Contacts of the helix formed by residues 23 - 34 (chain B) in PDB entry 1QBK
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 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLU 5.1 2.6 - - - +
22B SER* 1.3 89.0 + - - +
24B SER* 1.3 58.4 + - - +
25B PRO* 3.1 12.7 - - + -
26B ASP* 3.1 13.8 + - - +
27B THR* 2.6 37.5 + - - -
46C GLU* 4.5 0.4 - - - -
47C VAL* 3.3 40.3 + - - +
49C PRO* 5.0 7.7 - - - +
62C ASN* 5.0 7.2 + - - -
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Residues in contact with SER 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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23B GLN* 1.3 75.9 + - - +
25B PRO* 1.3 73.7 - - - +
27B THR* 3.0 14.4 - - - -
28B THR* 3.5 10.6 + - - -
46C GLU* 2.8 38.0 + - - +
47C VAL 4.3 2.6 + - - -
48C HIS* 5.7 1.0 + - - -
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Residues in contact with PRO 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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23B GLN* 3.5 13.2 - - + -
24B SER* 1.3 96.6 - - - +
26B ASP* 1.3 70.3 + - - +
27B THR 2.8 1.9 + - - -
28B THR* 3.5 1.5 + - - +
29B ILE* 3.0 44.9 + - + +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.1 36.1 - - + +
21B GLU 3.7 10.3 - - - +
22B SER* 4.0 4.7 - - - +
23B GLN* 3.5 26.9 - - - +
25B PRO* 1.3 81.7 - - - +
27B THR* 1.3 66.2 - - - +
29B ILE* 4.5 2.0 - - - -
30B GLN* 2.6 40.4 + - - +
31B ARG* 2.8 3.6 + - - -
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Residues in contact with THR 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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22B SER* 3.7 6.3 + - - -
23B GLN* 2.6 30.4 + - - -
24B SER 3.0 11.4 - - - +
25B PRO 2.8 0.6 + - - -
26B ASP* 1.3 80.0 - - - +
28B THR* 1.3 69.4 + - + +
29B ILE 2.6 10.5 + - - -
31B ARG* 2.7 38.4 + - - +
44C GLY* 3.0 37.0 - - - +
45C VAL 4.0 9.2 + - - +
46C GLU* 3.3 18.0 + - - +
47C VAL* 4.5 1.7 + - - +
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Residues in contact with THR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER 3.5 11.2 + - - +
25B PRO* 3.9 2.6 + - - +
27B THR* 1.3 88.5 - - + +
29B ILE* 1.3 60.9 + - - +
31B ARG* 4.1 11.6 - - - +
32B THR* 4.2 8.1 + - - -
43C LEU* 6.1 5.2 - - + -
44C GLY* 5.2 8.5 - - - +
46C GLU* 5.9 0.4 - - - +
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Residues in contact with ILE 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 PRO* 3.0 40.6 - - + +
26B ASP* 4.4 1.6 - - - -
27B THR 2.6 7.5 + - - -
28B THR* 1.3 80.0 - - - +
30B GLN* 1.3 64.4 + - - +
31B ARG 3.0 2.0 + - - -
32B THR* 3.2 21.5 + - - -
33B VAL* 4.1 5.6 + - + +
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Residues in contact with GLN 30 (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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15B ILE* 3.1 38.5 - - + +
18B LEU* 3.1 44.5 + - + +
19B LEU* 3.1 26.4 - - - +
22B SER* 4.3 1.6 + - - -
26B ASP* 2.6 32.4 + - + +
29B ILE* 1.3 71.9 - - - +
31B ARG* 1.3 71.8 + - - +
32B THR 2.9 11.4 + - - -
33B VAL* 3.2 9.6 + - + +
34B GLN* 3.1 25.3 + - - +
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Residues in contact with ARG 31 (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 LEU* 5.5 4.4 - - - +
22B SER* 3.0 25.7 + - - -
26B ASP 2.8 15.4 + - - -
27B THR* 2.7 60.2 + - - +
28B THR* 4.1 11.7 - - - +
29B ILE 3.0 0.8 - - - -
30B GLN* 1.3 95.8 - - - +
32B THR* 1.3 56.7 + - - +
34B GLN* 3.1 29.6 - - - +
35B GLN* 3.1 35.3 - - - +
44C GLY* 4.2 13.2 - - - -
45C VAL 4.2 8.9 + - - -
72C PHE* 3.0 30.6 - - - -
75C LEU* 5.6 1.1 - - - -
79C TYR* 5.0 6.1 - - - -
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Residues in contact with THR 32 (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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28B THR 4.2 8.3 + - - -
29B ILE* 3.4 13.5 + - - -
30B GLN 2.9 0.8 - - - -
31B ARG* 1.3 78.2 - - - +
33B VAL* 1.3 67.5 + - + +
34B GLN 3.2 1.3 - - - -
35B GLN* 3.0 13.1 + - - -
36B LYS* 3.1 30.3 + - + +
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Residues in contact with VAL 33 (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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15B ILE* 3.4 24.0 - - + -
29B ILE* 4.7 7.9 - - + +
30B GLN* 3.2 10.6 + - - +
32B THR* 1.3 77.9 - - - +
34B GLN* 1.3 54.8 + - - +
36B LYS* 3.3 37.3 - - - +
37B LEU* 2.8 43.3 - - + +
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Residues in contact with GLN 34 (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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15B ILE* 3.9 14.8 - - + -
19B LEU* 4.8 1.9 - - - +
30B GLN* 3.1 23.9 + - + +
31B ARG* 3.1 55.7 + - - +
33B VAL* 1.3 78.8 - - - +
35B GLN* 1.3 67.6 + - + +
36B LYS 3.5 0.4 - - - -
37B LEU* 4.3 6.8 + - - +
38B GLU* 2.5 28.0 - - - +
70B LEU* 5.3 17.2 - - + +
73B LYS* 3.7 7.3 + - - +
72C PHE* 3.2 23.2 - - - -
75C LEU* 4.4 9.7 - - - +
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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