Contacts of the helix formed by residues 32 - 46 (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 THR 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C GLY 4.5 0.9 - - - +
29C LEU* 2.4 38.7 + - + +
31C LEU* 1.3 81.5 - - - +
33C MET* 1.3 67.6 + - - +
34C PRO 3.4 0.2 - - - -
35C PHE* 2.9 21.3 + - - +
36C LEU* 3.3 22.9 + - - +
80C MET* 4.0 17.5 - - + +
83C ILE* 3.8 25.6 - - + -
84C ALA* 3.9 24.9 - - + +
264C LEU* 5.3 4.5 - - - +
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Residues in contact with MET 33 (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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26C ARG 5.5 0.4 - - - +
29C LEU* 3.9 11.9 - - + +
30C VAL* 3.4 29.6 + - + +
32C THR* 1.3 81.8 + - - +
34C PRO* 1.3 74.2 - - + +
35C PHE 3.0 1.6 + - - -
36C LEU* 3.1 9.4 + - - +
37C ILE* 3.1 31.7 + - + +
260C SER* 6.0 2.7 - - - +
382C TRP* 5.6 2.5 - - - -
183D SER* 5.1 2.7 - - - +
184D PHE* 6.1 2.0 - - + -
1I NAG 3.2 59.2 - - - +
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Residues in contact with PRO 34 (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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30C VAL 3.4 11.0 - - - +
31C LEU 4.1 5.8 - - - +
32C THR 3.6 2.9 - - - -
33C MET* 1.3 96.1 - - + +
35C PHE* 1.3 57.3 + - - +
37C ILE* 3.6 15.2 - - + +
38C ILE* 3.0 35.0 + - + +
600C ZDM 3.9 32.8 - - + -
183D SER* 4.0 26.9 - - - +
187D LEU* 3.6 18.7 - - + +
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.3 26.7 - - + -
32C THR 2.9 7.6 + - - +
34C PRO* 1.3 76.3 - - - +
36C LEU* 1.3 58.8 + - + +
37C ILE 3.1 1.1 - - - -
38C ILE* 2.9 13.1 + - + +
39C GLY 2.7 32.7 + - - -
76C THR* 3.6 21.7 - - + +
83C ILE* 3.5 29.4 - - + -
600C ZDM 3.8 25.4 - - + -
105D ALA* 4.0 16.4 - - + -
106D LEU* 3.7 42.2 - - + -
109D VAL* 3.8 23.3 - - + -
194D VAL* 5.2 1.8 - - + -
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Residues in contact with LEU 36 (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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32C THR* 3.3 19.5 + - - +
33C MET* 3.1 8.4 + - - +
35C PHE* 1.3 76.9 - - + +
37C ILE* 1.3 57.2 + - + +
40C SER* 2.8 36.6 + - - -
76C THR* 4.2 4.3 - - - -
77C PHE* 3.8 31.8 - - + +
80C MET* 3.6 33.4 - - + -
83C ILE* 6.5 0.7 - - + -
264C LEU* 3.7 29.6 - - + -
267C MET* 4.3 13.5 - - + -
379C ALA* 4.2 15.7 - - + -
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Residues in contact with ILE 37 (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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33C MET* 3.1 25.2 + - + +
34C PRO* 3.6 18.2 - - + +
35C PHE 3.1 0.4 - - - -
36C LEU* 1.3 77.9 - - + +
38C ILE* 1.3 63.8 + - - +
40C SER* 3.4 2.4 + - - -
41C ILE* 3.3 25.3 + - + +
379C ALA* 3.9 15.2 - - + +
380C VAL* 5.5 0.4 - - - -
381C THR* 3.2 39.5 - - + +
183D SER* 6.3 0.4 - - - -
184D PHE* 5.0 6.7 - - + -
187D LEU* 3.6 31.6 - - + -
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Residues in contact with ILE 38 (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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34C PRO* 3.0 21.7 + - + +
35C PHE* 2.9 18.7 + - + +
37C ILE* 1.3 72.3 - - - +
39C GLY* 1.3 71.0 + - - +
41C ILE* 2.9 21.8 + - - +
42C PHE* 3.6 10.2 - - + -
72C PRO* 5.7 1.1 - - + -
76C THR* 5.0 4.7 - - + -
600C ZDM 6.2 0.9 - - + -
187D LEU* 4.1 12.1 - - + +
190D GLY* 3.3 38.6 - - - +
191D PHE* 3.3 25.4 - - + +
194D VAL* 3.2 35.0 - - + -
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Residues in contact with GLY 39 (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 2.7 15.3 + - - -
