Contacts of the helix formed by residues 19 - 29 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B LYS 3.3 15.6 + - - +
16B VAL* 3.2 18.8 + - - +
18B GLU* 1.3 73.5 - - - +
20B ARG* 1.3 65.2 + - - +
21B HIS* 3.1 37.2 + - - +
22B LEU* 3.3 32.3 - - + +
23B LEU* 2.9 28.6 + - - +
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU 3.0 5.4 + - - -
19B GLN* 1.3 81.6 - - - +
21B HIS* 1.3 76.4 + - + +
23B LEU* 3.6 11.5 - - - +
24B ALA* 2.8 28.2 + - - +
92B LEU* 4.0 4.5 - - + +
95B TYR* 2.5 67.2 + - + +
96B TYR* 3.2 33.1 + - - -
161B ARG* 6.1 0.6 - - - +
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Residues in contact with HIS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 3.1 25.2 + - - +
20B ARG* 1.3 95.7 - - + +
22B LEU* 1.3 70.7 + - + +
23B LEU 3.0 0.9 - - - -
24B ALA* 3.2 3.1 + - - +
25B ILE* 2.9 33.6 + - + +
92B LEU* 4.1 14.8 - - + -
96B TYR* 4.7 0.4 - - - -
154B ILE* 4.1 34.1 - - + +
158B GLU* 2.6 30.1 + - + +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 4.1 35.0 - - + +
19B GLN* 3.3 27.3 + - + +
21B HIS* 1.3 79.9 - - + +
23B LEU* 1.3 50.5 + - - +
25B ILE* 3.9 10.6 - - + +
26B ARG* 2.7 45.4 + - + +
257B GLY 4.9 2.4 - - - +
258B VAL* 4.0 29.4 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ZDM 5.2 5.8 - - - +
17B ALA 4.6 5.8 - - - +
18B GLU* 4.3 8.7 - - - +
19B GLN 2.9 19.0 + - - +
20B ARG* 3.6 16.2 - - - +
22B LEU* 1.3 75.4 - - - +
24B ALA* 1.3 60.0 + - - +
26B ARG* 3.0 37.9 - - - +
27B ASP* 2.8 57.0 + - - +
91B ARG* 4.1 17.3 - - - +
95B TYR* 4.1 23.3 - - + -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG 2.8 22.6 + - - +
21B HIS* 3.2 5.8 + - - +
23B LEU* 1.3 72.7 - - - +
25B ILE* 1.3 58.8 + - + +
28B GLY* 2.9 28.6 + - - -
88B ILE* 3.9 16.2 - - + +
91B ARG* 4.0 13.7 - - + +
92B LEU* 3.7 37.2 - - + +
154B ILE* 5.4 2.5 - - + -
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B HIS 2.9 23.6 + - - +
22B LEU* 3.9 8.7 - - + +
24B ALA* 1.3 73.0 - - - +
26B ARG* 1.3 66.5 + - - +
28B GLY 3.8 0.2 - - - -
29B LEU* 2.9 46.0 + - + +
88B ILE* 3.5 28.1 - - + +
150B MET* 3.5 40.8 - - + -
154B ILE* 3.8 24.5 - - + -
257B GLY 4.1 9.4 - - - +
261B PRO* 4.7 1.3 - - + -
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.9 5.7 + - - +
17B ALA* 3.3 24.0 + - - +
22B LEU* 2.7 29.5 + - - +
23B LEU* 3.0 46.6 - - - +
25B ILE* 1.3 76.3 - - - +
27B ASP* 1.3 74.1 + - - +
29B LEU* 3.7 11.6 + - - +
30B VAL* 3.8 10.2 - - - +
33B MET* 5.3 1.4 - - - +
253B THR* 3.3 37.4 + - - +
254B ILE* 3.3 36.9 + - - +
257B GLY* 3.6 23.7 - - - +
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ALA* 5.4 7.8 - - - +
443A ZDM 3.7 36.0 + - - +
23B LEU* 2.8 33.3 + - - +
26B ARG* 1.3 86.5 + - - +
28B GLY* 1.3 66.5 + - - +
29B LEU 3.1 1.3 - - - -
30B VAL* 2.9 30.4 + - - +
31B LEU 4.1 0.9 + - - -
91B ARG* 3.2 31.0 + - + -
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Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ZDM 5.3 0.9 - - - -
24B ALA 2.9 19.3 + - - -
25B ILE 3.8 0.4 - - - -
27B ASP* 1.3 76.3 - - - +
29B LEU* 1.3 61.2 + - - +
31B LEU* 3.1 24.0 + - - +
84B ALA* 4.8 3.7 - - - -
87B GLY* 3.7 28.5 - - - -
88B ILE* 3.7 7.6 - - - -
91B ARG* 4.5 4.6 - - - +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 2.9 34.8 + - + +
26B ARG* 3.8 7.0 - - - +
27B ASP 3.1 0.6 - - - -
28B GLY* 1.3 71.1 - - - +
30B VAL* 1.3 59.5 + - - +
31B LEU 3.0 5.4 - - - -
32B THR* 2.7 36.0 + - + +
33B MET* 3.9 7.5 + - + +
84B ALA* 3.6 28.7 - - + -
88B ILE* 4.5 6.3 - - + -
146B LEU* 4.7 15.5 - - + -
150B MET* 5.8 0.7 - - + -
257B GLY* 4.4 3.6 - - - +
260B SER* 3.4 27.1 - - - +
261B PRO* 3.9 21.5 - - + -
264B LEU* 5.8 4.7 - - + -
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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