Contacts of the helix formed by residues 117 - 131 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PRO* 3.5 29.5 - - + +
113A ARG 3.0 11.0 + - - -
114A ALA 2.9 11.2 + - - +
116A HIS* 1.3 94.9 + + + +
118A ILE* 1.3 64.8 + - - +
119A ALA* 3.1 2.6 + - - -
120A GLU* 3.4 37.9 + - + -
121A ILE* 3.0 24.6 + - + +
212A MET* 2.9 35.8 - - + +
215A LYS* 5.9 2.9 - - + -
216A GLN* 4.7 11.6 + - - +
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA 3.5 6.3 - - - +
115A THR* 2.8 41.7 - - - +
116A HIS 3.8 0.8 - - - -
117A HIS* 1.3 76.6 - - - +
119A ALA* 1.3 59.9 + - - +
121A ILE* 3.0 8.3 + - - +
122A ILE* 2.8 33.2 + - + +
184A TRP* 4.0 16.2 - - + -
194A TRP* 3.7 56.1 - - + +
195A PRO* 4.8 6.3 - - + +
203A PRO* 4.9 12.6 - - + -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A HIS 3.1 0.6 - - - -
118A ILE* 1.3 79.2 - - - +
120A GLU* 1.3 68.9 + - - +
122A ILE* 3.0 9.4 + - - +
123A GLU* 3.0 25.7 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A HIS 4.5 1.4 - - - +
117A HIS* 3.4 51.4 - - + +
119A ALA* 1.3 84.7 - - - +
121A ILE* 1.3 64.0 + - - +
123A GLU* 3.8 8.3 - - + +
124A LEU* 3.1 25.5 + - - +
211A ALA* 3.6 26.0 - - - +
212A MET* 5.2 0.2 - - - -
214A CYS* 6.0 1.3 - - - -
215A LYS* 4.7 13.8 - - + +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA* 4.3 13.0 - - + +
117A HIS* 3.0 21.9 + - + +
118A ILE* 3.0 9.8 + - - +
120A GLU* 1.3 77.2 - - - +
122A ILE* 1.3 57.9 + - - +
124A LEU* 4.0 2.4 - - - +
125A THR* 2.8 34.5 + - - +
184A TRP* 4.3 23.6 - - + -
203A PRO* 3.7 25.4 - - + -
207A ILE* 3.5 23.8 - - + +
208A GLU* 3.8 26.9 - - + -
211A ALA* 3.6 20.9 - - + -
212A MET* 5.5 0.7 - - + -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 2.8 17.8 + - + +
119A ALA* 3.0 11.2 + - - +
121A ILE* 1.3 77.4 - - - +
123A GLU* 1.3 59.6 + - - +
125A THR* 3.1 8.4 + - - -
126A GLU* 2.9 40.0 + - + +
184A TRP* 5.7 3.8 - - + -
196A SER* 5.6 4.0 - - - -
197A PRO* 5.3 7.2 - - + -
198A TRP* 3.7 14.1 - - + -
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA 3.0 14.7 + - - +
120A GLU* 3.9 8.3 - - - +
121A ILE 3.5 0.2 - - - -
122A ILE* 1.3 77.4 - - - +
124A LEU* 1.3 65.2 + - - +
126A GLU* 2.8 28.0 + - - +
127A GLN* 2.9 13.6 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLU 3.1 14.9 + - - +
121A ILE 4.0 3.4 - - - +
123A GLU* 1.3 79.1 - - - +
125A THR* 1.3 62.6 + - - +
127A GLN* 3.3 7.1 + - - +
128A LEU* 3.2 39.8 + - + +
207A ILE* 3.9 12.1 - - + -
210A SER* 3.4 17.5 - - - +
211A ALA* 3.2 39.9 - - + +
214A CYS* 5.1 4.5 - - - -
241A GLN* 4.1 6.3 - - + +
242A SER* 5.9 0.2 - - - -
245A ALA* 3.8 20.0 - - + -
246A HIS* 4.9 11.2 - - + +
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Residues in contact with THR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 2.8 19.8 + - - +
122A ILE* 3.1 9.8 + - - -
123A GLU 3.1 0.6 - - - -
124A LEU* 1.3 79.4 - - - +
126A GLU* 1.3 60.5 + - - +
128A LEU* 3.3 12.6 + - - +
129A ILE* 3.2 21.0 + - - +
134A ALA* 4.9 0.2 - - - +
142A VAL* 3.7 28.5 - - + -
183A LEU* 4.3 16.8 + - + +
184A TRP* 4.7 3.8 - - + +
198A TRP* 3.3 27.3 - - + -
207A ILE* 4.0 13.2 - - - +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 2.9 19.8 + - - +
123A GLU* 2.8 23.8 + - - +
125A THR* 1.3 73.4 - - - +
127A GLN* 1.3 61.2 + - - +
129A ILE* 3.3 5.1 + - - +
130A ALA* 2.9 30.9 + - - +
197A PRO* 4.1 20.7 - - - +
198A TRP* 3.6 22.4 - - + -
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU 2.9 10.8 + - - +
124A LEU* 3.3 12.8 + - - +
126A GLU* 1.3 76.4 - - - +
128A LEU* 1.3 54.2 + - - +
130A ALA* 3.6 5.7 - - - +
131A LYS* 2.7 44.3 + - + +
245A ALA* 4.6 19.3 - - + +
246A HIS* 6.4 0.7 - - + -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.2 32.4 + - + +
125A THR* 3.6 9.0 - - - +
126A GLU 3.2 0.2 - - - -
127A GLN* 1.3 74.1 - - - +
129A ILE* 1.3 62.8 + - - +
131A LYS* 3.6 3.2 + - - -
132A GLY 3.4 2.8 + - - -
133A HIS* 2.8 35.0 + - + +
134A ALA* 3.3 12.7 + - + -
144A PHE* 4.0 17.7 - - + -
183A LEU* 3.7 25.1 - - + -
207A ILE* 4.7 1.3 - - + -
241A GLN* 3.6 26.9 - - + +
244A CYS* 3.9 16.8 - - + +
245A ALA* 3.7 20.9 - - + +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR 3.2 10.8 + - - +
126A GLU* 3.8 6.7 - - - +
128A LEU* 1.3 71.9 - - - +
130A ALA* 1.3 69.2 + - - +
132A GLY* 3.1 13.0 + - - -
134A ALA* 3.5 36.0 - - + +
135A TYR* 5.6 0.9 - - - -
136A VAL* 4.9 9.0 - - + +
142A VAL* 3.5 20.4 - - + -
198A TRP* 3.4 39.9 - - + +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU 2.9 18.0 + - - +
127A GLN* 3.6 7.4 - - - +
129A ILE* 1.3 80.3 - - - +
131A LYS* 1.3 60.0 + - + +
132A GLY 3.1 5.7 + - - -
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLN* 2.7 26.3 + - + +
128A LEU 4.3 0.7 - - - +
129A ILE 3.3 0.4 - - - -
130A ALA* 1.3 74.4 - - + +
132A GLY* 1.3 56.3 + - - -
133A HIS* 3.4 27.2 + - + +
244A CYS 3.6 17.9 + - - +
245A ALA* 3.7 22.7 - - - +
246A HIS 5.0 7.2 - - - +
247A ASP* 5.4 4.3 - - - +
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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