36C LEU 4.0 0.7 - - - -
38C ILE* 1.3 74.3 - - - +
40C SER* 1.3 61.5 + - - +
42C PHE* 3.0 22.8 + - - +
43C LEU* 3.1 11.2 + - - +
72C PRO* 4.6 6.1 - - - -
73C VAL* 3.9 6.6 - - - +
76C THR* 3.4 25.8 - - - +
77C PHE* 4.2 6.1 - - - -
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU 2.8 27.1 + - - -
37C ILE 3.8 2.5 - - - -
38C ILE 3.2 0.2 - - - -
39C GLY* 1.3 68.4 - - - +
41C ILE* 1.3 64.4 + - - +
43C LEU* 3.8 9.1 - - - +
44C ILE* 3.2 29.7 + - - +
77C PHE* 2.9 16.3 - - - -
378C ALA* 3.7 5.4 - - - -
379C ALA* 2.8 41.8 + - - -
380C VAL* 5.5 2.2 - - - -
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Residues in contact with ILE 41 (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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37C ILE* 3.3 20.9 + - + +
38C ILE* 2.9 10.5 + - - +
40C SER* 1.3 77.2 - - - +
42C PHE* 1.3 58.6 + - + +
44C ILE* 3.2 10.6 + - + +
45C ILE* 2.8 54.0 + - + +
191D PHE* 3.3 41.5 - - + -
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Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 3.6 26.0 - - + -
39C GLY 3.0 5.4 + - - +
41C ILE* 1.3 77.8 - - + +
43C LEU* 1.3 63.7 + - - +
44C ILE 2.8 1.9 + - - -
45C ILE* 3.0 15.9 + - + +
46C SER* 2.9 26.9 + - - -
69C LEU* 3.7 34.4 - - + +
72C PRO* 3.3 38.1 - - + -
73C VAL* 4.3 0.4 - - + -
191D PHE* 4.3 16.4 - + - -
194D VAL* 4.4 4.3 - - + -
195D THR* 3.6 27.4 - - - -
198D TRP* 3.8 29.4 - + - -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLY 3.1 11.9 + - - +
40C SER* 3.8 10.8 - - - +
41C ILE 3.3 0.2 - - - -
42C PHE* 1.3 75.8 - - - +
44C ILE* 1.3 59.8 - - + +
46C SER* 3.9 4.3 - - - +
47C THR* 3.0 34.7 + - + +
69C LEU 4.8 0.2 - - - -
73C VAL* 3.9 29.3 - - + +
77C PHE* 5.1 2.7 - - + -
271C ARG* 4.6 13.9 - - + +
274C PHE* 4.6 15.3 - - + -
275C GLN* 4.5 20.0 - - + -
378C ALA* 3.5 37.7 - - + +
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Residues in contact with ILE 44 (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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40C SER 3.2 15.1 + - - +
41C ILE* 3.5 11.4 - - + +
42C PHE 3.0 1.0 - - - -
43C LEU* 1.3 81.9 - - + +
45C ILE* 1.3 60.5 + - + +
46C SER 2.8 5.5 + - - -
47C THR* 3.5 12.0 + - - +
48C LEU* 3.2 33.5 + - + +
376C SER* 5.2 2.9 - - - +
378C ALA* 3.5 31.0 - - + -
380C VAL* 4.4 19.7 - - + -
392C LEU* 4.4 35.2 - - + +
395C GLY* 6.2 1.6 - - - -
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Residues in contact with ILE 45 (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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41C ILE* 2.8 43.2 + - + +
42C PHE* 3.8 15.3 - - + +
44C ILE* 1.3 76.4 - - + +
46C SER* 1.3 56.7 + - - +
47C THR 3.5 0.2 - - - -
48C LEU* 5.3 1.3 - - - -
53C TYR* 2.3 47.3 + - - +
57C MET* 5.1 7.4 - - + -
65C TRP* 4.1 0.3 - - - -
69C LEU* 3.7 17.5 - - + +
191D PHE* 5.8 2.2 - - + -
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Residues in contact with SER 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE 2.9 16.1 + - - -
43C LEU* 4.1 6.0 - - - +
44C ILE 2.8 1.0 - - - -
45C ILE* 1.3 80.3 - - - +
47C THR* 1.3 65.3 + - - +
48C LEU 3.9 0.9 - - - -
53C TYR* 5.1 0.4 - - - -
65C TRP* 4.4 5.7 - - - -
66C ASN* 3.0 36.0 + - - +
69C LEU* 3.3 32.3 + - - +
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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
------------------------------------------------------------
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