Contacts of the helix formed by residues 133 - 150 (chain R) in PDB entry 3LUE
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 ASN 133 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128R GLU* 2.9 31.9 + - + +
131R ASP* 3.3 4.9 - - + -
132R GLY* 1.3 74.7 - - - +
134R LEU* 1.3 56.7 + - - +
135R LYS* 3.2 11.6 + - - +
136R MET* 2.6 41.3 + - + +
137R THR* 2.6 36.6 + - - -
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Residues in contact with LEU 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R GLU* 3.2 37.9 - - + +
48R ARG* 4.2 16.8 - - - -
69R ILE* 4.2 17.5 - - + -
70R GLU* 3.8 26.9 - - + +
132R GLY 3.2 6.2 + - - +
133R ASN* 1.3 70.7 + - - +
135R LYS* 1.3 67.8 + - - +
137R THR* 3.1 2.7 + - - -
138R LEU* 2.8 40.5 + - + +
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Residues in contact with LYS 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R TRP* 4.7 24.4 - - + -
44R GLU* 3.7 25.9 + - - +
133R ASN* 3.2 9.5 + - - +
134R LEU* 1.3 78.2 - - - +
136R MET* 1.3 59.7 + - + +
138R LEU* 3.9 5.0 - - - +
139R GLY* 2.9 25.8 + - - -
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Residues in contact with MET 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I VAL* 2.1 45.8 - - + +
55I GLY* 5.6 0.2 - - - -
124R ILE* 4.2 23.5 - - + +
128R GLU* 3.0 50.0 - - + +
129R ILE* 4.1 5.8 - - + +
133R ASN* 2.6 28.1 + - - +
135R LYS* 1.3 71.1 - - + +
137R THR* 1.3 59.4 + - - +
139R GLY* 3.3 1.9 + - - +
140R MET* 2.9 28.6 + - - +
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Residues in contact with THR 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ILE* 3.8 38.5 + - + +
70R GLU* 5.3 2.1 - - - -
73R PHE* 4.7 9.4 - - + -
129R ILE* 4.2 22.6 + - + +
132R GLY* 4.3 4.7 - - - -
133R ASN 2.6 29.8 + - - -
134R LEU* 3.7 6.5 - - - -
136R MET* 1.3 74.1 - - - +
138R LEU* 1.3 65.8 + - - +
140R MET* 3.2 15.8 + - + +
141R ILE* 3.0 23.4 + - + +
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Residues in contact with LEU 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I ARG* 3.4 2.2 + - - -
43R TRP* 5.1 4.5 - - + -
44R GLU* 3.9 31.4 - - + +
47R GLN* 4.0 21.3 - - + +
48R ARG* 3.9 19.5 - - - +
51R PHE* 3.3 31.6 - - + -
69R ILE* 4.1 23.1 - - + -
134R LEU* 2.8 44.6 + - + +
135R LYS* 4.0 4.5 - - - +
137R THR* 1.3 73.7 - - - +
139R GLY* 1.3 62.1 + - - +
141R ILE* 3.4 0.8 + - - +
142R TRP 3.1 18.4 + - - -
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Residues in contact with GLY 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I ASN* 2.6 46.6 + - - -
124R ILE* 4.0 4.7 - - - -
135R LYS 2.9 17.8 + - - -
136R MET* 3.7 2.2 - - - -
137R THR 3.2 0.2 - - - -
138R LEU* 1.3 78.5 - - - +
140R MET* 1.3 59.0 + - - +
142R TRP 3.4 0.2 + - - -
143R THR* 2.8 16.3 + - - -
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Residues in contact with MET 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R PHE* 4.9 4.5 - - + -
79R LEU* 3.5 45.8 - - + -
111R LEU* 3.8 23.6 - - + -
114R ILE* 4.5 6.3 - - + -
121R LEU* 5.3 2.7 - - + -
124R ILE* 3.8 14.9 - - + +
129R ILE* 3.8 30.3 - - + -
136R MET 2.9 14.0 + - - +
137R THR* 3.5 15.7 - - + +
139R GLY* 1.3 76.3 - - - +
141R ILE* 1.3 75.8 + - + +
143R THR* 3.1 8.5 + - - -
144R ILE* 3.0 28.3 + - + +
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Residues in contact with ILE 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51R PHE* 4.0 16.4 - - + -
54R TRP* 4.7 1.6 - - + -
55R CYS* 3.8 23.1 - - - -
69R ILE* 4.3 15.3 - - + -
73R PHE* 3.7 28.5 - - + -
79R LEU* 4.3 9.9 - - + -
82R LEU* 4.3 6.7 - - + -
137R THR* 3.0 17.4 + - + +
138R LEU 4.0 3.6 - - - +
139R GLY 3.4 0.2 - - - -
140R MET* 1.3 86.2 - - + +
142R TRP* 1.3 61.2 + - - +
144R ILE* 3.1 9.1 + - + +
145R ILE* 2.7 45.6 + - + +
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Residues in contact with TRP 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I PHE 3.2 1.2 + - - -
