Contacts of the helix formed by residues 9 - 22 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F GLY 2.8 13.9 + - - -
8F ALA* 1.3 80.2 - - - +
10F PHE* 1.3 58.3 + - - -
11F ILE 3.7 1.1 - - - -
13F SER* 2.7 34.3 + - - -
31F ASP* 3.2 3.4 + - - -
41F ASN* 4.2 0.7 - - - -
177F HIS* 3.8 10.1 - - - -
400F NAP 3.5 24.2 - - - -
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Residues in contact with PHE 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLY* 1.3 70.6 - - - -
11F ILE* 1.3 67.2 + - + +
13F SER* 3.0 9.7 + - - -
14F ASN* 2.8 28.4 + - - -
170F VAL* 3.6 32.3 - - + -
171F TYR* 3.5 5.4 - - - -
172F GLY 3.2 34.1 - - - -
173F PRO 3.1 21.1 - - - -
174F ARG 3.1 24.9 - - - +
175F GLU* 3.6 17.0 - - + -
177F HIS* 3.5 2.4 - - + -
178F LYS* 4.0 9.4 - - + -
214F VAL* 3.6 12.6 - - + -
400F NAP 3.0 43.5 + - - +
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Residues in contact with ILE 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F PHE* 1.3 89.2 - - + +
12F GLY* 1.3 63.7 + - - +
14F ASN* 3.1 9.1 + - - +
15F ILE* 3.0 28.5 + - + +
75F GLU* 3.5 21.8 - - - +
167F TYR* 3.5 38.1 - - + +
170F VAL* 4.1 18.8 - - + -
214F VAL* 4.5 4.9 - - + -
217F VAL* 4.0 13.9 - - + -
400F NAP 2.8 46.7 + - + +
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Residues in contact with GLY 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 3.7 15.4 - - - +
6F GLY 3.5 19.4 + - - -
7F GLY* 3.8 6.1 - - - -
9F GLY 4.3 0.2 - - - -
10F PHE 3.3 0.4 - - - -
11F ILE* 1.3 79.2 - - - +
13F SER* 1.3 61.5 + - - +
15F ILE* 3.0 7.0 + - - +
16F VAL* 2.9 24.3 + - - +
75F GLU* 4.0 14.8 - - - +
400F NAP 4.4 0.8 + - - -
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Residues in contact with SER 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLY 3.3 18.1 + - - -
9F GLY 2.7 24.5 + - - -
10F PHE 3.0 8.3 + - - -
12F GLY* 1.3 75.9 - - - +
14F ASN* 1.3 56.9 + - - +
16F VAL* 3.2 7.5 + - - +
17F LYS* 2.9 24.3 + - - +
41F ASN* 3.6 30.1 - - - +
45F LEU* 3.4 8.7 - - - +
174F ARG* 3.3 22.3 - - - +
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Residues in contact with ASN 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F PHE* 2.8 22.2 + - - -
11F ILE 3.1 9.2 + - - +
13F SER* 1.3 80.1 + - - +
15F ILE* 1.3 59.2 + - - +
17F LYS* 3.4 12.0 + - - +
18F ALA* 3.0 28.1 + - - +
173F PRO* 2.9 29.5 + - - +
174F ARG* 3.8 14.1 + - - +
214F VAL* 3.5 38.1 - - + +
215F GLY* 5.3 1.6 + - - -
218F ALA* 3.9 12.5 - - + +
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Residues in contact with ILE 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 4.4 5.4 - - + -
11F ILE* 3.0 19.4 + - + +
12F GLY* 3.4 7.4 - - - +
14F ASN* 1.3 75.4 - - - +
16F VAL* 1.3 65.9 + - - +
18F ALA* 3.2 7.3 + - - +
19F LEU* 2.9 36.9 + - + +
73F PHE* 4.0 26.5 - - + -
75F GLU* 3.6 32.3 - - + +
218F ALA* 4.6 8.5 - - - -
221F ASN* 3.5 39.0 - - + +
222F LEU* 4.4 8.7 - - + -
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Residues in contact with VAL 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 4.2 17.5 - - + -
7F GLY 4.2 8.5 - - - +
12F GLY 2.9 19.3 + - - +
13F SER 3.2 8.0 + - - +
15F ILE* 1.3 75.9 - - - +
17F LYS* 1.3 58.7 + - - +
19F LEU* 3.1 11.2 + - - +
20F ASN* 2.8 29.9 + - - +
27F ILE* 4.0 11.2 - - + -
29F VAL* 4.1 21.8 - - + -
42F LEU* 4.8 1.1 - - + -
45F LEU* 3.7 21.5 - - + -
47F ILE* 3.8 24.9 - - + -
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Residues in contact with LYS 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F SER 2.9 14.3 + - - +
14F ASN* 3.7 15.0 - - - +
15F ILE 3.3 0.2 - - - -
16F VAL* 1.3 75.1 - - - +
18F ALA* 1.3 59.5 + - - +
20F ASN* 3.1 7.1 + - + +
21F ASP* 2.8 60.4 + - - +
45F LEU* 3.9 27.3 - - + +
174F ARG* 4.0 20.8 - - - +
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Residues in contact with ALA 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ASN 3.0 17.0 + - - +
15F ILE* 3.5 5.8 - - - +
16F VAL 3.2 0.2 - - - -
17F LYS* 1.3 78.1 - - - +
19F LEU* 1.3 61.8 + - - +
21F ASP* 3.2 12.4 + - - +
22F LYS* 3.1 18.2 + - - +
218F ALA* 4.0 19.5 - - + -
219F ASP* 5.3 4.9 - - - +
222F LEU* 3.8 27.3 - - + +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ILE* 3.9 44.9 - - + -
4F VAL* 4.2 7.0 - - + -
15F ILE* 2.9 33.1 + - + +
16F VAL 3.1 6.3 + - - +
18F ALA* 1.3 72.3 - - - +
20F ASN* 1.3 67.1 + - - +
22F LYS* 3.0 9.9 + - - +
24F ILE* 2.9 40.7 + - + +
27F ILE* 3.9 23.1 - - + -
73F PHE* 4.4 4.3 - - + -
222F LEU* 3.8 27.4 - - + -
225F LEU* 5.0 3.8 - - + -
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Residues in contact with ASN 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F VAL* 2.8 17.1 + - - -
17F LYS* 3.3 12.6 - - + +
19F LEU* 1.3 77.1 - - - +
21F ASP* 1.3 57.3 + - - +
23F GLY* 2.7 26.3 + - - -
24F ILE 2.9 19.0 + - - -
25F THR* 3.8 9.4 - - + +
27F ILE* 3.8 4.0 - - - +
45F LEU* 3.6 15.5 - - + +
46F ASN* 2.8 54.4 + - - +
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Residues in contact with ASP 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F LYS* 2.8 51.7 + - - +
18F ALA* 3.2 12.4 + - - +
20F ASN* 1.3 78.9 - - - +
22F LYS* 1.3 61.5 + - + +
23F GLY 3.2 1.3 + - - -
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Residues in contact with LYS 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ALA 3.1 12.0 + - - +
19F LEU* 3.0 12.2 + - - +
21F ASP* 1.3 77.7 - - + +
23F GLY* 1.3 59.5 + - - +
24F ILE* 3.3 16.5 + - + +
222F LEU* 3.8 25.1 - - + -
226F GLU* 3.1 29.7 + - - +
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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