Contacts of the helix formed by residues 70 - 77 (chain C) in PDB entry 3QNQ
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 GLY 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ASN 3.8 6.8 + - - -
67C VAL* 3.2 13.6 + - - -
68C ALA 2.8 1.6 - - - -
69C LEU* 1.3 81.0 - - - +
71C TYR* 1.3 67.0 + - - +
72C PRO 3.7 0.2 - - - -
73C VAL* 3.5 10.1 + - - +
74C SER* 3.3 18.5 + - - -
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Residues in contact with TYR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C VAL* 3.8 15.1 - - + +
68C ALA* 2.8 23.6 + - + +
70C GLY* 1.3 73.7 - - - +
72C PRO* 1.4 77.6 - - + +
73C VAL 3.0 1.1 - - - -
74C SER* 2.7 21.5 + - - -
75C ALA* 3.2 7.1 + - - +
800C CIT 3.6 19.7 + - - -
113D LEU* 3.7 8.2 - - + +
116D PRO 5.2 4.0 - - - -
198D TRP* 3.8 7.0 - - + -
201D ARG* 2.9 43.4 + - - +
202D LEU* 3.8 22.4 - - + -
205D GLU* 2.5 29.3 + - - -
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Residues in contact with PRO 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 5.7 2.0 - - + -
39C GLY* 4.7 3.6 - - - -
42C PHE* 3.3 53.4 - - + -
68C ALA 3.3 9.9 - - - +
69C LEU 4.4 2.2 - - - -
70C GLY 4.1 0.2 - - - -
71C TYR* 1.4 93.3 - - + +
73C VAL* 1.3 63.2 + - + +
75C ALA* 2.9 12.5 + - - +
76C THR* 3.1 20.9 + - + +
113D LEU* 3.4 14.5 - - + -
194D VAL* 5.4 3.6 - - + +
198D TRP* 3.4 20.4 - - + -
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLY* 3.9 7.9 - - - +
42C PHE* 4.3 1.6 - - + -
43C LEU* 3.9 37.5 - - + +
69C LEU 3.3 25.4 - - - +
70C GLY* 3.6 8.7 - - - +
71C TYR 2.9 0.8 + - - -
72C PRO* 1.3 74.4 - - - +
74C SER* 1.3 58.1 + - - +
76C THR* 3.8 5.6 - - - -
77C PHE* 3.1 42.9 + - + +
78C ASN* 3.5 1.9 + - - +
271C ARG* 3.8 29.4 + - - +
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLY 3.3 9.1 + - - -
71C TYR* 2.7 17.2 + - - -
73C VAL* 1.3 75.8 - - - +
75C ALA* 1.3 60.4 + - - +
78C ASN* 3.1 42.6 + - - +
79C ILE* 4.2 0.7 - - - +
117D PHE* 3.8 40.0 - - - +
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C TYR 3.2 2.6 + - - +
72C PRO* 2.9 8.5 + - + +
74C SER* 1.3 75.9 - - - +
76C THR* 1.3 56.7 + - + +
79C ILE* 2.7 26.8 - - - +
109D VAL* 3.8 26.1 - - + +
112D LEU* 4.2 4.0 - - + +
113D LEU* 3.7 48.2 - - + +
117D PHE* 4.9 6.3 - - + -
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Residues in contact with THR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 3.6 46.4 - - + +
36C LEU* 4.2 5.1 - - - +
38C ILE* 5.0 5.8 - - + -
39C GLY* 3.4 20.1 - - - +
72C PRO* 3.2 16.3 + - + +
73C VAL 3.4 3.1 + - - -
75C ALA* 1.3 85.2 - - + +
77C PHE* 1.3 78.1 + - - +
78C ASN 3.2 0.4 - - - -
79C ILE* 2.9 15.7 + - - +
80C MET* 3.1 13.2 + - - +
83C ILE* 5.1 2.2 - - - +
109D VAL* 4.5 11.7 - - + -
194D VAL* 5.7 1.6 - - + -
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Residues in contact with PHE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 3.8 28.9 - - + +
39C GLY 4.2 0.7 - - - -
40C SER* 2.9 37.5 - - - -
43C LEU* 5.1 2.7 - - + -
73C VAL* 3.1 23.5 + - + +
76C THR* 1.3 91.0 + - - +
78C ASN* 1.3 58.3 + - - +
79C ILE 2.8 6.2 + - - -
80C MET* 3.5 18.2 + - - +
142C GLY* 3.9 6.9 - - - -
143C SER 4.1 1.7 + - - -
267C MET* 3.7 27.6 - - + -
268C ASP* 3.4 12.9 - - - +
271C ARG* 3.3 39.3 - - + +
377C GLY 3.7 14.4 - - - -
378C ALA* 4.6 2.0 - - - -
379C ALA* 4.1 6.7 - - + -
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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