Contacts of the helix formed by residues 62 - 76 (chain M) in PDB entry 6MUO
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 SER 62 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1M MET* 6.0 0.9 - - - +
5M VAL* 4.2 1.1 - - - -
30M PHE* 5.3 2.2 - - - -
60M ARG* 3.4 14.7 - - - +
61M ALA* 1.3 77.2 - - - +
63M ILE* 1.3 60.0 + - - +
64M SER* 3.9 7.8 + - - -
65M ASP* 3.4 30.8 + - - +
66M ALA* 3.0 30.0 + - - +
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Residues in contact with ILE 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M ASP* 4.6 13.7 + - - +
4M THR* 4.9 8.1 - - - +
5M VAL* 3.7 28.7 - - + +
8M PHE* 4.2 28.9 - - + -
62M SER* 1.3 70.2 - - - +
64M SER* 1.3 72.4 + - - +
66M ALA* 3.9 2.0 - - + -
67M ALA* 3.1 22.7 + - - +
146M GLN* 4.5 24.9 + - + +
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Residues in contact with SER 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M SER* 3.2 8.0 - - - -
63M ILE* 1.3 87.5 - - - +
65M ASP* 1.3 68.9 + - - +
67M ALA* 3.4 15.4 + - - +
68M LEU* 3.6 6.2 + - - +
118M ASN* 5.5 0.9 + - - -
121M VAL* 4.1 30.4 - - - +
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Residues in contact with ASP 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M TRP* 3.6 16.8 + - - -
30M PHE* 4.2 27.1 - - + -
60M ARG* 5.2 4.9 - - - +
62M SER* 3.4 18.9 + - - +
64M SER* 1.3 80.7 - - - +
66M ALA* 1.3 62.2 + - - +
67M ALA 3.3 0.2 - - - -
68M LEU* 3.3 29.9 + - + +
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Residues in contact with ALA 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M VAL* 5.3 2.0 - - + -
8M PHE* 3.4 22.2 - - + -
9M ILE* 3.8 34.7 - - + +
28M TRP* 4.4 9.6 - - - -
30M PHE* 6.2 0.2 - - - -
61M ALA* 6.2 0.2 - - - -
62M SER 3.0 20.1 + - - +
63M ILE* 4.2 7.0 - - + +
65M ASP* 1.3 73.9 - - - +
67M ALA* 1.3 64.9 + - - +
68M LEU 3.2 0.7 - - - -
69M LEU* 3.3 19.1 + - - +
70M ASP 4.0 1.2 + - - -
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Residues in contact with ALA 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M PHE* 4.1 11.4 - - - -
63M ILE 3.1 18.9 + - - +
64M SER* 3.4 8.7 - - - +
65M ASP 3.3 0.2 - - - -
66M ALA* 1.3 77.6 - - - +
68M LEU* 1.3 61.4 + - - +
70M ASP* 3.2 15.2 + - - +
71M ILE* 3.4 16.8 + - + +
121M VAL 5.2 8.5 - - - +
134M ARG* 3.8 23.8 - - + +
146M GLN* 4.7 6.7 - - - +
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Residues in contact with LEU 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M TRP* 3.6 28.0 - - + +
64M SER 3.6 5.3 + - - +
65M ASP* 3.3 24.6 + - + +
66M ALA 3.2 1.0 - - - -
67M ALA* 1.3 76.7 - - - +
69M LEU* 1.3 63.9 + - - +
70M ASP 3.3 0.2 - - - -
71M ILE* 3.2 23.4 + - + +
72M ILE* 3.4 26.3 + - + +
122M SER* 6.1 0.2 - - - -
123M PHE* 3.7 31.0 - - + +
124M ARG* 4.5 15.0 - - + -
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Residues in contact with LEU 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M ILE* 5.0 9.6 - - + -
12M THR* 4.1 22.4 - - + +
13M ILE* 4.3 22.7 - - + -
16M ILE* 5.2 6.7 - - + -
24M ILE* 3.9 23.5 - - + +
25M LEU* 4.8 5.2 - - + -
28M TRP* 3.4 60.5 - - + +
66M ALA 3.3 13.6 + - - +
67M ALA 3.2 0.6 - - - -
68M LEU* 1.3 79.9 - - - +
70M ASP* 1.3 59.2 + - - +
72M ILE* 3.8 2.2 + - + +
73M TYR* 3.3 20.3 + - - +
