Contacts of the helix formed by residues 47 - 58 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ARG* 3.8 29.6 - - + +
38F CYS 5.6 4.5 - - - +
40F LYS 4.4 6.7 - - - +
41F THR* 4.0 5.4 - - - +
45F GLY 3.6 11.7 - - - +
46F TRP* 1.3 76.6 - - - +
48F LEU* 1.3 65.0 + - - +
49F ASP* 3.7 7.7 + - - +
50F GLN* 3.0 35.0 + - - +
51F CYS* 3.1 23.7 + - - -
80F PHE* 3.7 9.2 - - - -
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LEU* 4.9 3.8 - - + -
34F TYR* 3.6 41.1 - - + +
37F LEU* 3.9 31.2 + - + +
38F CYS* 4.1 14.0 + - - +
40F LYS 4.7 1.2 + - - -
47F THR* 1.3 71.5 - - - +
49F ASP* 1.3 66.9 + - - +
51F CYS* 3.0 20.4 + - + +
52F ILE* 3.1 19.4 + - + +
80F PHE* 3.5 35.1 - - + -
83F LEU* 3.9 28.5 - - + -
84F PHE* 6.1 0.2 - - + -
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Residues in contact with ASP 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 6.1 1.9 - - - +
143B ARG* 3.3 24.0 + - - +
14F GLU* 5.2 6.6 - - - +
34F TYR* 2.7 36.3 + - - -
38F CYS* 6.0 1.7 - - - +
47F THR* 3.3 8.1 + - - +
48F LEU* 1.3 78.6 - - - +
50F GLN* 1.3 61.0 + - + +
52F ILE* 3.4 7.4 + - - +
53F GLN* 3.0 35.5 + - - +
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Residues in contact with GLN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 5.5 1.6 + - - -
45F GLY 3.6 11.1 - - - +
46F TRP* 3.4 48.2 - - + -
47F THR* 3.0 39.4 + - - +
48F LEU 3.1 0.6 - - - -
49F ASP* 1.3 80.6 - - + +
51F CYS* 1.3 62.4 + - - +
53F GLN* 3.7 13.2 + - - +
54F THR 5.2 0.7 + - - -
70F VAL* 4.5 3.6 - - - +
200F ALA* 6.0 1.6 - - - -
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Residues in contact with CYS 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F TRP* 3.2 28.5 - - - +
47F THR 3.1 15.0 + - - -
48F LEU* 3.0 13.1 + - + +
50F GLN* 1.3 80.1 - - - +
52F ILE* 1.3 66.1 + - + +
53F GLN 3.7 0.2 + - - -
54F THR* 4.5 2.3 + - - +
69F MET* 3.2 6.3 - - + -
70F VAL* 3.0 40.9 + - - +
76F THR* 3.7 20.2 - - - -
80F PHE* 4.0 10.3 - - - -
84F PHE* 3.9 15.0 - - + -
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Residues in contact with ILE 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG* 4.5 2.5 - - - +
16F PRO* 4.4 7.2 - - + -
25F MET* 3.6 28.5 - - + -
29F LEU* 4.3 22.9 - - + -
34F TYR* 4.4 8.5 - - + -
48F LEU* 3.1 19.3 + - + +
49F ASP* 3.6 20.6 - - - +
51F CYS* 1.3 78.7 - - + +
53F GLN* 1.3 66.7 + - - +
54F THR 3.3 2.5 - - - -
55F GLY* 2.9 14.5 + - - -
56F VAL* 3.1 25.9 + - + +
68F GLY 4.0 5.8 - - - -
69F MET* 4.2 2.5 - - + -
83F LEU* 3.9 20.2 - - + -
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Residues in contact with GLN 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ARG* 4.0 9.6 + - - -
204B ARG* 3.9 23.5 + - + +
205B ASP* 3.1 29.3 + - - +
49F ASP* 3.0 19.9 + - - +
50F GLN* 4.1 10.8 - - - +
51F CYS 3.5 2.8 - - - -
52F ILE* 1.3 75.8 - - - +
54F THR* 1.3 65.5 + - - +
56F VAL* 3.1 6.2 + - - +
57F ASP* 2.8 56.7 + - - +
199F ALA 4.2 13.2 - - - +
200F ALA* 5.9 0.7 - - - -
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Residues in contact with THR 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLN 5.2 0.6 + - - -
51F CYS 4.5 2.6 + - - +
53F GLN* 1.3 78.4 - - - +
55F GLY* 1.3 60.5 + - - +
57F ASP 3.4 0.2 + - - -
58F ASN* 2.9 45.0 + - - +
68F GLY* 3.8 20.2 - - - +
69F MET* 3.8 11.0 - - - +
70F VAL* 4.3 16.8 - - + +
196F LEU* 2.7 31.3 + - - +
199F ALA* 4.1 12.5 + - - +
200F ALA* 4.0 14.7 - - + +
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Residues in contact with GLY 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F HIS* 3.1 22.3 - - - -
23F ASN* 3.1 12.4 + - - -
25F MET* 3.5 10.0 - - - +
52F ILE 2.9 6.3 + - - -
54F THR* 1.3 83.0 - - - +
56F VAL* 1.3 59.2 + - - +
58F ASN* 3.4 5.2 - - - +
68F GLY* 3.0 30.9 + - - -
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Residues in contact with VAL 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG* 4.0 12.1 - - - +
205B ASP* 3.6 34.0 - - + +
206B TRP 4.8 6.4 - - - +
16F PRO* 3.9 31.2 - - + -
17F ASP 5.4 3.1 - - - +
18F LEU* 4.3 5.6 - - + -
21F HIS* 2.8 27.5 + - + +
25F MET* 4.1 10.3 - - + -
52F ILE* 3.1 20.8 + - + +
53F GLN* 3.1 6.9 + - - +
55F GLY* 1.3 77.4 - - - +
57F ASP* 1.3 62.9 + - - +
59F PRO* 4.6 1.2 - - - +
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Residues in contact with ASP 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LYS* 3.6 23.9 + - - +
203B ALA 4.3 5.9 - - - +
204B ARG* 3.7 13.6 - - - +
205B ASP* 2.7 32.2 + - - +
206B TRP* 4.9 9.2 - - + +
53F GLN* 2.8 33.8 + - - +
54F THR 3.9 3.1 - - - +
56F VAL* 1.3 77.5 - - - +
58F ASN* 1.3 59.7 + - - +
59F PRO* 3.4 9.3 - - - +
199F ALA* 3.8 25.7 - - + +
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Residues in contact with ASN 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LYS* 4.8 4.5 + - - -
23F ASN* 3.3 17.2 + - - -
54F THR* 2.9 38.7 + - - +
55F GLY* 3.4 5.1 - - - +
56F VAL 3.3 0.2 - - - -
57F ASP* 1.3 83.9 - - - +
59F PRO* 1.3 66.7 - - - +
60F GLY* 3.1 6.0 + - - +
66F THR* 4.4 4.1 + - + +
195F PRO* 3.3 37.8 + - - +
196F LEU* 3.3 27.8 - - + +
199F ALA* 4.0 5.5 - - - +
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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