Contacts of the helix formed by residues 73 - 78 (chain M) in PDB entry 3J7Y
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 PRO 73 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64M ARG* 5.3 3.6 - - - +
66M GLY 3.8 9.4 - - - +
67M PHE* 4.9 10.1 - - + -
68M GLU* 3.7 9.9 - - + +
71M GLN 3.3 4.0 - - - +
72M THR* 1.3 87.6 - - + +
74M PHE* 1.3 60.1 + - - +
75M TYR* 3.5 40.6 - - + +
76M ILE* 3.1 24.4 + - + +
77M ARG* 2.9 30.2 + - - +
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Residues in contact with PHE 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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1143 PHE* 3.8 14.8 - + - -
1243 ARG* 4.0 4.9 - - - -
1503 CYS* 3.8 15.9 - - - -
1543 GLN* 3.2 61.2 - - + +
1573 LEU* 5.2 8.3 - - + -
1583 LEU* 4.1 15.0 - - + -
2867A C 3.8 10.3 - - - +
2868A C 4.2 14.1 - - - -
68M GLU* 2.9 24.0 + - - +
73M PRO* 1.3 73.0 - - - +
75M TYR* 1.3 67.8 + - + +
76M ILE 3.5 0.2 + - - -
77M ARG* 3.5 15.1 + - + +
78M ILE* 3.2 41.2 + - + +
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Residues in contact with TYR 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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1073 VAL* 4.5 4.0 - - + -
1093 ALA* 3.9 18.2 - - + -
1103 VAL* 3.9 20.4 - - + -
1133 ARG* 2.8 32.7 + - - -
1143 PHE* 4.0 14.9 - - + -
1573 LEU* 4.6 4.9 - - + -
1583 LEU* 4.7 3.4 - - + -
1613 MET* 3.9 20.9 - - + -
1750A G 3.9 1.6 + - - -
1751A A 2.7 29.7 + - - -
64M ARG* 3.3 22.5 + - - -
65M LEU 4.9 1.1 + - - -
66M GLY* 3.7 25.8 - - - -
67M PHE 4.6 1.9 + - - -
73M PRO* 3.5 19.5 - - + +
74M PHE* 1.3 83.2 - - + +
76M ILE* 1.3 84.6 + - + +
78M ILE 4.1 0.5 + - - -
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Residues in contact with ILE 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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1133 ARG* 3.4 18.7 + - - +
1750A G 3.6 37.9 - - - +
2897A A 5.4 3.6 - - + -
2898A U 3.1 35.5 + - + +
64M ARG* 5.5 1.8 - - - +
72M THR* 5.2 5.6 - - + -
73M PRO* 3.1 27.9 + - + -
75M TYR* 1.3 107.8 - - + +
77M ARG* 1.3 62.2 - - - +
78M ILE 3.3 3.7 + - - +
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Residues in contact with ARG 77 (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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1273 ALA* 3.7 6.1 - - - +
2867A C 5.5 0.2 - - - -
2868A C 2.3 48.8 + - - +
2897A A 2.7 42.9 + - - +
2898A U 3.1 12.8 - - - +
2916A G 3.3 38.7 + - - +
2917A G 2.7 28.3 + - - +
68M GLU* 5.5 0.2 - - - -
72M THR* 2.6 40.4 + - - +
73M PRO 2.9 18.2 + - - +
74M PHE* 3.5 10.0 + - + +
76M ILE* 1.3 76.9 - - - +
78M ILE* 1.3 61.7 + - + +
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Residues in contact with ILE 78 (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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1133 ARG* 3.1 33.7 + - + +
1143 PHE* 3.5 28.3 - - + -
1243 ARG* 3.6 27.4 - - + +
1253 ARG 3.4 21.3 - - - +
1273 ALA* 4.4 4.5 - - + -
2868A C 5.1 3.4 - - - +
2898A U 3.7 2.3 - - - +
74M PHE* 3.2 51.7 + - + +
76M ILE 3.3 2.2 - - - +
77M ARG* 1.3 83.2 - - + +
79M PRO* 1.3 77.5 - - + +
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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