Contacts of the helix formed by residues 66 - 74 (chain M) in PDB entry 3J0S
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 66 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M VAL* 3.4 9.6 - - + +
65M ASP* 1.3 107.3 + - - +
67M PRO* 1.4 66.5 - - - +
68M TYR 3.1 6.5 + - - +
69M ALA* 3.3 27.6 - - + +
70M THR* 3.5 8.8 + - - -
146M ARG* 5.0 11.6 + - - -
162M GLU* 5.1 12.8 - - - +
164M LYS* 4.4 20.6 + - - -
165M PRO* 5.9 1.4 - - - +
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Residues in contact with PRO 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M LYS* 3.3 35.9 - - + +
55M ILE* 3.8 22.8 - - + +
56M LEU 4.8 3.8 - - - +
59M ASP* 5.2 2.7 - - + -
60M VAL* 3.2 36.6 - - + +
64M VAL* 4.2 7.1 - - + +
65M ASP 3.6 2.7 - - - +
66M ASP* 1.4 86.7 - - - +
68M TYR* 1.3 57.9 + - - +
69M ALA 3.0 6.9 + - - -
70M THR* 3.2 17.0 + - - +
71M PHE* 3.3 14.6 + - - +
85M TYR* 4.4 2.2 - - - -
162M GLU* 5.1 6.5 - - + +
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Residues in contact with TYR 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M ASP* 3.1 4.1 - - - +
67M PRO* 1.3 75.7 - - - +
69M ALA* 1.3 64.5 + - - +
71M PHE* 4.7 18.6 - + - -
72M VAL* 4.8 2.9 - - + +
85M TYR* 3.2 37.9 + + - +
102M ILE* 5.8 3.8 - - + -
135M LEU* 4.9 7.9 - - + +
142M GLU 4.4 1.6 + - - -
143M VAL* 2.8 32.5 + - + +
144M LYS* 4.0 9.3 - - - +
145M ASP 3.6 21.4 + - - -
146M ARG* 3.6 33.3 + - - +
148M THR* 5.0 2.1 - - - +
149M LEU* 3.7 36.0 + - + +
161M LEU* 5.1 3.6 - - + -
162M GLU* 5.3 10.1 - - + -
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Residues in contact with ALA 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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66M ASP* 3.3 20.9 - - + +
67M PRO 3.0 1.0 + - - -
68M TYR* 1.3 77.1 - - - +
70M THR* 1.3 63.6 + - - +
71M PHE 3.1 3.1 - - - +
72M VAL* 3.1 20.7 + - - +
73M LYS* 2.9 40.5 + - - +
146M ARG* 5.5 1.1 - - - +
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Residues in contact with THR 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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55M ILE* 4.7 8.5 - - + -
64M VAL* 3.6 28.9 - - + +
66M ASP 3.5 2.8 + - - -
67M PRO* 3.2 11.2 + - - +
69M ALA* 1.3 77.2 - - - +
71M PHE* 1.3 57.9 + - - +
73M LYS* 3.1 11.5 + - + +
74M MET* 2.9 49.0 + - + +
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Residues in contact with PHE 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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35M ALA* 4.4 12.6 - - + -
37M LEU* 4.1 11.7 - - + -
55M ILE* 3.4 28.0 - - + +
67M PRO 3.3 8.9 + - - +
68M TYR* 4.7 15.7 - + - -
69M ALA 4.5 3.4 - - - +
70M THR* 1.3 80.7 - - - +
72M VAL* 1.3 62.2 + - + +
74M MET* 3.5 7.0 + - + +
75M LEU* 3.1 54.9 + - + +
83M ALA* 3.7 21.1 - - + -
85M TYR* 4.6 10.3 - + + -
102M ILE* 3.5 40.2 - - + -
143M VAL* 4.0 18.6 - - + -
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Residues in contact with VAL 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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68M TYR* 4.8 4.3 - - + +
69M ALA* 3.1 25.7 + - - +
71M PHE* 1.3 80.0 - - + +
73M LYS* 1.3 68.4 + - + +
75M LEU* 3.5 9.0 + - - +
140M TYR* 3.2 37.6 - - + +
143M VAL* 3.6 31.2 - - + +
144M LYS* 3.7 44.2 - - + +
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Residues in contact with LYS 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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69M ALA* 2.9 29.2 + - - +
70M THR* 3.3 12.1 - - + +
72M VAL* 1.3 85.4 - - + +
74M MET* 1.3 57.7 + - + +
75M LEU 3.3 2.9 + - - -
76M PRO* 4.4 9.5 - - - +
140M TYR* 4.6 7.0 + - + -
144M LYS* 4.7 15.4 - - - +
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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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37M LEU* 3.9 11.0 - - + -
52M GLY 5.2 0.4 - - - +
53M LYS* 3.4 53.7 - - + +
54M GLU 3.9 8.5 - - - +
55M ILE* 4.1 20.6 - - + -
70M THR* 2.9 37.5 + - + +
71M PHE* 3.7 9.9 - - - +
73M LYS* 1.3 74.9 - - + +
75M LEU* 1.3 60.1 + - + +
76M PRO* 3.4 7.2 - - - +
81M ARG* 3.3 18.4 + - - -
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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
------------------------------------------------------------
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