Contacts of the helix formed by residues 19 - 30 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS 3.3 9.7 + - - +
16A VAL* 3.1 21.9 + - + +
18A GLU* 1.3 73.9 - - - +
20A ARG* 1.3 87.4 + - - +
21A HIS* 4.1 12.9 + - + +
22A LEU* 4.0 25.0 - - + +
23A LEU* 3.0 24.6 + - - +
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Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU 3.2 6.2 + - - -
19A GLN* 1.3 85.3 + - - +
21A HIS* 1.3 81.2 + - + +
23A LEU* 3.7 12.2 - - - +
24A ALA* 3.0 24.9 + - - +
92A LEU* 4.0 5.7 - - + +
95A TYR* 3.3 33.6 + - + -
96A TYR* 3.0 45.4 + - - -
158A GLU* 5.1 0.2 + - - -
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Residues in contact with HIS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 3.3 10.7 + - + +
20A ARG* 1.3 95.9 - - + +
22A LEU* 1.3 66.5 + - + +
23A LEU 2.9 4.5 - - - -
24A ALA* 3.0 4.7 + - - +
25A ILE* 2.8 36.4 + - - +
92A LEU* 3.8 24.9 - - + -
154A ILE* 4.1 31.0 - - + +
158A GLU* 3.4 31.4 + - - -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.8 30.3 - - + +
19A GLN* 3.5 23.0 + - + +
21A HIS* 1.3 82.2 - - + +
23A LEU* 1.3 55.8 + - - +
25A ILE* 3.9 16.3 - - + +
26A ARG* 2.8 34.7 + - - +
257A GLY 3.9 3.5 - - - +
258A VAL* 3.9 33.7 - - + +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 4.8 6.3 - - - +
18A GLU* 5.1 3.1 - - - +
19A GLN 3.0 18.1 + - - +
20A ARG* 3.7 12.1 - - - +
21A HIS 2.9 0.4 - - - -
22A LEU* 1.3 75.9 - - - +
24A ALA* 1.3 65.4 + - - +
25A ILE 3.2 0.9 - - - -
26A ARG* 3.2 28.0 - - - +
27A ASP* 2.9 50.5 + - - +
91A ARG* 3.5 22.4 - - - +
92A LEU* 6.5 0.4 - - - -
95A TYR* 3.6 37.7 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG 3.0 18.3 + - - +
21A HIS* 3.0 7.2 + - - +
23A LEU* 1.3 74.8 - - + +
25A ILE* 1.3 54.6 + - + +
27A ASP 3.8 0.2 - - - -
28A GLY* 2.8 34.3 + - - -
88A ILE* 3.7 17.4 - - + +
91A ARG* 3.9 13.9 - - - +
92A LEU* 3.4 37.9 - - + -
154A ILE* 5.6 0.4 - - + -
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A HIS* 2.8 22.0 + - + +
22A LEU* 3.9 15.5 - - + +
24A ALA* 1.3 73.4 - - - +
26A ARG* 1.3 68.1 + - - +
29A LEU* 3.0 36.1 + - + +
88A ILE* 3.7 25.6 - - + -
150A MET* 3.8 35.4 - - + -
154A ILE* 3.9 25.8 - - + -
257A GLY 3.7 14.4 - - - +
258A VAL* 5.6 0.7 - - - -
261A PRO* 4.6 2.5 - - + -
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.9 6.5 + - - +
17A ALA* 3.6 33.8 + - - +
22A LEU* 2.8 30.6 + - - +
23A LEU* 3.2 44.9 + - - +
25A ILE* 1.3 75.2 - - - +
27A ASP* 1.3 70.5 + - - +
29A LEU* 3.8 6.4 + - - +
30A VAL* 3.1 19.6 + - + +
253A THR* 3.7 38.5 + - + +
254A ILE* 3.6 29.5 + - - +
257A GLY* 3.6 22.9 - - - +
258A VAL* 5.4 2.0 - - - +
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Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 2.9 43.9 + - - +
26A ARG* 1.3 89.4 + - - +
28A GLY* 1.3 64.7 + - - +
29A LEU 3.3 0.4 - - - -
30A VAL* 3.4 24.9 + - - +
31A LEU* 4.2 2.4 + - - +
91A ARG* 3.9 4.2 + - + -
253A THR* 5.6 1.7 - - - +
600A ZDM 2.6 49.1 + - - +
179B ALA* 4.5 10.7 - - - +
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Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 2.8 19.3 + - - -
25A ILE 3.8 0.7 - - - -
27A ASP* 1.3 76.8 - - - +
29A LEU* 1.3 62.8 + - - +
31A LEU* 3.1 23.1 + - - +
32A THR* 4.3 3.1 + - - +
84A ALA* 4.7 2.1 - - - -
87A GLY* 3.5 33.3 - - - -
88A ILE* 3.7 6.5 - - - -
91A ARG* 4.8 1.0 - - - +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.0 27.3 + - + +
26A ARG 4.0 5.6 - - - +
27A ASP 3.3 0.2 - - - -
28A GLY* 1.3 71.3 - - - +
30A VAL* 1.3 56.8 + - - +
31A LEU 2.9 11.0 + - - -
32A THR* 2.8 33.3 + - + +
33A MET* 3.5 6.8 + - - +
84A ALA* 3.5 28.5 - - + -
88A ILE* 4.6 7.4 - - + +
146A LEU* 4.8 15.5 - - + -
150A MET* 5.7 1.1 - - + -
257A GLY* 5.1 4.0 - - - +
260A SER* 3.5 26.7 - - - +
261A PRO* 3.7 26.9 - - + -
264A LEU* 5.6 5.8 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 3.1 23.1 - - + +
27A ASP* 3.4 24.9 - - - +
28A GLY 3.1 0.4 - - - -
29A LEU* 1.3 74.6 - - - +
31A LEU* 1.3 59.4 + - - +
33A MET* 3.6 17.4 - - + +
34A PRO* 3.6 17.5 - - - +
253A THR* 6.5 0.4 - - + -
600A ZDM 4.1 14.1 - - + +
179B ALA* 4.6 16.2 - - + +
183B SER* 3.2 23.3 + - - +
1E NAG 4.3 21.3 - - + +
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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