Contacts of the helix formed by residues 37 - 47 (chain Q) in PDB entry 3K9Q
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 ASP 37 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194P GLY* 5.9 2.2 - - - -
36Q THR* 1.3 84.3 + - - +
38Q ASP* 1.3 66.1 + - - +
39Q ASP* 3.7 15.3 - - - +
40Q MET* 3.2 21.3 + - - +
41Q LEU* 3.1 25.0 + - - +
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Residues in contact with ASP 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q ASP* 1.3 73.7 - - - +
39Q ASP* 1.3 67.1 + - - +
41Q LEU* 3.2 5.6 + - - +
42Q ALA* 2.8 29.5 + - - +
60Q VAL* 3.8 21.7 - - + +
61Q VAL 4.4 2.6 - - - +
63Q GLY* 4.1 4.2 + - - -
64Q GLY* 3.4 32.3 + - - +
65Q PHE* 4.0 5.2 - - + -
74Q SER* 2.4 34.9 + - - -
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Residues in contact with ASP 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P GLY 5.1 1.9 - - - +
196P LYS* 2.7 39.9 + - - +
37Q ASP* 3.6 17.1 + - - +
38Q ASP* 1.3 79.2 - - - +
40Q MET* 1.3 62.7 + - - +
42Q ALA* 4.0 1.9 - - - +
43Q HIS* 3.2 21.7 + - - +
60Q VAL* 4.1 15.5 - - + +
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Residues in contact with MET 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P PRO* 3.8 9.0 - - + -
191P HIS 3.8 17.3 - - - +
194P GLY* 3.6 38.8 - - - +
195P ASP 3.9 10.8 - - - +
196P LYS* 4.1 13.9 - - + -
199P ALA* 3.9 14.4 - - - -
36Q THR* 3.3 28.5 - - + +
37Q ASP* 3.2 8.4 + - - +
39Q ASP* 1.3 79.8 + - - +
41Q LEU* 1.3 63.8 + - - +
43Q HIS* 3.2 6.2 + - - +
44Q LEU* 2.9 51.3 + - + +
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Residues in contact with LEU 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P PRO* 5.1 3.1 - - + -
10Q PHE* 3.7 40.4 - - + +
32Q VAL* 4.1 14.6 - - + -
34Q ASP* 4.0 12.6 - - + -
36Q THR* 3.5 24.0 - - + +
37Q ASP 3.1 15.3 + - - +
38Q ASP* 3.2 12.8 + - - +
40Q MET* 1.3 75.9 - - - +
42Q ALA* 1.3 64.1 + - - +
44Q LEU* 3.1 6.0 + - + +
45Q LEU* 3.0 23.7 + - - +
65Q PHE* 4.1 12.6 - - + -
74Q SER* 4.0 27.1 - - - +
75Q PHE 5.2 3.6 - - - +
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Residues in contact with ALA 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q ASP 2.8 19.5 + - - +
39Q ASP 4.0 1.8 - - - +
41Q LEU* 1.3 73.0 - - - +
43Q HIS* 1.3 57.5 - - - +
45Q LEU* 3.4 5.3 + - - +
46Q LYS* 3.0 38.2 + - + +
58Q VAL* 3.7 27.0 - - + +
60Q VAL* 3.8 21.8 - - + +
65Q PHE* 4.7 11.0 - - + -
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Residues in contact with HIS 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276O ASP* 4.9 1.9 - - + +
277O GLU 3.6 35.4 + - - -
196P LYS* 3.6 48.0 + - + +
200P ARG* 4.3 11.4 + - - -
39Q ASP 3.2 12.0 + - - +
40Q MET* 3.4 9.2 - - - +
42Q ALA* 1.3 80.6 - - - +
44Q LEU* 1.3 67.8 + - + +
46Q LYS* 3.2 15.5 + - - +
47Q TYR* 3.1 56.4 + + + +
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Residues in contact with LEU 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188P ASP* 4.2 14.4 - - + -
189P ALA* 3.4 46.7 - - - +
190P PRO* 3.4 12.8 - - + -
199P ALA* 4.3 12.6 - - + -
200P ARG* 4.4 12.1 - - - -
10Q PHE 5.4 0.7 - - - +
15Q ARG* 3.1 36.5 + - - +
19Q ARG* 4.9 0.3 + - - -
40Q MET* 2.9 37.4 + - + +
41Q LEU* 4.1 4.7 - - + +
43Q HIS* 1.3 76.2 - - + +
45Q LEU* 1.3 64.0 + - - +
47Q TYR 3.1 17.5 - - - +
48Q ASP* 4.8 4.3 - - - +
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Residues in contact with LEU 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q PHE* 4.1 14.1 - - + -
15Q ARG* 3.8 12.4 - - + +
18Q PHE* 3.9 26.5 - - + -
19Q ARG* 3.1 31.7 + - + +
41Q LEU 3.0 12.6 + - - +
42Q ALA 3.5 6.7 - - - +
44Q LEU* 1.3 78.6 - - - +
46Q LYS* 1.3 61.5 + - - +
54Q PHE* 3.2 24.8 - - + +
58Q VAL* 4.1 17.9 - - + -
65Q PHE* 3.9 27.4 - - + -
67Q VAL* 4.0 18.4 - - + -
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Residues in contact with LYS 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276O ASP* 3.6 31.7 + - - -
42Q ALA* 3.0 25.9 + - + +
43Q HIS* 3.2 14.2 + - - +
45Q LEU* 1.3 76.3 - - - +
47Q TYR* 1.3 81.5 + - + +
53Q ARG* 3.4 6.1 - - - +
54Q PHE* 2.8 34.3 + - + +
58Q VAL* 3.9 39.2 + - + +
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Residues in contact with TYR 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274O THR* 4.9 1.2 + - - -
276O ASP* 2.5 35.8 + - + +
278O ILE* 3.8 16.8 - - + +
282O ASP* 3.3 29.2 - - - +
188P ASP* 3.9 6.8 - - - +
200P ARG* 3.6 16.7 + - - +
43Q HIS* 3.1 39.6 + + + +
44Q LEU* 3.1 20.3 - - - +
46Q LYS* 1.3 106.2 - - + +
48Q ASP* 1.3 61.6 + - - +
53Q ARG* 3.6 37.2 + - + +
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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