Contacts of the helix formed by residues 113 - 127 (chain B) in PDB entry 3LSU
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 SER 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B ILE* 3.9 11.7 + - - +
108B ASP* 3.6 8.9 + - - -
111B PHE* 3.2 3.9 - - - +
112B GLY* 1.3 78.8 - - - +
114B LEU* 1.3 64.4 + - - +
115B ASP* 3.6 10.5 + - - +
116B GLU* 3.0 32.7 + - - +
117B LEU* 3.2 15.9 + - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLY 6.0 1.1 - - - +
98B PRO* 4.0 21.1 - - + -
99B PRO* 3.7 31.0 - - + -
107B ILE* 3.8 25.0 - - + +
108B ASP* 4.0 4.2 + - - +
113B SER* 1.3 73.6 - - - +
115B ASP* 1.3 61.9 + - - +
117B LEU* 3.1 7.3 + - + +
118B ILE* 2.8 44.8 + - + +
195B TRP* 3.6 37.9 - - + +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B SER* 3.2 9.7 + - - +
114B LEU* 1.3 84.2 - - - +
116B GLU* 1.3 56.6 + - + +
118B ILE* 3.3 16.2 + - - +
119B MLY 2.9 57.7 + - - +
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 3.1 27.5 - - + +
112B GLY* 3.3 8.3 - - - -
113B SER* 3.0 34.9 + - - +
114B LEU 3.2 0.2 - - - -
115B ASP* 1.3 74.6 - - + +
117B LEU* 1.3 60.2 + - - +
119B MLY 3.4 13.8 + - + +
120B LEU* 3.0 29.1 + - - +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ILE* 3.8 36.8 - - + -
111B PHE* 3.7 37.1 - - + +
113B SER 3.2 8.9 + - - +
114B LEU* 3.1 10.6 + - + +
116B GLU* 1.3 77.6 - - - +
118B ILE* 1.3 58.4 + - - +
120B LEU* 3.4 3.7 + - + +
121B THR* 2.8 34.8 + - - +
136B ILE* 4.0 32.1 - - + -
146B LEU* 5.2 0.4 - - + -
148B VAL* 3.7 26.2 - - + -
195B TRP* 4.2 9.6 - - + -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 2.8 40.5 + - + +
115B ASP* 3.6 15.9 - - - +
117B LEU* 1.3 78.6 - - + +
119B MLY 1.3 60.2 + - + +
121B THR* 3.2 7.4 + - - -
122B ASN* 2.9 35.7 + - - +
187B MLY 6.3 2.2 - - - -
190B TRP* 3.5 62.8 - - + +
195B TRP* 4.4 11.0 - - + +
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Residues in contact with MLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASP* 2.9 43.6 + - - +
116B GLU* 3.9 13.7 - - + +
117B LEU 3.3 0.2 - - - -
118B ILE* 1.3 77.2 + - + +
120B LEU* 1.3 64.7 + - - +
122B ASN* 3.3 9.3 + - - +
123B THR* 3.0 27.5 + - - +
187B MLY 5.1 19.3 - - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 3.7 31.0 - - + -
116B GLU 3.0 17.9 + - - +
117B LEU* 3.6 3.6 - - + +
119B MLY 1.3 75.1 + - - +
121B THR* 1.3 64.7 + - - +
123B THR* 3.1 10.9 + - + -
124B MLY 3.0 38.5 + - - +
147B ASP* 5.6 0.4 - - - +
148B VAL* 3.7 23.8 - - + +
141D SER* 3.7 32.1 - - - +
160D PRO* 6.4 0.2 - - + -
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU 2.8 21.8 + - - -
118B ILE 3.2 4.7 + - - -
120B LEU* 1.3 77.0 - - - +
122B ASN* 1.3 57.5 + - - +
124B MLY 3.0 3.8 + - - +
125B LEU* 2.8 37.0 + - + +
134B ALA* 4.1 16.4 - - + -
136B ILE* 3.7 26.3 - - + +
148B VAL* 3.7 19.8 - - + +
167B ILE* 4.8 3.8 - - + -
190B TRP* 3.6 27.6 - - + -
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Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ILE* 2.9 27.0 + - - +
119B MLY 3.8 9.8 - - - +
121B THR* 1.3 75.9 - - - +
123B THR* 1.3 57.7 + - - +
125B LEU* 3.8 9.9 - - - +
126B ALA* 3.0 29.3 + - - +
186B PHE* 3.3 29.2 + - + +
187B MLY 4.0 16.8 - - - +
190B TRP* 2.8 33.8 + - - +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B MLY 3.0 15.6 + - - +
120B LEU* 3.1 16.7 + - + -
122B ASN* 1.3 78.0 - - - +
124B MLY 1.3 64.5 + - + +
126B ALA* 3.4 6.4 + - + +
127B GLY* 3.1 18.9 + - - -
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Residues in contact with MLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 3.0 31.0 + - + +
121B THR 3.5 6.7 - - - +
123B THR* 1.3 77.1 + - + +
125B LEU* 1.3 64.0 + - - +
127B GLY 3.1 3.1 + - - -
128B VAL* 3.4 4.3 + - - +
134B ALA* 4.5 5.2 - - + -
147B ASP* 5.2 3.1 - - - -
148B VAL* 3.5 50.5 - - + +
149B VAL* 4.7 0.9 - - - -
150B GLN* 2.8 64.0 + - + +
139D ASN* 5.3 3.6 - - - -
141D SER* 4.0 21.5 - - - -
160D PRO* 4.1 24.1 - - - +
161D LEU* 5.8 6.7 - - - -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 2.8 29.8 + - + +
122B ASN* 3.8 17.7 - - - +
123B THR 3.3 0.2 - - - -
124B MLY 1.3 72.0 + - - +
126B ALA* 1.3 63.1 + - - +
128B VAL* 3.1 24.7 + - - +
133B TRP 4.4 0.2 - - - -
134B ALA* 3.5 32.8 - - + +
167B ILE* 3.6 41.1 - - + +
169B ALA* 3.8 17.8 - - + +
182B MLY 5.3 1.2 + - - +
186B PHE* 3.7 37.6 - - + -
190B TRP* 4.8 1.8 - - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASN 3.0 18.2 + - - +
123B THR* 3.7 6.3 - - - +
124B MLY 3.3 0.2 - - - -
125B LEU* 1.3 77.1 - - - +
127B GLY* 1.3 58.2 + - - +
128B VAL 3.2 2.1 + - - +
129B GLN* 5.3 1.2 - - - +
182B MLY 3.3 37.0 + - + -
183B ALA* 6.0 4.9 - - + -
186B PHE* 3.7 15.4 - - + -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLN* 4.7 4.0 + - - -
123B THR 3.1 12.8 + - - -
124B MLY 3.1 4.9 + - - -
125B LEU 3.0 1.2 - - - -
126B ALA* 1.3 76.6 - - - +
128B VAL* 1.3 58.6 + - - +
129B GLN* 3.2 20.4 + - - +
150B GLN* 3.5 17.9 + - - -
152B TYR* 3.6 7.1 + - - -
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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