Contacts of the helix formed by residues 9 - 22 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6Q GLY 2.7 14.5 + - - -
8Q ALA* 1.3 79.8 - - - +
10Q PHE* 1.3 57.0 + - - -
11Q ILE 3.7 0.9 - - - -
13Q SER* 2.7 34.5 + - - -
31Q ASP* 3.2 3.6 + - - -
41Q ASN* 4.2 0.4 - - - -
177Q HIS* 3.8 8.7 - - - -
400Q NAP 3.4 25.4 - - - -
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Residues in contact with PHE 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q GLY* 1.3 70.4 - - - -
11Q ILE* 1.3 67.7 + - + +
13Q SER* 3.0 9.2 + - - -
14Q ASN* 2.8 28.3 + - - -
170Q VAL* 3.6 31.6 - - + -
171Q TYR* 3.5 5.2 - - - -
172Q GLY 3.2 34.1 - - - -
173Q PRO 3.1 22.0 - - - -
174Q ARG 3.1 25.4 - - - +
175Q GLU* 3.6 15.5 - - + -
177Q HIS* 3.5 2.2 - - + -
178Q LYS* 4.0 9.6 - - + -
214Q VAL* 3.6 12.6 - - + -
400Q NAP 2.9 43.5 + - - +
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Residues in contact with ILE 11 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q PHE* 1.3 87.5 - - + +
12Q GLY* 1.3 61.9 + - - +
14Q ASN* 3.1 5.5 + - - +
15Q ILE* 3.0 28.4 + - + +
75Q GLU* 3.5 22.9 - - - +
167Q TYR* 3.5 37.5 - - + +
170Q VAL* 4.1 19.7 - - + -
214Q VAL* 4.5 7.9 - - + -
217Q VAL* 4.0 14.6 - - + -
400Q NAP 2.7 47.4 + - + +
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Residues in contact with GLY 12 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q VAL* 3.7 14.9 - - - +
6Q GLY 3.5 19.4 + - - -
7Q GLY* 3.8 6.7 - - - -
10Q PHE 3.3 0.4 - - - -
11Q ILE* 1.3 79.4 - - - +
13Q SER* 1.3 61.2 + - - +
15Q ILE* 3.0 6.0 + - - +
16Q VAL* 2.9 24.6 + - - +
75Q GLU* 4.0 15.0 - - - +
400Q NAP 4.2 0.6 + - - -
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Residues in contact with SER 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q GLY 3.3 17.4 + - - -
9Q GLY 2.7 24.1 + - - -
10Q PHE 3.0 8.7 + - - -
12Q GLY* 1.3 75.9 - - - +
14Q ASN* 1.3 56.2 + - - +
16Q VAL* 3.2 8.5 + - - +
17Q LYS* 2.9 24.3 + - - +
41Q ASN* 3.6 29.9 - - - +
45Q LEU* 3.4 8.1 - - - +
174Q ARG* 3.3 22.3 - - - +
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Residues in contact with ASN 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Q PHE* 2.8 22.4 + - - -
11Q ILE* 3.1 8.9 + - + +
13Q SER* 1.3 80.7 + - - +
15Q ILE* 1.3 60.2 + - - +
17Q LYS* 3.7 11.2 - - - +
18Q ALA* 3.0 28.4 + - - +
173Q PRO* 2.9 29.4 + - - +
174Q ARG* 3.8 15.0 + - - +
214Q VAL* 3.5 37.9 - - + +
215Q GLY* 5.3 1.7 + - - -
218Q ALA* 3.9 13.0 - - + +
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Residues in contact with ILE 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q VAL* 4.4 5.8 - - + -
11Q ILE* 3.0 20.9 + - + +
12Q GLY* 3.4 7.4 - - - +
14Q ASN* 1.3 75.4 - - - +
16Q VAL* 1.3 65.4 + - - +
18Q ALA* 3.2 6.9 + - - +
19Q LEU* 2.9 37.1 + - + +
73Q PHE* 4.0 26.9 - - + -
75Q GLU* 3.6 32.5 - - + +
218Q ALA* 4.6 8.3 - - - -
