Contacts of the helix formed by residues 12 - 25 (chain Q) in PDB entry 5IYB
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 ALA 12 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11Q PRO* 1.3 75.8 - - - +
13Q ALA* 1.3 62.6 + - - +
15Q LYS* 3.2 17.1 - - + +
16Q ARG* 3.0 22.9 + - - +
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Residues in contact with ALA 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PRO* 5.1 0.9 - - + -
12Q ALA* 1.3 76.0 - - - +
14Q LEU* 1.3 53.9 + - - +
16Q ARG* 3.2 7.3 + - - +
17Q LEU* 2.8 35.0 + - - +
194Q THR* 3.9 21.4 - - + +
197Q VAL* 5.2 11.7 - - + -
198Q ASN* 4.6 9.6 - - - +
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Residues in contact with LEU 14 (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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11Q PRO* 3.2 23.5 + - + +
13Q ALA* 1.3 78.6 - - - +
15Q LYS* 1.3 59.3 + - + +
17Q LEU* 3.2 8.7 + - + +
18Q ALA* 2.7 40.7 + - + +
38Q ILE* 6.1 3.1 - - + -
102Q VAL* 2.0 54.7 - - + -
103Q VAL* 4.9 9.8 - - + +
198Q ASN* 4.0 19.6 - - - +
201Q TYR* 6.3 2.7 - - + -
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Residues in contact with LYS 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PRO* 2.9 29.0 + - + +
12Q ALA* 3.2 18.6 - - + +
14Q LEU* 1.3 80.0 - - + +
16Q ARG* 1.3 57.1 + - - +
18Q ALA* 3.4 8.5 - - - +
19Q LYS* 3.0 34.1 + - - +
38Q ILE* 3.8 36.4 - - + +
39Q ARG* 4.1 28.5 - - + +
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Residues in contact with ARG 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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12Q ALA 3.0 13.4 + - - +
13Q ALA* 3.7 8.7 - - - +
15Q LYS* 1.3 72.7 - - - +
17Q LEU* 1.3 61.8 + - - +
18Q ALA 3.1 1.3 - - - -
19Q LYS* 2.9 31.1 + - - +
20Q TYR* 2.8 31.6 + - - +
206R LYS* 5.7 9.4 - - - +
207R SER* 4.7 17.4 - - - +
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Residues in contact with LEU 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 ALA 2.8 21.4 + - - +
14Q LEU* 3.2 8.9 + - + +
16Q ARG* 1.3 72.3 - - - +
18Q ALA* 1.3 57.7 + - - +
20Q TYR* 3.2 12.8 - - + +
21Q VAL* 3.0 31.6 + - + +
102Q VAL* 5.9 1.1 - - + -
103Q VAL* 4.0 27.6 - - + -
107Q LEU* 4.2 15.0 - - + -
188Q TYR* 6.3 0.2 - - + -
191Q LEU* 4.0 36.1 - - + +
194Q THR* 4.0 17.0 - - + +
195Q GLU* 4.5 9.4 - - + -
198Q ASN* 3.9 19.5 - - - +
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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 LEU* 2.7 23.3 + - + +
15Q LYS* 3.4 8.3 - - - +
17Q LEU* 1.3 74.1 - - - +
19Q LYS* 1.3 58.9 + - - +
21Q VAL* 3.0 10.6 + - - +
22Q ILE* 2.9 35.2 + - + +
38Q ILE* 3.6 25.1 - - + -
103Q VAL* 4.6 13.4 - - + +
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Residues in contact with LYS 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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15Q LYS* 3.0 25.5 + - - +
16Q ARG* 2.9 44.2 + - - +
18Q ALA* 1.3 74.8 - - - +
20Q TYR* 1.3 58.9 + - - +
22Q ILE* 3.1 30.0 - - + +
23Q ARG 3.5 0.3 + - - -
35Q ASP* 3.0 26.4 + - - +
38Q ILE* 5.4 4.0 - - + +
