Contacts of the helix formed by residues 95 - 108 (chain E) in PDB entry 3LVQ
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 ARG 95 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E LEU* 3.6 22.5 - - + +
22E ASP* 2.7 45.2 + - - -
23E ALA* 5.6 0.8 - - - +
71E ARG* 4.7 0.8 - - - +
89E ASP* 5.8 2.4 + - - +
92E ASP* 3.1 39.4 + - - +
94E ASP* 1.3 86.3 - - + +
96E ILE* 1.3 63.6 + - - +
97E ASP 3.4 2.2 - - - +
98E GLU* 3.2 40.2 + - + +
99E ALA* 3.1 17.3 + - - +
473E VAL* 5.8 0.2 - - - +
478E MET 5.2 0.2 + - - -
479E GLN* 3.4 26.3 + - - +
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Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E VAL* 3.7 28.3 - - + -
89E ASP 5.6 1.1 - - - +
92E ASP 3.7 7.9 + - - +
93E ARG 3.8 14.6 - - - +
94E ASP 3.7 0.6 - - - -
95E ARG* 1.3 77.6 - - - +
97E ASP* 1.3 64.1 + - - +
99E ALA* 2.9 8.7 + - + +
100E ARG* 2.7 32.4 + - - +
130E MET* 4.1 17.0 - - + -
135E ILE* 4.2 13.7 - - + -
138E LYS* 4.0 35.7 - - + +
139E LEU* 3.6 27.8 - - + -
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Residues in contact with ASP 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ASP 5.4 1.3 + - - +
95E ARG 3.4 0.8 - - - -
96E ILE* 1.3 87.9 - - - +
98E GLU* 1.3 56.3 + - - +
100E ARG* 3.4 35.6 + - - +
101E GLN* 3.1 34.7 + - - +
138E LYS* 4.2 7.5 - - - +
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Residues in contact with GLU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 3.8 8.8 - - + +
68E ASP* 3.9 5.7 - - - +
71E ARG* 3.4 34.4 + - - +
95E ARG* 3.2 45.2 + - - +
96E ILE 3.0 0.8 - - - -
97E ASP* 1.3 76.2 - - - +
99E ALA* 1.3 59.2 + - - +
101E GLN* 3.3 11.7 + - + +
102E GLU* 3.1 35.9 + - + +
684E MG 4.0 8.4 - - - -
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Residues in contact with ALA 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 3.7 16.3 - - + +
86E PHE* 3.3 25.5 - - + -
87E VAL 5.8 0.2 - - - +
88E VAL* 4.2 15.9 - - + -
95E ARG 3.1 11.5 + - - +
96E ILE* 2.9 17.3 + - + +
98E GLU* 1.3 74.4 - - - +
100E ARG* 1.3 64.3 + - - +
103E LEU* 3.1 27.0 + - - +
139E LEU* 4.2 3.1 - - + +
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Residues in contact with ARG 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE 2.7 12.1 + - - +
97E ASP* 3.4 48.6 + - - +
99E ALA* 1.3 77.8 - - - +
101E GLN* 1.3 76.4 + - - +
103E LEU* 3.8 1.9 - - - +
104E HIS* 3.0 52.1 + - - +
138E LYS 3.4 20.9 - - - +
139E LEU* 3.5 35.8 - - + +
140E GLY* 4.6 2.9 - - - +
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Residues in contact with GLN 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASP* 3.1 17.4 + - - +
98E GLU* 3.3 13.0 + - - +
100E ARG* 1.3 101.4 + - - +
102E GLU* 1.3 59.3 + - + +
104E HIS* 3.4 5.2 + - - +
105E ARG* 2.8 42.4 + - - +
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Residues in contact with GLU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 3.7 21.1 - - + -
71E ARG* 3.2 34.4 + - - +
74E TRP* 4.1 18.3 - - + -
86E PHE* 4.5 4.3 - - + -
98E GLU* 3.1 19.0 + - + +
99E ALA 4.5 1.3 - - - +
101E GLN* 1.3 77.8 + - - +
103E LEU* 1.3 67.2 + - - +
105E ARG* 2.8 53.4 + - - +
106E ILE* 3.1 29.1 + - - +
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E LEU* 4.4 14.1 - - + -
86E PHE* 3.6 43.8 - - + -
99E ALA 3.1 19.7 + - - +
100E ARG 3.8 1.3 - - - +
102E GLU* 1.3 77.1 - - - +
104E HIS* 1.3 74.8 + - + +
106E ILE* 3.0 15.3 + - - +
107E ILE* 3.1 26.3 + - + +
117E ILE* 4.6 2.7 - - + -
119E ILE* 4.3 13.7 - - + -
139E LEU* 4.1 19.1 - - + -
141E LEU* 4.0 27.4 - - + -
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Residues in contact with HIS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ARG* 3.0 38.3 + - + +
101E GLN* 3.7 5.4 - - - +
103E LEU* 1.3 87.7 - - + +
105E ARG* 1.3 62.5 + - - +
106E ILE 3.0 1.4 + - - -
107E ILE* 3.6 17.1 - - + +
108E ASN* 3.2 31.0 + - - +
139E LEU 3.0 25.7 + - - -
140E GLY* 4.0 17.9 + - - -
141E LEU* 4.6 3.8 - - + +
144E ILE* 5.0 9.6 - - + +
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Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ARG* 5.3 12.1 + - - +
72E PRO* 5.5 6.1 - - - +
74E TRP* 6.3 0.6 - - - -
75E ARG* 6.0 5.5 - - - +
78E TYR* 4.2 6.3 + - - -
101E GLN* 2.8 28.2 + - - +
102E GLU* 2.8 44.2 + - - +
103E LEU 3.2 0.4 - - - -
104E HIS* 1.3 72.2 - - - +
106E ILE* 1.3 60.3 + - + +
108E ASN* 4.5 2.1 - - - +
109E ASP* 4.1 13.2 + - - +
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Residues in contact with ILE 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 3.7 26.0 - - + -
74E TRP* 4.3 10.8 - - + -
78E TYR* 3.4 35.9 - - + +
84E LEU* 4.3 14.4 - - + -
86E PHE* 4.2 20.0 - - + -
102E GLU 3.1 21.1 - - - +
103E LEU* 3.0 6.8 + - - +
105E ARG* 1.3 78.3 - - + +
107E ILE* 1.3 60.2 + - + +
108E ASN 3.0 4.3 - - - -
109E ASP* 2.8 27.2 + - - +
112E MET* 3.6 28.5 - - + +
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Residues in contact with ILE 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E LEU* 4.3 13.9 - - + -
103E LEU* 3.6 27.4 - - + +
104E HIS* 3.6 25.8 - - + +
106E ILE* 1.3 75.3 - - - +
108E ASN* 1.3 73.0 + - - +
109E ASP 3.4 4.3 + - - +
112E MET* 4.6 1.8 - - + -
113E ARG* 4.8 1.6 + - - +
115E ALA* 6.5 0.2 - - + -
117E ILE* 3.7 32.1 - - + -
141E LEU* 6.5 0.4 - - + -
144E ILE* 4.6 24.5 - - + -
147E ARG* 3.2 45.7 + - + +
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Residues in contact with ASN 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E HIS* 3.2 19.0 + - - +
105E ARG* 5.0 2.5 - - - +
106E ILE 3.0 0.8 + - - -
107E ILE* 1.3 92.2 - - - +
109E ASP* 1.3 64.4 + - - +
110E ARG* 3.4 2.8 + - - -
144E ILE* 5.8 1.9 - - - +
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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