221Q ASN* 3.5 38.4 - - + +
222Q LEU* 4.5 7.9 - - + -
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Residues in contact with VAL 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q VAL* 4.2 17.0 - - + -
7Q GLY 4.2 8.3 - - - +
12Q GLY 2.9 18.9 + - - +
13Q SER 3.2 8.0 + - - +
15Q ILE* 1.3 76.5 - - - +
17Q LYS* 1.3 57.4 + - - +
19Q LEU* 3.1 11.2 + - - +
20Q ASN* 2.8 30.6 + - - +
27Q ILE* 4.0 11.0 - - + -
29Q VAL* 4.1 21.8 - - + -
42Q LEU* 4.7 1.6 - - + -
45Q LEU* 3.7 22.0 - - + -
47Q ILE* 3.8 25.4 - - + -
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Residues in contact with LYS 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Q SER 2.9 14.2 + - - +
14Q ASN* 3.7 15.5 - - - +
15Q ILE 3.3 0.4 - - - -
16Q VAL* 1.3 75.5 - - - +
18Q ALA* 1.3 59.4 + - - +
20Q ASN* 3.1 7.2 + - + +
21Q ASP* 2.9 61.0 + - - +
45Q LEU* 3.9 27.6 - - + +
174Q ARG* 4.1 20.2 - - - +
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Residues in contact with ALA 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q ASN 3.0 17.4 + - - +
15Q ILE* 3.5 6.1 - - - +
17Q LYS* 1.3 78.2 - - - +
19Q LEU* 1.3 60.6 + - - +
21Q ASP* 3.2 11.6 + - - +
22Q LYS* 3.1 18.9 + - - +
218Q ALA* 4.0 20.0 - - + +
219Q ASP* 5.3 4.3 - - - +
222Q LEU* 3.8 26.8 - - + +
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Residues in contact with LEU 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q ILE* 3.8 46.0 - - + -
4Q VAL* 4.2 7.0 - - + -
15Q ILE* 2.9 32.6 + - + +
16Q VAL 3.4 5.6 - - - +
18Q ALA* 1.3 71.9 - - - +
20Q ASN* 1.3 67.2 + - - +
22Q LYS* 3.0 11.0 + - + +
23Q GLY 3.3 0.3 + - - -
24Q ILE* 2.9 39.4 + - + +
27Q ILE* 3.9 22.7 - - + -
73Q PHE* 4.4 4.0 - - + -
222Q LEU* 3.9 26.2 - - + -
225Q LEU* 5.1 3.1 - - + -
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Residues in contact with ASN 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q VAL* 2.8 16.0 + - - +
17Q LYS* 3.1 12.1 + - + +
19Q LEU* 1.3 76.2 - - - +
21Q ASP* 1.3 57.5 + - - +
23Q GLY* 2.7 26.5 + - - -
24Q ILE 2.9 19.2 + - - -
25Q THR* 3.8 8.6 - - + +
27Q ILE* 3.8 4.4 - - - +
44Q ASP 5.0 0.2 - - - +
45Q LEU* 3.6 15.3 - - + +
46Q ASN* 2.8 55.4 + - - +
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Residues in contact with ASP 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q LYS* 2.9 50.9 + - - +
18Q ALA* 3.2 13.1 + - - +
20Q ASN* 1.3 78.5 - - - +
22Q LYS* 1.3 60.4 + - + +
23Q GLY 3.2 0.7 + - - -
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Residues in contact with LYS 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q ALA 3.1 12.3 + - - +
19Q LEU* 3.0 11.8 + - - +
21Q ASP* 1.3 78.6 - - + +
23Q GLY* 1.3 60.0 + - - +
24Q ILE* 3.3 17.4 + - + +
222Q LEU* 3.8 24.0 - - + -
226Q GLU* 3.1 31.0 + - - +
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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