Contacts of the helix formed by residues 84 - 91 (chain M) in PDB entry 4ADV
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 CYS 84 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M LEU* 3.4 22.9 - - - +
82M LEU* 2.7 14.0 + - + +
83M GLY* 1.3 75.0 - - - +
85M TYR* 1.3 65.7 + - - +
86M ARG* 3.5 17.5 - - - -
87M GLY* 3.1 23.9 + - - -
88M LEU* 2.9 22.8 + - - +
68S HIS* 4.0 11.4 - - + -
72S GLU* 3.0 33.2 - - + +
73S PHE* 4.2 4.2 - - + +
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Residues in contact with TYR 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1226A C 5.0 0.5 + - - -
1320A C 4.2 7.6 - - - +
1321A U 3.5 32.3 + - - -
1322A C 3.0 28.3 + - - -
83M GLY 4.0 0.2 + - - -
84M CYS* 1.3 70.5 - - - +
86M ARG* 1.3 66.4 + - - +
88M LEU* 3.2 17.5 + - + +
89M ARG* 2.9 78.0 + - + +
95M PRO 5.2 6.2 + - - -
96M VAL* 5.7 6.1 - - - -
101M THR* 5.3 4.2 - - - +
72S GLU* 2.7 24.7 + - - +
74S ALA 5.8 2.5 - - - +
75S PRO* 5.5 9.2 - - + -
76S THR* 6.0 2.2 - - - -
77S ARG* 4.3 11.0 + - - -
79S TYR* 5.8 3.8 - + - -
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Residues in contact with ARG 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309A G 3.3 34.4 + - - +
1310A G 3.1 25.9 + - - -
79M LEU* 3.1 39.7 - - + +
80M MET* 6.2 0.9 - - + -
84M CYS* 3.2 11.8 - - - -
85M TYR* 1.3 79.8 - - - +
87M GLY* 1.3 53.0 + - - +
89M ARG* 2.9 3.3 + - - -
90M HIS* 2.6 42.5 + - + +
96M VAL* 3.0 31.9 - - + +
2S ARG* 4.5 22.2 - - - +
68S HIS* 4.9 9.5 + - - -
72S GLU* 3.1 16.7 + - - +
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Residues in contact with GLY 87 (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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80M MET* 3.6 41.1 - - - +
84M CYS* 3.1 11.6 + - - -
86M ARG* 1.3 79.1 - - - +
88M LEU* 1.3 57.4 + - - +
90M HIS* 2.7 21.2 + - - +
91M ARG* 2.8 18.4 + - - +
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Residues in contact with LEU 88 (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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80M MET 5.0 0.2 + - - -
82M LEU 5.2 0.4 + - - +
83M GLY* 3.9 25.4 - - - +
84M CYS 2.9 19.3 + - - +
85M TYR* 3.5 19.7 - - + +
87M GLY* 1.3 74.3 - - - +
89M ARG* 1.3 61.8 + - + +
91M ARG* 3.9 10.7 - - + +
92M ARG* 2.9 32.2 - - - +
75S PRO* 4.4 18.6 - - + -
79S TYR* 4.1 21.1 - - - +
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Residues in contact with ARG 89 (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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1225A A 4.6 0.2 + - - -
1226A C 2.7 36.2 + - - -
85M TYR* 2.9 60.2 + - + +
86M ARG 3.4 6.7 - - - +
87M GLY 2.9 0.6 - - - -
88M LEU* 1.3 78.9 + - - +
90M HIS* 1.3 64.1 + - - +
91M ARG 3.2 2.0 - - - -
92M ARG* 3.2 9.9 + - - +
94M LEU* 2.9 66.6 + - - +
95M PRO 4.3 6.1 - - - +
96M VAL* 3.4 15.3 - - + -
101M THR* 4.5 2.9 - - - +
77S ARG* 4.2 8.5 - - - +
79S TYR* 3.7 36.4 - - - -
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Residues in contact with HIS 90 (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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1308A U 3.0 30.2 + - - -
1309A G 2.8 34.7 + - - -
76M ILE* 4.0 25.6 - - + +
80M MET* 4.2 11.7 - - + -
86M ARG* 2.6 31.2 + - + +
87M GLY* 2.7 11.3 + - - +
89M ARG* 1.3 75.6 - - - +
91M ARG* 1.3 56.0 + - - +
92M ARG 3.1 3.4 + - - -
93M GLY* 3.6 8.4 + - - +
94M LEU 4.7 0.7 - - - -
96M VAL* 3.5 10.4 - - + +
108M ARG* 4.5 6.8 + - - +
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Residues in contact with ARG 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M MET* 4.7 20.6 - - + -
87M GLY 2.8 14.7 + - - +
88M LEU* 3.9 17.5 + - + +
90M HIS* 1.3 76.6 - - - +
92M ARG* 1.3 63.9 + - + +
93M GLY 3.6 0.2 - - - -
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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