Contacts of the helix formed by residues 96 - 111 (chain m) in PDB entry 5M32
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 GLY 96 (chain m).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166h GLU* 3.3 27.6 + - - +
167h LEU* 5.4 2.2 - - - +
170h LYS* 5.0 2.9 - - - -
171h HIS* 5.7 4.7 - - - -
95m LEU* 1.3 75.4 - - - +
97m GLU* 1.3 56.1 + - - -
98m SER 3.1 6.1 - - - -
99m GLU* 2.7 33.9 + - - +
100m ILE* 3.1 13.5 + - - +
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Residues in contact with GLU 97 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162h LYS* 4.8 1.9 + - - -
166h GLU* 3.2 8.3 - - - +
170h LYS* 2.4 32.9 + - - +
206h HIS* 2.8 45.1 - - - +
96m GLY* 1.3 68.2 - - - -
98m SER* 1.3 55.1 + - - +
99m GLU 3.1 0.4 - - - -
100m ILE* 3.7 14.7 - - + +
101m ARG* 2.7 35.6 + - - +
130m LYS* 4.5 24.7 - - + +
131m THR 6.3 0.2 - - - -
132m VAL* 4.8 13.5 - - + +
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Residues in contact with SER 98 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162h LYS* 3.7 21.3 - - - +
206h HIS* 6.3 1.1 - - - -
97m GLU* 1.3 84.6 - - - +
99m GLU* 1.3 85.5 + - - +
101m ARG* 3.2 9.7 - - - +
102m ASP* 3.0 36.1 + - - +
132m VAL* 5.3 8.7 - - - -
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Residues in contact with GLU 99 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159h LYS* 6.0 1.7 - - - +
162h LYS* 4.7 6.7 - - - -
166h GLU* 4.7 0.9 - - - +
87m GLU* 5.5 0.5 - - - +
91m ALA* 3.9 5.0 - - - +
94m ASN 5.5 0.2 - - - -
95m LEU* 3.7 39.4 - - + +
96m GLY* 2.7 40.2 + - - +
98m SER* 1.3 100.2 + - - +
100m ILE* 1.3 58.7 + - - +
101m ARG 3.2 0.4 - - - -
102m ASP* 3.6 8.3 - - + +
103m ALA* 2.9 27.4 + - - +
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Residues in contact with ILE 100 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171h HIS* 6.1 1.6 - - - +
88m LEU* 3.8 24.9 - - + +
91m ALA* 3.3 33.0 - - + +
92m GLU* 4.8 8.7 - - + +
95m LEU 3.8 1.6 - - - +
96m GLY* 3.1 34.2 + - - +
97m GLU* 3.7 9.0 - - + +
99m GLU* 1.3 73.5 - - - +
101m ARG* 1.3 60.6 + - - +
103m ALA* 3.7 4.0 - - - +
104m MET* 2.9 32.4 + - + +
130m LYS* 3.7 36.8 - - + +
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Residues in contact with ARG 101 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m GLU 2.7 23.3 + - - +
98m SER* 3.2 12.8 - - - +
100m ILE* 1.3 74.4 - - - +
102m ASP* 1.3 66.4 + - - +
104m MET* 3.2 11.9 + - - +
105m MET* 2.9 69.5 + - - +
127m THR* 4.2 4.7 - - - -
130m LYS* 4.6 15.5 - - - +
132m VAL* 4.0 18.6 - - + +
135m GLY 4.2 6.5 + - - -
136m HIS* 3.0 63.6 + - - +
139m ASP* 4.8 5.5 + - - -
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Residues in contact with ASP 102 (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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98m SER* 3.0 25.1 + - - +
99m GLU* 3.5 8.8 + - + +
100m ILE 3.4 0.2 - - - -
101m ARG* 1.3 85.6 + - - +
103m ALA* 1.3 60.9 + - - +
105m MET* 3.0 18.0 + - + +
106m ALA* 2.9 23.2 + - - +
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Residues in contact with ALA 103 (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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84m LEU* 4.7 3.9 - - - +
87m GLU* 3.6 17.7 - - + +
88m LEU* 3.5 37.5 - - + +
99m GLU 2.9 18.8 + - - +
100m ILE* 3.7 5.6 - - - +
101m ARG 3.3 0.2 - - - -
102m ASP* 1.3 75.4 - - - +
104m MET* 1.3 59.2 + - - +
105m MET 3.1 0.7 - - - -
106m ALA* 3.1 11.1 + - - +
107m LYS* 3.0 25.9 + - - +
