Contacts of the helix formed by residues 47 - 58 (chain B) in PDB entry 1QK1
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 THR 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B CYS 5.7 4.3 - - - +
40B LYS 4.4 7.4 - - - +
41B THR* 4.0 9.9 - - - +
45B GLY 3.6 11.9 - - - +
46B TRP* 1.3 78.9 - - - +
48B LEU* 1.3 65.1 + - - +
49B ASP* 3.8 7.9 + - - +
50B GLN* 2.9 34.1 + - - +
51B CYS* 3.1 24.8 + - - -
80B PHE* 3.7 8.5 - - - -
5H ARG* 4.5 23.8 - - + +
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Residues in contact with LEU 48 (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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29B LEU* 4.9 4.3 - - + -
34B TYR* 3.6 39.9 - - + +
37B LEU* 3.9 32.1 - - + +
38B CYS* 4.1 13.6 + - - +
40B LYS 4.8 1.0 + - - -
47B THR* 1.3 71.9 - - - +
49B ASP* 1.3 69.1 + - - +
51B CYS* 3.0 19.5 + - + +
52B ILE* 3.1 19.8 + - + +
80B PHE* 3.5 35.0 - - + -
83B LEU* 3.9 28.3 - - + -
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 5.2 6.2 - - - +
34B TYR* 2.7 35.9 + - - -
38B CYS* 6.0 1.5 - - - +
47B THR* 3.3 8.1 + - - +
48B LEU* 1.3 80.0 - - - +
50B GLN* 1.3 58.3 + - + +
52B ILE* 3.5 7.4 + - - +
53B GLN* 3.0 35.0 + - - +
142F THR* 6.0 2.6 - - - +
143F ARG* 3.2 24.9 + - - +
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Residues in contact with GLN 50 (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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45B GLY 3.6 10.6 - - - +
46B TRP* 3.4 48.8 - - + -
47B THR* 2.9 40.3 + - - +
48B LEU 3.2 0.8 - - - -
49B ASP* 1.3 77.0 - - + +
51B CYS* 1.3 66.0 + - - +
53B GLN* 3.8 13.3 + - - +
54B THR 5.2 0.5 + - - -
70B VAL* 4.5 3.8 - - - +
200B ALA* 6.0 2.3 - - - -
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Residues in contact with CYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TRP* 3.3 29.2 - - - +
47B THR 3.1 14.8 + - - -
48B LEU* 3.0 13.1 + - + +
50B GLN* 1.3 79.1 - - - +
52B ILE* 1.3 64.3 + - + +
53B GLN 3.6 0.3 + - - -
54B THR* 4.4 2.3 - - - +
69B MET* 3.3 6.0 - - + -
70B VAL* 3.0 40.6 + - - +
76B THR* 3.8 18.4 - - - -
80B PHE* 3.9 11.4 - - - -
84B PHE* 3.9 15.5 - - + -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 4.4 7.0 - - + -
25B MET* 3.6 29.6 - - + -
29B LEU* 4.2 22.9 - - + -
34B TYR* 4.4 8.5 - - + -
48B LEU* 3.1 19.9 + - + +
49B ASP* 3.6 20.4 - - - +
51B CYS* 1.3 78.7 - - + +
53B GLN* 1.3 66.3 + - - +
54B THR 3.3 3.1 - - - -
55B GLY* 2.9 13.7 + - - -
56B VAL* 3.1 25.9 + - + +
68B GLY 4.0 6.7 - - - -
69B MET* 4.2 2.2 - - + -
83B LEU* 3.9 20.4 - - + -
143F ARG* 4.4 2.9 - - - +
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Residues in contact with GLN 53 (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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49B ASP* 3.0 19.0 + - - +
50B GLN* 4.1 10.3 - - - +
51B CYS 3.5 2.8 - - - -
52B ILE* 1.3 76.4 - - - +
54B THR* 1.3 62.6 + - - +
56B VAL* 3.1 5.6 + - - +
57B ASP* 2.8 56.6 + - - +
199B ALA 4.2 14.1 - - - +
200B ALA* 5.9 0.4 - - - -
143F ARG* 4.0 9.4 + - - -
204F ARG* 3.9 21.4 + - + +
205F ASP* 3.1 30.9 + - - +
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Residues in contact with THR 54 (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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50B GLN 5.2 0.4 + - - -
51B CYS 4.4 3.5 + - - +
53B GLN* 1.3 78.9 - - - +
55B GLY* 1.3 60.2 + - - +
57B ASP 3.5 0.2 + - - -
58B ASN* 2.8 45.2 + - - +
68B GLY* 3.8 20.0 - - - +
69B MET* 3.8 11.4 - - - +
70B VAL* 4.3 16.2 - - + -
196B LEU* 2.7 30.1 + - - +
199B ALA* 4.0 12.6 + - - +
200B ALA* 4.0 15.0 - - + +
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Residues in contact with GLY 55 (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* 3.1 13.5 - - - -
23B ASN* 3.1 21.1 + - - -
25B MET* 3.5 10.2 - - - +
52B ILE 2.9 6.3 + - - -
54B THR* 1.3 77.4 - - - +
56B VAL* 1.3 59.5 + - - +
58B ASN 3.4 4.6 - - - +
68B GLY* 2.9 36.9 + - - -
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Residues in contact with VAL 56 (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 PRO* 3.9 30.1 - - + -
17B ASP 5.4 3.8 - - - +
18B LEU* 4.3 6.1 - - + -
21B HIS* 2.8 27.1 + - + +
25B MET* 4.1 10.5 - - + -
52B ILE* 3.1 21.2 + - + +
53B GLN* 3.6 9.4 - - - +
55B GLY* 1.3 75.7 - - - +
57B ASP* 1.3 62.8 + - - +
59B PRO* 4.6 0.9 - - - +
143F ARG* 4.1 12.6 - - - +
205F ASP* 3.6 32.0 - - + +
206F TRP 4.7 6.6 - - - +
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Residues in contact with ASP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLN* 2.8 34.5 + - - +
54B THR 4.0 3.4 - - - +
56B VAL* 1.3 77.7 - - - +
58B ASN* 1.3 60.0 + - - +
59B PRO* 3.4 9.3 - - - +
199B ALA* 3.8 25.3 - - + +
191F LYS* 3.5 26.0 + - - +
203F ALA 4.3 5.7 - - - +
204F ARG* 3.7 14.0 + - - +
205F ASP* 2.6 32.3 + - - +
206F TRP 4.9 8.2 - - - +
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Residues in contact with ASN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN* 3.3 16.3 + - - -
54B THR* 2.8 38.6 + - - +
55B GLY* 3.4 5.1 - - - +
56B VAL 3.3 0.6 - - - -
57B ASP* 1.3 84.7 - - - +
59B PRO* 1.3 66.9 - - - +
60B GLY* 3.1 5.8 + - - +
66B THR* 4.7 4.6 + - - +
195B PRO* 3.4 35.4 + - - +
196B LEU* 3.3 30.0 - - + +
199B ALA* 4.0 5.5 - - - +
191F LYS* 4.8 4.9 + - - -
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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