159R ASP* 4.9 9.2 + - - -
161R ARG* 4.2 11.7 - - - +
206R LYS* 6.4 1.6 - - + -
207R SER* 3.3 18.1 + - - +
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Residues in contact with TYR 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q ARG* 2.8 14.6 + - - +
17Q LEU* 3.2 18.8 - - + +
19Q LYS* 1.3 78.0 - - - +
21Q VAL* 1.3 73.6 + - + +
23Q ARG* 3.3 6.0 + - + +
24Q GLY* 3.1 19.8 + - - -
25Q PHE* 6.4 1.3 - + - -
107Q LEU* 5.6 7.6 - - + -
184Q ILE* 5.4 6.1 - - - +
187Q ILE* 5.1 12.6 - - + +
188Q TYR* 5.2 7.0 - + - +
191Q LEU* 3.5 38.3 - - + +
207R SER* 4.7 9.2 - - - -
208R CYS 6.0 1.8 - - - -
210R PHE* 3.5 40.3 - + + +
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Residues in contact with VAL 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 LEU* 3.0 21.5 + - + +
18Q ALA* 3.0 12.3 + - - +
20Q TYR* 1.3 85.5 - - + +
22Q ILE* 1.3 66.3 + - + +
24Q GLY* 5.3 0.2 - - - -
25Q PHE* 3.1 55.3 + - + +
34Q LEU* 5.9 2.9 - - + -
71Q PHE* 5.0 12.6 - - + -
103Q VAL* 4.5 23.1 - - + -
106Q LYS* 5.6 4.0 - - + -
107Q LEU* 4.7 16.4 - - + -
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Residues in contact with ILE 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* 2.9 17.4 + - + +
19Q LYS* 3.1 32.8 - - + +
21Q VAL* 1.3 80.6 - - + +
23Q ARG* 1.3 65.5 + - + +
25Q PHE* 3.7 4.6 + - - -
26Q TYR 3.5 20.8 + - - +
31Q ALA* 3.6 38.0 - - + +
34Q LEU* 3.8 39.7 - - + -
35Q ASP* 4.5 13.0 - - + +
38Q ILE* 5.0 6.5 - - + -
161R ARG* 6.4 0.2 - - - +
207R SER* 5.2 0.4 - - - +
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Residues in contact with ARG 23 (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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19Q LYS 3.7 0.4 - - - +
20Q TYR* 3.3 9.3 + - + +
22Q ILE* 1.3 84.4 - - + +
24Q GLY* 1.3 61.3 + - - +
25Q PHE 4.5 2.4 - - - +
26Q TYR 4.5 3.3 - - - +
31Q ALA* 5.6 0.9 - - - -
205R ASP* 5.4 9.4 - - - -
207R SER* 1.7 56.5 + - - +
208R CYS* 2.3 34.9 - - - +
209R GLN* 1.9 59.1 - - - +
210R PHE* 5.9 0.2 - - + -
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Residues in contact with GLY 24 (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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20Q TYR* 3.1 12.2 + - - -
21Q VAL 4.1 0.4 - - - -
23Q ARG* 1.3 79.7 - - - +
25Q PHE* 1.3 67.1 - - - +
209R GLN* 4.4 8.0 - - - +
210R PHE* 2.6 53.4 - - - -
219R LEU* 4.7 4.2 - - - +
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Residues in contact with PHE 25 (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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20Q TYR* 6.4 1.3 - + - -
21Q VAL* 3.1 49.7 + - + +
22Q ILE* 4.1 2.5 - - - +
23Q ARG 3.5 1.3 - - - +
24Q GLY* 1.3 84.9 - - - +
26Q TYR* 1.3 80.9 + + + +
34Q LEU* 6.4 2.0 - - + -
69Q ASP* 5.6 1.3 - - - -
71Q PHE* 4.1 28.3 - + + -
106Q LYS* 4.6 17.0 - - + -
107Q LEU* 5.6 6.1 - - + -
110Q MET* 3.4 48.2 - - + -
209R GLN* 6.0 0.3 - - - +
210R PHE* 5.2 4.5 - + - -
219R LEU* 3.5 27.5 - - + +
223R VAL* 5.4 6.5 - - + -
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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