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Residues in contact with MET 104 (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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88m LEU* 4.2 24.9 - - + -
100m ILE* 2.9 16.3 + - + +
101m ARG* 3.4 10.8 - - - +
103m ALA* 1.3 75.9 - - - +
105m MET* 1.3 51.1 + - - +
106m ALA 3.4 0.2 - - - -
107m LYS* 3.8 12.1 - - + +
108m ALA* 2.6 37.3 + - - +
123m ALA* 5.4 4.2 - - + +
126m LYS* 3.9 46.9 - - + +
127m THR* 4.1 21.5 - - - +
130m LYS* 3.7 38.8 - - + +
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Residues in contact with MET 105 (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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101m ARG* 2.9 40.3 + - - +
102m ASP* 3.0 22.1 + - + +
104m MET* 1.3 95.7 - - - +
106m ALA* 1.3 59.5 + - - +
108m ALA* 3.5 9.9 - - + -
109m GLU* 2.8 55.6 + - - +
127m THR* 3.4 39.0 - - + +
136m HIS* 4.0 2.2 - - - +
140m ILE* 4.5 11.2 - - + -
143m TYR* 6.4 0.9 - - - -
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Residues in contact with ALA 106 (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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84m LEU* 3.7 25.8 - - + +
87m GLU* 5.4 3.4 - - + +
102m ASP 2.9 11.6 + - - +
103m ALA* 3.1 12.5 + - - +
105m MET* 1.3 76.8 - - - +
107m LYS* 1.3 52.7 + - - +
110m TYR* 2.7 41.8 + - + +
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Residues in contact with LYS 107 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81m LEU 5.6 3.4 + - - -
84m LEU* 4.6 8.7 - - + +
85m ASP* 4.5 16.6 + - - +
88m LEU* 4.1 26.7 - - - -
103m ALA 3.0 15.6 + - - +
104m MET* 4.1 12.6 - - + +
106m ALA* 1.3 75.9 - - - +
108m ALA* 1.3 55.3 + - - +
110m TYR* 4.8 1.1 - - - -
111m LEU* 2.6 43.9 + - + +
119m GLY 4.3 1.7 - - - +
123m ALA* 4.6 15.2 - - + +
126m LYS* 5.2 13.5 - - + -
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Residues in contact with ALA 108 (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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104m MET 2.6 23.9 + - - +
105m MET* 3.4 20.2 + - + -
106m ALA 3.1 0.4 - - - -
107m LYS* 1.3 78.2 - - - +
109m GLU* 1.3 55.9 + - - +
111m LEU* 3.6 1.0 - - - -
112m CYS* 2.7 39.2 + - - +
123m ALA* 4.7 9.2 - - + +
124m PHE* 3.6 29.9 - - + -
143m TYR* 4.5 0.7 - - + -
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Residues in contact with GLU 109 (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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105m MET* 2.8 57.0 + - - +
108m ALA* 1.3 73.9 - - - +
110m TYR* 1.3 59.5 + - - +
113m ARG* 2.9 29.1 + - - +
143m TYR* 3.3 38.9 + - + +
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Residues in contact with TYR 110 (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 GLU* 5.8 11.0 - - + +
81m LEU* 6.3 1.6 - - - -
84m LEU* 5.9 2.7 - - + -
106m ALA* 2.7 23.7 + - + +
107m LYS* 4.8 1.1 - - - -
109m GLU* 1.3 78.4 - - - +
111m LEU* 1.3 56.8 + - - +
112m CYS 3.2 4.0 + - - -
113m ARG* 3.2 7.2 + - - +
114m ILE* 3.2 18.4 + - - +
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Residues in contact with LEU 111 (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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107m LYS* 2.6 32.2 + - + +
108m ALA 3.6 2.7 - - - -
110m TYR* 1.3 75.5 - - - +
112m CYS* 1.3 57.6 + - - +
114m ILE* 4.0 16.8 + - + +
115m GLY 4.9 0.3 + - - -
116m ASP 4.7 1.9 + - - +
119m GLY* 3.1 21.4 - - - +
120m ALA* 3.1 22.7 + - - +
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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