Contacts of the helix formed by residues 47 - 58 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 4.0 25.7 + - + -
38G CYS 5.7 4.3 - - - +
40G LYS 4.4 7.6 - - - +
41G THR* 4.0 10.3 - - - +
45G GLY 3.6 11.0 - - - +
46G TRP* 1.3 79.4 - - - +
48G LEU* 1.3 65.3 + - - +
49G ASP* 3.7 7.8 + - - +
50G GLN* 3.0 33.7 + - - +
51G CYS* 3.1 24.1 + - - -
80G PHE* 3.7 9.4 - - - -
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Residues in contact with LEU 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G LEU* 4.8 4.3 - - + -
34G TYR* 3.7 39.3 - - + +
37G LEU* 3.8 33.4 + - + +
38G CYS* 4.1 13.4 + - + +
40G LYS 4.8 1.0 + - - -
47G THR* 1.3 71.5 - - - +
49G ASP* 1.3 68.7 + - - +
51G CYS* 3.0 19.6 + - + +
52G ILE* 3.1 19.7 + - + +
69G MET* 5.8 0.2 - - + -
80G PHE* 3.5 35.0 - - + -
83G LEU* 3.9 28.0 - - + -
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Residues in contact with ASP 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C THR* 6.0 2.1 - - - +
143C ARG* 3.3 23.9 + - - +
14G GLU* 5.2 5.9 - - - +
34G TYR* 2.7 35.8 + - - -
38G CYS* 6.0 1.3 - - - +
47G THR* 3.3 8.3 + - - +
48G LEU* 1.3 78.7 - - - +
50G GLN* 1.3 64.0 + - + +
52G ILE* 3.6 6.9 - - - +
53G GLN* 3.0 31.2 + - - +
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Residues in contact with GLN 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.1 37.2 + - - +
45G GLY 3.6 2.6 - - - +
46G TRP* 3.5 48.2 - - + -
47G THR* 3.0 35.4 + - - +
48G LEU 3.1 0.6 - - - -
49G ASP* 1.3 78.6 - - + +
51G CYS* 1.3 64.1 + - - +
53G GLN* 3.7 13.4 + - - +
54G THR 5.1 0.5 + - - -
70G VAL* 4.5 3.5 - - - +
200G ALA* 5.9 1.9 - - - -
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Residues in contact with CYS 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G TRP* 3.3 28.0 - - - +
47G THR 3.1 14.8 + - - -
48G LEU* 3.0 14.0 + - + +
50G GLN* 1.3 79.8 - - - +
52G ILE* 1.3 65.7 + - + +
53G GLN 3.7 0.3 + - - -
54G THR* 4.4 2.4 - - - +
69G MET* 3.2 6.6 - - + -
70G VAL* 3.1 40.1 + - - +
76G THR* 3.7 19.5 - - - -
80G PHE* 4.0 11.0 - - - -
84G PHE* 3.8 15.0 - - + -
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Residues in contact with ILE 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ARG* 4.5 2.5 - - - +
16G PRO* 4.4 7.2 - - + -
25G MET* 3.6 28.7 - - + -
29G LEU* 4.2 22.9 - - + -
34G TYR* 4.4 8.5 - - + -
48G LEU* 3.6 20.6 - - + +
49G ASP* 3.6 19.7 - - - +
51G CYS* 1.3 79.8 - - + +
53G GLN* 1.3 67.3 + - - +
54G THR 3.2 2.9 - - - -
55G GLY* 2.8 14.9 + - - -
56G VAL* 3.1 24.9 + - + +
68G GLY 4.0 6.3 - - - -
69G MET* 4.2 2.0 - - + -
83G LEU* 3.9 20.4 - - + -
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Residues in contact with GLN 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ARG* 4.1 9.8 + - - -
204C ARG* 4.0 21.6 + - + +
205C ASP* 3.1 29.0 + - - +
49G ASP* 3.0 20.4 + - - +
50G GLN* 4.1 10.5 - - - +
51G CYS 3.5 2.2 - - - -
52G ILE* 1.3 75.7 - - - +
54G THR* 1.3 64.4 + - - +
56G VAL* 3.1 6.6 + - - +
57G ASP* 2.8 57.0 + - - +
199G ALA 4.2 13.5 - - - +
200G ALA* 6.0 0.7 - - - -
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Residues in contact with THR 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G GLN 5.1 0.4 + - - -
51G CYS 4.4 3.5 + - - +
53G GLN* 1.3 77.6 - - - +
55G GLY* 1.3 60.1 + - - +
58G ASN* 2.9 45.2 + - - +
68G GLY* 3.8 20.2 - - - +
69G MET* 3.8 11.4 - - - +
70G VAL* 4.3 16.8 - - + -
196G LEU* 2.7 30.8 + - - +
199G ALA* 4.0 12.4 + - - +
200G ALA* 4.0 16.1 - - + +
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Residues in contact with GLY 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G HIS* 3.1 21.8 - - - -
23G ASN* 3.1 12.6 + - - -
25G MET* 3.5 10.2 - - - +
52G ILE 2.8 6.7 + - - -
54G THR* 1.3 77.0 - - - +
56G VAL* 1.3 59.2 + - - -
58G ASN 3.4 4.9 - - - +
68G GLY* 2.9 37.5 + - - -
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Residues in contact with VAL 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ARG* 4.1 12.3 - - - +
205C ASP* 3.7 31.6 - - + +
206C TRP 4.9 5.5 - - - +
16G PRO* 3.9 31.2 - - + -
17G ASP 5.4 3.1 - - - +
18G LEU* 4.2 5.6 - - + -
21G HIS* 2.8 26.9 + - + +
25G MET* 4.1 10.8 - - + -
52G ILE* 3.5 21.1 - - + +
53G GLN* 3.1 10.4 + - - +
55G GLY* 1.3 76.5 - - - +
57G ASP* 1.3 62.0 + - - +
59G PRO* 4.6 1.0 - - - +
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Residues in contact with ASP 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C LYS* 3.6 25.6 + - - +
203C ALA 4.3 5.3 - - - +
204C ARG* 3.8 13.8 - - - +
205C ASP* 2.8 21.0 + - - +
206C TRP* 5.0 7.8 - - - +
53G GLN* 2.8 46.9 + - - +
54G THR 4.0 3.4 - - - +
56G VAL* 1.3 77.1 - - - +
58G ASN* 1.3 66.2 + - - +
59G PRO* 3.4 9.7 - - - +
199G ALA* 3.8 19.2 - - + +
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Residues in contact with ASN 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C LYS* 4.9 4.3 + - - -
23G ASN* 3.3 16.8 + - - -
54G THR* 2.9 38.9 + - - +
55G GLY* 3.4 5.0 - - - +
56G VAL 3.3 0.2 - - - -
57G ASP* 1.3 82.2 - - - +
59G PRO* 1.3 67.2 - - - +
60G GLY* 3.2 4.9 + - - +
66G THR* 4.6 4.4 + - - +
195G PRO* 3.4 36.4 + - - +
196G LEU* 3.3 28.1 - - + +
199G ALA* 4.0 5.9 - - - +
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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