91I TYR* 1.2 79.3 - + + +
92I ASN* 3.7 0.7 - - - +
95I ARG* 1.6 76.0 - - + +
96I VAL* 2.8 36.3 - - - -
97I ALA* 5.1 0.2 - - + -
51R PHE* 5.0 0.9 - + - -
138R LEU 3.1 10.0 + - - +
139R GLY 3.8 1.6 - - - +
141R ILE* 1.3 76.0 - - - +
143R THR* 1.3 55.7 + - - +
145R ILE* 2.9 24.2 + - + +
146R LEU* 2.7 41.1 + - + +
150R ILE* 4.1 19.7 - - + -
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Residues in contact with THR 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I HIS* 4.1 15.7 + - + +
91I TYR* 4.5 3.9 - - + +
92I ASN* 3.3 10.9 + - - -
114R ILE* 4.4 6.7 - - + -
119R VAL* 3.1 36.3 - - + -
120R LYS 5.6 0.7 - - - +
121R LEU* 4.6 7.4 - - + -
124R ILE* 4.4 5.9 - - - +
139R GLY 2.8 19.9 + - - -
140R MET* 3.1 13.0 + - - -
142R TRP* 1.3 81.2 - - - +
144R ILE* 1.3 57.4 + - - +
146R LEU* 3.9 3.9 - - - +
147R ARG* 2.9 31.0 + - - +
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Residues in contact with ILE 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R TRP* 4.2 11.7 - - + -
79R LEU* 3.9 24.5 - - + -
82R LEU* 4.9 5.8 - - + -
83R LEU* 3.8 14.8 - - + -
86R ILE* 3.5 27.5 - - + +
114R ILE* 3.4 39.0 - - + -
140R MET* 3.0 16.8 + - + +
141R ILE* 3.5 16.2 - - + +
142R TRP 3.1 0.2 - - - -
143R THR* 1.3 75.9 - - - +
145R ILE* 1.3 60.8 + - - +
147R ARG* 4.6 0.7 - - - -
148R PHE* 2.9 37.7 + - + +
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Residues in contact with ILE 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I ARG* 3.9 1.1 - - - +
51R PHE* 3.7 36.1 - - + -
54R TRP* 3.6 54.1 - - + +
141R ILE* 2.7 30.7 + - + +
142R TRP* 3.4 24.2 - - + +
144R ILE* 1.3 72.6 - - - +
146R LEU* 1.3 63.9 + - - +
149R ALA* 3.0 27.5 + - + +
150R ILE* 3.5 10.7 + - + +
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Residues in contact with LEU 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I TYR* 1.0 92.4 - - + +
96I VAL 3.7 9.0 - - - +
97I ALA* 3.9 16.2 - - + -
98I PRO* 4.2 0.9 - - + -
99I GLU* 4.4 6.5 - - - +
142R TRP* 2.7 23.9 + - + +
143R THR 3.9 2.2 - - - +
145R ILE* 1.3 77.0 - - - +
147R ARG* 1.3 62.8 + - - +
150R ILE* 3.2 52.7 + - + +
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Residues in contact with ARG 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114R ILE* 5.7 0.2 - - + -
117R LYS* 3.3 43.7 + - + +
119R VAL* 3.6 25.8 - - + -
143R THR* 2.9 20.1 + - + +
144R ILE* 4.6 0.2 - - - -
146R LEU* 1.3 80.2 - - - +
148R PHE* 1.3 85.7 + - + +
149R ALA 3.9 0.2 + - - -
150R ILE 4.8 2.4 + - - -
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Residues in contact with PHE 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R TRP* 5.7 0.4 - - + -
83R LEU* 3.9 14.4 - - + -
86R ILE* 3.4 40.6 - - + +
87R SER* 3.8 33.2 - - - -
89R GLU* 5.4 0.2 - - - -
113R PHE* 3.7 15.7 - + - -
114R ILE* 4.6 11.7 - - + -
117R LYS* 3.5 35.9 - - + -
144R ILE* 2.9 26.2 + - + +
147R ARG* 1.3 93.4 - - + +
149R ALA* 1.3 59.8 + - + +
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Residues in contact with ALA 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R TRP* 4.2 26.2 - - + +
58R HIS* 5.8 1.3 - - - +
145R ILE* 3.0 17.5 + - + +
148R PHE* 1.3 79.5 - - - +
150R ILE* 1.3 69.3 + - + +
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Residues in contact with ILE 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ALA* 3.7 7.0 - - + -
99I GLU* 3.5 26.2 - - - +
100I GLU* 3.4 25.1 - - - +
142R TRP* 4.1 29.4 - - + -
145R ILE* 4.2 12.3 - - + +
146R LEU* 3.2 33.1 + - + +
147R ARG 4.7 2.0 - - - -
148R PHE 3.9 0.4 - - - -
149R ALA* 1.3 88.6 - - + +
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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
------------------------------------------------------------
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