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Residues in contact with ASP 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M PHE* 4.5 16.8 - - + -
12M THR* 4.4 14.5 - - + +
15M LYS* 4.3 12.1 + - - +
66M ALA 4.0 1.0 + - - -
67M ALA 3.2 12.2 + - - +
69M LEU* 1.3 77.0 - - - +
71M ILE* 1.3 59.3 + - - +
73M TYR* 3.4 20.8 - - - +
74M MET* 3.1 25.5 + - - +
134M ARG* 3.5 19.9 + - - +
149M PRO* 4.4 2.7 - - - +
151M TYR* 2.1 32.6 + - - -
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Residues in contact with ILE 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M ALA* 3.4 18.4 - - + +
68M LEU* 3.2 23.7 + - + +
70M ASP* 1.3 75.6 - - - +
72M ILE* 1.3 66.1 + - + +
74M MET* 3.2 12.8 + - - +
75M GLN* 3.3 18.4 + - - +
121M VAL 5.3 0.2 - - - +
122M SER* 3.5 34.5 - - - +
124M ARG* 5.0 10.1 - - + -
132M TRP* 3.8 37.8 - - + +
134M ARG* 3.7 21.5 - - + +
151M TYR* 4.6 9.6 - - + -
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Residues in contact with ILE 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M ILE* 4.4 23.8 - - + -
27M ALA* 4.0 17.5 - - + +
28M TRP* 3.8 30.3 - - + -
68M LEU* 3.4 32.6 + - + +
69M LEU* 4.2 3.8 - - - +
71M ILE* 1.3 75.7 - - + +
73M TYR* 1.3 61.9 + - - +
75M GLN* 3.2 24.5 + - - +
76M PHE* 3.5 23.6 + - + -
124M ARG* 4.1 28.3 - - + +
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Residues in contact with TYR 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M THR* 5.3 6.1 - - + -
15M LYS* 3.3 57.6 + - + +
16M ILE* 3.6 35.4 - - + -
20M GLU* 5.6 0.4 - - - -
24M ILE* 5.0 11.6 - - + +
69M LEU 3.3 14.8 + - - +
70M ASP* 3.4 24.9 - - - +
71M ILE 3.2 0.6 - - - -
72M ILE* 1.3 79.7 - - - +
74M MET* 1.3 70.9 + - + +
76M PHE* 3.5 2.0 + - - -
77M HIS* 3.4 60.7 + + + +
80M GLN* 4.8 10.2 + - - -
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Residues in contact with MET 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M LYS* 5.7 4.3 - - - +
70M ASP* 3.1 13.4 + - - +
71M ILE 3.2 9.5 + - - +
73M TYR* 1.3 88.4 - - + +
75M GLN* 1.3 65.1 + - - +
76M PHE 3.3 0.5 + - - -
77M HIS* 3.4 20.1 + - + +
78M GLN* 3.3 16.1 + - - +
80M GLN* 6.1 1.6 - - + +
81M LYS* 3.7 37.0 - - + -
83M TRP* 4.6 9.4 - - + -
132M TRP* 4.5 10.5 - - + -
151M TYR* 3.6 51.1 - - + +
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Residues in contact with GLN 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M ILE* 3.3 15.8 + - - +
72M ILE* 3.2 17.4 + - + +
74M MET* 1.3 77.1 - - - +
76M PHE* 1.3 76.7 + - + +
77M HIS 3.5 0.2 - - - -
78M GLN* 3.1 31.2 + - - +
124M ARG* 3.3 38.2 + - - +
126M THR* 3.7 6.5 + - - +
132M TRP* 3.2 53.7 - - + +
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Residues in contact with PHE 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M GLU* 4.1 23.7 - - - +
23M THR* 4.5 18.4 - - + -
24M ILE* 3.6 29.6 - - + -
27M ALA* 5.8 4.5 - - + -
72M ILE* 3.5 17.2 + - + +
73M TYR* 3.5 5.3 + - - +
74M MET 3.2 0.6 - - - -
75M GLN* 1.3 94.5 - - + +
77M HIS* 1.3 72.0 + - + +
78M GLN 3.7 1.1 - - - -
79M HIS* 4.8 4.3 + - - -
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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
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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