Contacts of the helix formed by residues 47 - 58 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.5 42.1 + - + +
38H CYS 5.7 4.3 - - - +
40H LYS 4.4 6.7 - - - +
41H THR* 4.0 8.3 - - - +
45H GLY 3.6 0.9 - - - +
46H TRP* 1.3 77.3 - - - +
48H LEU* 1.3 65.9 + - - +
49H ASP* 3.7 7.7 + - - +
50H GLN* 3.0 33.7 + - - +
51H CYS* 3.1 24.1 + - - -
80H PHE* 3.7 8.7 - - - -
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Residues in contact with LEU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H LEU* 4.9 4.7 - - + -
34H TYR* 3.7 39.3 - - + +
37H LEU* 3.9 32.5 + - + +
38H CYS* 4.1 12.5 + - - +
40H LYS 4.8 1.2 + - - -
47H THR* 1.3 74.6 - - - +
49H ASP* 1.3 64.3 + - - +
51H CYS* 3.0 18.9 + - + +
52H ILE* 3.1 20.4 + - + +
69H MET* 5.8 0.2 - - + -
80H PHE* 3.5 36.1 - - + -
83H LEU* 3.9 27.4 - - + -
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Residues in contact with ASP 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D THR* 6.0 1.9 - - - +
143D ARG* 3.3 24.6 + - - +
14H GLU* 5.2 6.4 - - - +
34H TYR* 2.7 35.8 + - - -
38H CYS* 6.1 1.3 - - - +
47H THR* 3.3 8.7 + - - +
48H LEU* 1.3 79.6 - - - +
50H GLN* 1.3 64.9 + - + +
52H ILE* 3.5 7.3 + - - +
53H GLN* 3.0 30.7 + - - +
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Residues in contact with GLN 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 3.8 14.3 + - - +
45H GLY 3.6 10.6 - - - +
46H TRP* 3.4 48.0 - - + -
47H THR* 3.0 38.5 + - - +
48H LEU 3.2 0.8 - - - -
49H ASP* 1.3 78.0 - - + +
51H CYS* 1.3 66.4 + - - +
53H GLN* 3.8 13.1 + - - +
54H THR 5.2 0.3 + - - -
70H VAL* 4.5 4.2 - - - +
200H ALA* 6.0 1.7 - - - -
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Residues in contact with CYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H TRP* 3.3 28.9 - - - +
47H THR 3.1 15.5 + - - -
48H LEU* 3.0 13.1 + - + +
50H GLN* 1.3 79.1 - - - +
52H ILE* 1.3 65.6 + - + +
53H GLN 3.6 0.3 + - - -
54H THR* 4.4 2.3 - - - +
69H MET* 3.3 7.1 - - + -
70H VAL* 3.1 39.7 + - - +
76H THR* 3.7 19.7 - - - -
80H PHE* 3.9 11.4 - - - -
84H PHE* 3.8 15.5 - - + -
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Residues in contact with ILE 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ARG* 4.5 2.9 - - - +
16H PRO* 4.4 7.0 - - + -
25H MET* 3.6 28.7 - - + -
29H LEU* 4.2 22.7 - - + -
34H TYR* 4.4 9.2 - - + -
48H LEU* 3.1 21.3 + - + +
49H ASP* 3.7 19.5 - - - +
51H CYS* 1.3 80.5 - - + +
53H GLN* 1.3 65.9 + - - +
54H THR 3.3 2.7 - - - -
55H GLY* 2.8 15.2 + - - -
56H VAL* 3.1 25.1 + - + +
68H GLY 4.0 6.1 - - - -
69H MET* 4.5 2.2 - - + -
83H LEU* 3.9 19.7 - - + -
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Residues in contact with GLN 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ARG* 4.2 9.6 + - - -
204D ARG* 3.9 24.0 + - + +
205D ASP* 3.2 29.7 + - - +
49H ASP* 3.0 18.7 + - - +
50H GLN* 4.1 10.8 - - - +
51H CYS 3.4 2.8 + - - -
52H ILE* 1.3 77.0 - - - +
54H THR* 1.3 63.6 + - - +
56H VAL* 3.0 7.1 + - - +
57H ASP* 2.8 55.7 + - - +
199H ALA 4.2 13.0 - - - +
200H ALA* 5.9 0.7 - - - -
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Residues in contact with THR 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H GLN 5.2 0.4 + - - -
51H CYS 4.4 3.3 + - - +
53H GLN* 1.3 78.8 - - - +
55H GLY* 1.3 61.2 + - - +
57H ASP 3.5 0.2 + - - -
58H ASN* 2.8 48.1 + - - +
68H GLY* 3.8 19.7 - - - +
69H MET* 3.8 11.0 - - - +
70H VAL* 4.3 16.2 - - + -
196H LEU* 2.7 31.4 + - - +
199H ALA* 4.1 9.6 + - - +
200H ALA* 4.0 16.7 - - + +
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Residues in contact with GLY 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H HIS* 3.1 22.7 - - - -
23H ASN* 3.1 11.8 + - - -
25H MET* 3.5 9.8 - - - +
52H ILE 2.8 6.6 + - - -
54H THR* 1.3 82.9 - - - +
56H VAL* 1.3 62.2 + - - +
58H ASN 3.4 4.2 - - - +
68H GLY* 3.0 30.4 + - - -
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Residues in contact with VAL 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ARG* 4.2 12.6 - - - +
205D ASP* 3.7 32.7 - - + +
206D TRP 4.8 5.7 - - - +
16H PRO* 3.9 30.1 - - + -
17H ASP 5.4 3.1 - - - +
18H LEU* 4.2 5.2 - - + -
21H HIS* 2.8 27.8 + - + +
25H MET* 4.1 10.5 - - + -
52H ILE* 3.1 19.9 + - + +
53H GLN* 3.0 11.5 + - - +
55H GLY* 1.3 78.3 - - - +
57H ASP* 1.3 62.8 + - - +
59H PRO* 4.5 1.4 - - - +
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Residues in contact with ASP 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D LYS* 3.4 26.8 + - - +
203D ALA 4.2 5.9 - - - +
204D ARG* 3.7 13.3 + - - +
205D ASP* 2.8 32.3 + - - +
206D TRP 5.0 7.5 - - - +
53H GLN* 2.8 32.6 + - - +
54H THR 4.0 3.4 - - - +
56H VAL* 1.3 78.1 - - - +
58H ASN* 1.3 64.7 + - - +
59H PRO* 3.4 9.3 - - - +
199H ALA* 3.8 19.8 - - + +
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Residues in contact with ASN 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D LYS* 4.8 4.5 + - - -
23H ASN* 3.3 17.2 + - - -
54H THR* 2.8 39.1 + - - +
55H GLY* 3.4 5.3 - - - +
56H VAL 3.3 0.4 - - - -
57H ASP* 1.3 83.6 - - - +
59H PRO* 1.3 67.7 - - - +
60H GLY* 3.0 6.3 + - - +
66H THR* 4.7 3.6 + - - +
195H PRO* 3.4 36.9 + - - +
196H LEU* 3.3 27.7 - - + +
199H ALA* 4.0 6.1 - - - +
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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
------------------------------------------------------------
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