Contacts of the helix formed by residues 117 - 131 (chain B) in PDB entry 1LI5
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 HIS 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B PRO* 3.6 28.7 - - + +
113B ARG 3.4 10.3 + - - -
114B ALA 3.1 9.0 + - - +
116B HIS* 1.3 97.8 + - + +
118B ILE* 1.3 59.4 + - - +
119B ALA* 3.3 2.5 - - - +
120B GLU* 3.8 19.5 - - + +
121B ILE* 2.9 31.2 + - + +
212B MET* 3.3 34.0 + - + +
215B LYS* 5.2 8.5 - - + -
216B GLN* 4.4 11.2 + - - -
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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 ALA 4.1 10.1 - - - +
115B THR* 4.0 13.5 - - - +
116B HIS 3.7 2.0 + - - -
117B HIS* 1.3 73.6 - - - +
119B ALA* 1.3 60.1 + - - +
121B ILE* 3.1 5.0 + - + +
122B ILE* 2.8 31.8 + - + +
184B TRP* 4.0 15.7 - - + -
194B TRP* 3.7 61.0 - - + +
195B PRO* 5.7 0.9 - - + -
196B SER 6.3 0.9 - - - +
203B PRO* 4.0 25.6 - - + -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B HIS* 3.3 0.6 - - - +
118B ILE* 1.3 79.3 - - - +
120B GLU* 1.3 54.6 + - - +
122B ILE* 4.0 4.9 - - - +
123B GLU* 2.7 38.1 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B HIS* 3.4 30.6 + - + +
119B ALA* 1.3 78.6 - - - +
121B ILE* 1.3 63.5 + - - +
123B GLU* 3.8 5.3 - - - +
124B LEU* 3.1 24.4 + - - +
211B ALA* 3.6 24.1 - - + +
214B CYS* 6.2 0.2 - - - -
215B LYS* 5.6 4.7 - - + -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ALA* 4.2 13.9 - - + +
117B HIS* 2.9 28.1 + - + +
118B ILE* 3.1 10.7 + - + +
120B GLU* 1.3 76.8 - - - +
122B ILE* 1.3 63.0 + - - +
124B LEU* 3.2 5.5 + - - +
125B THR* 3.0 26.0 + - - +
183B LEU 4.9 0.2 - - - +
184B TRP* 4.1 22.9 - - + -
203B PRO* 3.9 26.7 - - + -
207B ILE* 3.6 25.6 - - + +
208B GLU* 4.1 23.8 - - + +
211B ALA* 3.7 18.4 - - + -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 2.8 24.2 + - + +
119B ALA* 4.0 5.6 - - - +
121B ILE* 1.3 72.5 - - - +
123B GLU* 1.3 56.7 + - - +
125B THR* 3.0 3.7 + - - -
126B GLU* 2.8 37.0 + - - +
184B TRP* 5.5 3.6 - - + -
196B SER* 5.4 5.4 - - - -
197B PRO* 5.2 8.5 - - + -
198B TRP* 3.6 25.2 - - + -
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Residues in contact with GLU 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 ALA 2.7 23.7 + - - +
120B GLU* 3.8 6.1 - - - +
122B ILE* 1.3 72.2 - - - +
124B LEU* 1.3 58.0 + - - +
126B GLU* 3.4 7.1 + - - +
127B GLN* 3.0 28.6 + - - +
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Residues in contact with LEU 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 GLU 3.1 18.6 + - - +
121B ILE 3.4 4.7 - - - +
122B ILE 3.1 0.2 - - - -
123B GLU* 1.3 75.1 - - - +
125B THR* 1.3 64.8 + - - +
127B GLN* 3.3 6.7 + - + +
128B LEU* 3.1 29.0 + - + +
207B ILE* 3.6 24.0 - - + -
210B SER* 3.8 15.0 - - - +
211B ALA* 3.6 32.1 - - + +
214B CYS* 5.0 3.4 - - - -
241B GLN* 5.0 4.9 - - + +
242B SER* 5.6 0.7 - - - -
245B ALA* 3.8 15.9 - - + -
246B HIS* 3.5 35.7 - - + +
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Residues in contact with THR 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 ILE* 3.0 18.8 + - - +
122B ILE* 3.0 2.5 + - - -
124B LEU* 1.3 75.0 - - - +
126B GLU* 1.3 58.2 + - - +
128B LEU* 2.9 12.5 + - - +
129B ILE* 2.9 26.2 + - - +
142B VAL* 3.5 33.4 - - + -
183B LEU* 3.9 20.1 + - + +
184B TRP* 4.9 2.9 - - + +
198B TRP* 3.5 27.0 - - + -
207B ILE* 4.1 15.0 - - - +
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Residues in contact with GLU 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 ILE 2.8 20.6 + - - +
123B GLU* 3.5 8.7 - - - +
125B THR* 1.3 74.0 - - - +
127B GLN* 1.3 52.1 + - - +
129B ILE* 3.1 5.4 + - - +
130B ALA* 2.7 37.8 + - - +
198B TRP* 3.9 15.6 - - + -
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Residues in contact with GLN 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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123B GLU 3.0 17.4 + - - +
124B LEU* 3.6 9.0 - - + +
125B THR 3.2 0.2 - - - -
126B GLU* 1.3 77.3 - - - +
128B LEU* 1.3 59.1 + - - +
130B ALA* 3.8 7.8 + - - +
131B LYS* 3.2 26.7 + - - +
245B ALA* 4.9 18.8 - - + +
246B HIS* 6.1 1.6 - - + -
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Residues in contact with LEU 128 (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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124B LEU* 3.1 19.1 + - + +
125B THR* 2.9 10.6 + - - +
127B GLN* 1.3 76.8 - - - +
129B ILE* 1.3 63.0 + - - +
130B ALA 3.3 0.2 - - - -
131B LYS* 3.4 2.1 + - - -
132B GLY 3.1 4.5 + - - -
133B HIS* 2.8 36.6 + - + +
134B ALA* 3.9 11.2 - - + -
144B PHE* 4.2 11.2 - - + -
183B LEU* 3.6 32.5 - - + -
207B ILE* 4.8 3.1 - - + -
241B GLN* 3.6 31.6 - - + +
244B CYS* 3.9 15.0 - - + +
245B ALA* 3.7 21.5 - - + +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR 2.9 12.3 + - - +
126B GLU* 3.6 6.1 - - - +
128B LEU* 1.3 75.9 - - - +
130B ALA* 1.3 66.1 + - - +
132B GLY* 2.9 14.4 + - - -
134B ALA* 3.5 34.2 - - + +
135B TYR* 4.6 1.8 - - - +
136B VAL* 5.0 6.3 - - + -
142B VAL* 3.8 16.2 - - + -
198B TRP* 3.1 48.5 - - + +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLU 2.7 18.4 + - - +
127B GLN* 3.8 10.1 - - - +
129B ILE* 1.3 78.8 - - - +
131B LYS* 1.3 57.0 + - - +
132B GLY 3.7 0.3 + - - -
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Residues in contact with LYS 131 (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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127B GLN 3.2 17.1 + - - +
128B LEU 3.4 0.6 + - - +
129B ILE 3.1 1.2 - - - -
130B ALA* 1.3 75.9 - - + +
132B GLY* 1.3 65.0 + - - +
133B HIS* 3.5 27.1 + - + +
244B CYS 4.7 5.8 - - - +
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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