6 + - - -
25O THR* 3.8 8.2 - - + +
27O ILE* 3.8 4.2 - - - +
45O LEU* 3.6 15.9 - - + +
46O ASN* 2.8 55.0 + - - +
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Residues in contact with ASP 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O LYS* 2.9 51.2 + - - +
18O ALA* 3.2 12.1 + - - +
20O ASN* 1.3 78.5 - - - +
22O LYS* 1.3 62.1 + - + +
23O GLY 3.2 1.4 + - - -
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Residues in contact with LYS 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O ALA 3.1 11.0 + - - +
19O LEU* 3.0 11.5 + - + +
21O ASP* 1.3 78.1 - - + +
23O GLY* 1.3 59.6 - - - +
24O ILE* 3.3 16.7 + - + +
222O LEU* 3.8 23.8 - - + -
226O GLU* 3.1 32.1 + - - +
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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