Contacts of the helix formed by residues 38 - 48 (chain G) in PDB entry 3MQ6
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 ALA 38 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ARG 3.6 17.5 - - - +
19B CYS 2.7 19.6 + - - +
21B GLN* 3.9 16.6 - - + -
36G GLN* 3.3 2.7 + - - -
37G LEU* 1.3 69.3 - - - +
39G GLN* 1.3 64.2 + - - +
40G GLN 3.3 2.5 - - - -
41G ASN* 3.1 16.0 + - + +
42G MET* 2.9 25.3 + - - +
13R G 4.2 0.7 - - - -
14R G 3.6 11.4 - - - +
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Residues in contact with GLN 39 (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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37G LEU 2.9 5.7 + - - -
38G ALA* 1.3 71.6 - - - +
40G GLN* 1.3 66.5 + - + +
42G MET* 3.2 12.9 + - - +
43G LEU* 3.0 38.3 + - + +
96G LYS* 2.9 24.0 + - - +
97G VAL* 3.8 31.9 - - + +
100G ASP* 2.9 37.5 + - - +
101G ILE* 4.5 4.1 - - + +
104G ILE* 4.2 11.7 - - - +
152G ARG* 5.1 0.6 - - - +
13R G 3.8 4.2 - - - +
14R G 3.0 28.1 + - - +
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Residues in contact with GLN 40 (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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39G GLN* 1.3 82.4 - - + +
41G ASN* 1.3 65.2 + - - +
43G LEU* 3.3 3.6 + - + -
44G ALA* 3.1 9.9 + - - +
104G ILE* 6.3 1.6 - - + -
213G ARG* 2.9 43.0 + - - +
216G GLN* 3.0 38.8 + - - +
14R G 3.0 37.2 + - - +
15R A 3.2 27.9 + - - -
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Residues in contact with ASN 41 (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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16B THR 3.0 25.2 + - - +
17B GLU* 3.2 24.7 - - - +
18B ARG 2.8 26.8 + - - +
19B CYS* 4.3 2.7 - - - -
21B GLN* 4.0 2.8 - - - +
38G ALA* 3.1 19.7 + - - +
40G GLN* 1.3 79.0 - - - +
42G MET* 1.3 53.3 + - - +
44G ALA* 3.3 6.2 + - - +
45G TYR* 2.8 36.2 + - - +
213G ARG* 6.1 0.7 - - - -
14R G 4.8 0.4 + - - -
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Residues in contact with MET 42 (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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19B CYS* 3.7 29.2 - - + +
37G LEU* 3.8 16.4 - - + -
38G ALA 2.9 34.4 + - - +
39G GLN* 3.3 10.8 - - - +
40G GLN 3.2 0.2 - - - -
41G ASN* 1.3 74.3 - - - +
43G LEU* 1.3 59.6 + - - +
46G THR* 2.9 36.2 + - - -
71G PRO* 3.6 38.4 - - + +
72G VAL* 3.8 13.2 - - + -
75G ALA* 3.9 11.4 - - + -
97G VAL* 3.6 23.3 - - + -
101G ILE* 5.1 1.3 - - + -
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Residues in contact with LEU 43 (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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39G GLN* 3.0 22.7 + - + +
40G GLN* 3.6 2.2 - - + +
41G ASN 3.3 0.2 - - - -
42G MET* 1.3 76.2 - - - +
44G ALA* 1.3 57.3 + - - +
47G PHE* 2.7 44.9 + - + +
48G GLY 3.3 0.9 + - - -
71G PRO* 5.6 0.2 - - - -
101G ILE* 3.4 26.9 - - + -
104G ILE* 3.7 37.7 - - + -
105G VAL* 3.9 16.2 - - + -
211G LEU* 3.6 25.5 - - + +
216G GLN* 3.4 27.1 - - - +
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Residues in contact with ALA 44 (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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40G GLN 3.1 15.6 + - - +
41G ASN* 3.8 6.1 - - - +
43G LEU* 1.3 76.7 - - - +
45G TYR* 1.3 59.3 + - - +
48G GLY* 2.9 26.3 + - - +
211G LEU 3.2 17.9 + - - +
212G THR* 4.3 10.1 - - - -
213G ARG* 4.3 7.6 - - + +
216G GLN* 4.1 3.4 - - - +
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Residues in contact with TYR 45 (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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2B PRO* 2.7 54.2 - - + +
5B TYR* 3.6 9.3 - + - -
6B SER 3.0 28.1 + - - -
9B ALA* 4.0 12.3 - - + -
10B THR* 3.0 29.8 + - - -
13B LEU* 4.1 26.7 - - + -
17B GLU 5.8 0.2 - - - +
19B CYS* 3.9 17.9 - - - -
41G ASN 2.8 22.5 + - - +
42G MET 3.8 2.5 - - - +
44G ALA* 1.3 75.6 - - - +
46G THR* 1.3 68.3 + - - +
48G GLY* 4.3 1.4 + - - -
74G ASN* 3.8 28.7 - - + -
78G GLU* 5.7 0.9 - - - -
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Residues in contact with THR 46 (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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2B PRO* 3.6 6.6 - - - +
3B PHE* 3.2 36.6 + - + +
42G MET* 2.9 21.2 + - - -
45G TYR* 1.3 76.0 - - - +
47G PHE* 1.3 76.2 + - + +
48G GLY 3.6 0.4 + - - -
49G GLU 5.2 0.3 + - - -
50G VAL* 4.6 2.3 - - - +
70G ARG* 3.8 28.3 - - + -
71G PRO* 3.5 22.9 + - + +
74G ASN* 3.1 20.5 + - - +
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Residues in contact with PHE 47 (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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3B PHE* 3.7 22.9 - + - -
43G LEU* 2.7 29.0 + - + +
46G THR* 1.3 83.3 - - + +
48G GLY* 1.3 65.2 + - - +
49G GLU 3.0 5.0 + - - -
50G VAL* 3.1 37.7 + - + +
52G PRO* 3.9 19.5 - - + -
67G VAL* 3.4 29.4 - - + -
68G ILE* 5.1 0.4 - - - -
71G PRO* 3.4 26.2 - - + -
101G ILE* 4.6 0.9 - - + -
105G VAL* 3.8 29.6 - - + -
210G GLY* 3.3 0.2 - - - -
211G LEU* 2.9 30.4 + - + -
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Residues in contact with GLY 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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2B PRO* 6.1 0.4 - - - +
43G LEU 3.3 0.8 + - - -
44G ALA* 2.9 26.4 + - - -
45G TYR 4.3 1.2 + - - -
46G THR 3.6 1.4 - - - -
47G PHE* 1.3 77.3 - - - +
49G GLU* 1.3 65.5 + - - +
209G ALA* 4.3 0.7 - - - +
210G GLY* 3.3 14.7 + - - -
211G LEU 4.1 11.2 - - - -
212G THR* 3.5 21.1 - - - +
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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
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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