Contacts of the helix formed by residues 19 - 29 (chain C) in PDB entry 3QNQ
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 GLN 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C LYS 3.4 11.9 + - - +
16C VAL* 2.5 23.1 + - + +
18C GLU* 1.3 69.4 - - - +
20C ARG* 1.3 68.7 + - - +
21C HIS* 2.7 46.3 + - - +
22C LEU* 3.3 28.1 - - + +
23C LEU* 3.1 19.6 + - - +
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLU 3.3 6.3 + - - -
19C GLN* 1.3 74.4 + - - +
21C HIS* 1.3 81.4 + - + +
23C LEU* 2.8 16.7 + - - +
24C ALA* 2.7 34.3 + - - +
92C LEU* 4.4 2.5 - - + -
95C TYR* 3.2 57.1 + - + +
96C TYR* 2.9 35.8 + - - -
161C ARG* 4.9 5.1 - - - +
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Residues in contact with HIS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C GLN* 2.7 20.6 + - - +
20C ARG* 1.3 95.0 + - + +
22C LEU* 1.3 52.7 + - - +
24C ALA* 2.7 28.0 + - - +
25C ILE* 2.8 23.4 + - + +
92C LEU* 3.9 10.8 - - + -
154C ILE* 4.0 33.0 - - + +
158C GLU* 2.9 28.2 + - + -
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 4.0 28.3 - - + -
19C GLN* 3.3 28.9 + - + +
21C HIS* 1.3 78.2 - - - +
23C LEU* 1.3 56.6 + - - +
25C ILE* 3.8 14.0 - - + +
26C ARG* 2.8 39.1 + - + +
257C GLY 4.6 3.6 - - - +
258C VAL* 3.5 42.2 - - + -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ALA 4.6 7.9 - - - +
18C GLU* 5.4 1.8 - - - +
19C GLN 3.1 13.9 + - - +
20C ARG* 2.8 18.9 + - - +
22C LEU* 1.3 75.9 - - - +
24C ALA* 1.3 65.1 + - + +
26C ARG* 3.2 32.6 - - - +
27C ASP* 3.1 44.8 + - - +
91C ARG* 3.7 31.6 - - + +
92C LEU* 6.5 0.2 - - + -
95C TYR* 3.9 23.3 - - + -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG 2.7 13.5 + - - +
21C HIS* 2.7 10.0 + - - +
23C LEU* 1.3 71.7 - - + +
25C ILE* 1.3 58.6 + - - +
27C ASP* 3.8 0.5 - - - +
28C GLY* 2.9 28.2 + - - -
88C ILE* 3.8 16.6 - - + +
91C ARG* 3.9 13.1 - - + +
92C LEU* 3.6 44.9 - - + +
154C ILE* 5.8 1.1 - - + -
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C HIS* 2.8 24.6 + - + +
22C LEU* 3.8 12.8 - - + +
24C ALA* 1.3 72.1 - - - +
26C ARG* 1.3 63.4 + - - +
27C ASP 3.0 1.2 + - - -
28C GLY* 4.0 0.2 - - - -
29C LEU* 3.2 34.0 + - + +
88C ILE* 4.0 14.5 - - + +
150C MET* 3.8 42.2 - - + -
154C ILE* 3.9 27.6 - - + -
257C GLY 4.0 16.2 - - - +
261C PRO* 4.9 1.3 - - + -
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 4.0 6.7 + - - +
17C ALA* 3.4 34.6 + - - +
22C LEU* 2.8 26.1 + - + +
23C LEU* 3.2 50.8 - - - +
24C ALA 3.3 0.2 - - - -
25C ILE* 1.3 77.2 - - - +
27C ASP* 1.3 69.0 + - - +
29C LEU* 4.1 4.7 + - - +
30C VAL* 3.3 21.5 + - + +
33C MET* 5.5 0.5 - - - +
253C THR* 3.6 28.2 + - - +
254C ILE* 3.7 31.0 + - - +
257C GLY* 4.1 22.4 - - - -
258C VAL* 6.3 0.6 - - - +
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Residues in contact with ASP 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 3.1 40.9 + - - +
26C ARG* 1.3 91.5 - - - +
28C GLY* 1.3 64.6 + - - +
29C LEU 3.4 0.4 - - - -
30C VAL* 3.5 22.6 - - - +
31C LEU* 4.1 3.3 + - - +
87C GLY 5.1 0.4 - - - -
91C ARG* 3.8 6.4 + - + -
600C ZDM 2.7 50.2 + - - +
179D ALA* 5.0 8.8 - - - +
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Residues in contact with GLY 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA 2.9 12.6 + - - -
25C ILE 4.0 0.2 - - - -
27C ASP* 1.3 74.4 - - - +
29C LEU* 1.3 53.6 + - - +
30C VAL 2.9 4.9 - - - -
31C LEU* 2.7 35.7 + - - +
32C THR* 3.9 2.9 + - - +
84C ALA* 5.0 2.8 - - - -
87C GLY* 3.4 36.2 + - - -
88C ILE* 3.6 6.7 - - - -
91C ARG* 4.9 0.2 - - - +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.2 27.6 + - + +
26C ARG* 4.1 6.3 - - - +
28C GLY* 1.3 75.3 - - - +
30C VAL* 1.3 58.6 + - - +
32C THR* 2.4 36.1 + - + +
33C MET* 3.6 11.7 + - + +
80C MET* 6.0 0.7 - - + -
84C ALA* 3.9 24.9 - - + -
88C ILE* 4.4 6.8 - - + +
146C LEU* 4.4 18.6 - - + +
150C MET* 5.4 1.6 - - + -
257C GLY* 4.8 3.8 - - - +
260C SER* 3.6 24.7 - - - +
261C PRO* 3.7 28.0 - - + -
264C LEU* 5.8 3.8 - - + -
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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