Contacts of the helix formed by residues 170 - 182 (chain A) in PDB entry 3LIO
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 VAL 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A TYR* 5.1 0.7 - - - -
167A TYR* 3.0 22.3 + - - +
168A ARG* 3.3 2.1 - - + -
169A ASN* 1.3 94.1 - - - +
171A ARG* 1.3 64.5 + - - +
172A PRO* 3.8 16.6 - - + -
173A ASP* 3.0 43.3 + - + +
174A TYR 3.3 7.3 + - - -
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Residues in contact with ARG 171 (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 2.9 25.7 + - - -
115A VAL* 3.4 26.4 + - + +
117A ASN* 2.8 23.6 + - - +
118A PHE* 5.1 0.2 - - - +
119A GLY 3.1 28.5 + - - +
158A LEU* 3.1 33.1 + - + +
160A GLU* 5.3 3.4 - - - +
163A TYR* 2.9 39.4 + - + +
169A ASN 3.2 7.4 + - - +
170A VAL* 1.3 72.6 - - - +
172A PRO* 1.3 70.5 - - + +
174A TYR* 3.0 9.9 + - - +
175A LEU* 2.8 28.1 + - + +
159B TRP* 5.8 2.8 - - - -
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Residues in contact with PRO 172 (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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115A VAL* 4.2 15.0 - - + -
169A ASN 5.2 0.2 - - - +
170A VAL* 3.3 15.7 - - + -
171A ARG* 1.3 93.7 - - + +
173A ASP* 1.3 59.7 + - - +
175A LEU* 3.3 11.7 + - + +
176A LYS* 3.0 32.5 + - + +
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Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 3.5 31.3 + - + -
170A VAL* 3.0 31.6 + - + +
172A PRO* 1.3 79.9 - - - +
174A TYR* 1.4 65.5 + - - +
176A LYS* 3.2 22.7 + - - +
177A GLY 3.1 15.8 + - - -
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Residues in contact with TYR 174 (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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18A ILE* 4.4 14.6 - - + -
76A TYR* 2.7 35.6 + + - -
156A VAL* 4.9 4.8 - - + -
157A ASP 2.7 30.7 + - - -
158A LEU* 3.9 18.2 - - + -
162A ALA* 3.7 17.5 - - + +
163A TYR* 3.5 35.4 - + + -
167A TYR* 3.6 30.0 - + + -
170A VAL 3.3 3.5 + - - +
171A ARG* 3.0 12.5 + - - +
173A ASP* 1.4 81.3 - - - +
175A LEU* 1.3 64.3 - - + +
177A GLY* 2.9 5.5 + - - -
178A PHE* 2.9 32.2 + + + +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.7 6.7 - - + -
111A ASN* 3.7 29.4 - - - +
114A ALA* 3.8 26.9 - - + -
115A VAL* 3.6 31.9 - - + +
156A VAL* 4.7 13.9 - - + -
158A LEU* 4.7 6.5 - - + -
171A ARG* 2.8 21.1 + - + +
172A PRO* 3.7 7.0 - - + +
173A ASP 3.2 0.2 - - - -
174A TYR* 1.3 81.6 - - + +
176A LYS* 1.3 64.9 + - - +
178A PHE* 3.1 16.8 + - + +
179A TRP* 3.0 29.7 + - + -
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Residues in contact with LYS 176 (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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17A HIS* 5.4 0.2 - - - -
172A PRO 3.0 20.1 + - - +
173A ASP* 3.4 23.8 + - - +
175A LEU* 1.3 75.4 - - - +
177A GLY* 1.3 62.8 + - - +
179A TRP* 3.4 10.2 + - + +
180A SER* 3.2 24.6 + - - -
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Residues in contact with GLY 177 (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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17A HIS* 3.9 27.8 - - - -
18A ILE* 5.7 1.3 - - - -
167A TYR* 4.2 8.9 + - - -
173A ASP 3.1 9.1 + - - -
174A TYR* 2.9 9.3 + - - -
176A LYS* 1.3 76.3 - - - +
178A PHE* 1.4 63.5 + - - +
180A SER* 3.0 12.0 + - - -
181A LEU* 3.2 21.0 + - - +
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Residues in contact with PHE 178 (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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18A ILE* 5.9 1.5 - - - +
76A TYR* 5.2 2.7 - + - -
79A SER* 4.3 8.5 - - - -
80A LEU* 3.8 24.5 - - + -
110A LEU* 5.0 5.2 - - + -
154A LEU* 5.0 9.9 - - + -
155A THR 3.8 13.0 - - - -
156A VAL* 3.2 39.5 - - + -
174A TYR* 2.9 21.8 + + + +
175A LEU* 3.1 18.4 + - + +
177A GLY* 1.4 76.0 - - - +
179A TRP* 1.4 98.2 + + - +
181A LEU* 2.9 9.7 + - - -
182A VAL* 2.8 47.1 + - + +
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Residues in contact with TRP 179 (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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85A GLY* 3.2 18.5 - - - -
86A GLY 3.4 8.0 + - - +
103A PHE* 4.0 25.1 - + + -
106A PHE* 3.6 35.9 - + - -
107A LYS* 3.5 50.3 - - + +
110A LEU* 3.9 28.5 - - + -
111A ASN* 2.9 27.8 + - - +
154A LEU* 6.3 0.4 - - + -
175A LEU* 3.0 34.0 + - - +
176A LYS* 4.0 9.0 - - - +
177A GLY 3.3 0.2 - - - -
178A PHE* 1.4 94.8 - + - +
180A SER* 1.3 58.3 + - - +
182A VAL* 3.5 14.1 - - + +
184A TRP* 4.2 9.0 - + - -
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Residues in contact with SER 180 (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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17A HIS* 3.5 36.4 + - - -
81A SER 4.8 0.5 - - - +
84A GLY 3.7 5.2 - - - +
85A GLY* 3.3 16.6 + - - -
86A GLY 4.9 1.3 - - - +
176A LYS 3.2 11.6 + - - -
177A GLY 3.0 10.4 + - - -
179A TRP* 1.3 77.9 - - - +
181A LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 181 (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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14A LEU* 3.9 39.7 - - + +
17A HIS* 3.7 24.0 - - + -
18A ILE* 3.7 37.7 - - + -
80A LEU* 3.4 17.8 - - + -
81A SER 2.8 42.8 + - - +
82A PRO* 5.0 2.2 - - + -
84A GLY* 3.8 1.2 - - - -
85A GLY 3.6 2.0 - - - -
177A GLY 3.3 11.9 - - - +
178A PHE* 2.9 6.1 + - - +
180A SER* 1.3 78.8 - - - +
182A VAL* 1.3 69.7 + - - +
183A ASN 3.2 0.3 + - - -
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER 3.5 7.4 - - - +
84A GLY* 3.2 2.9 - - - -
85A GLY* 2.8 27.1 + - - +
86A GLY 4.5 0.7 - - - +
154A LEU* 3.5 31.0 - - + -
178A PHE* 2.8 33.1 + - + +
179A TRP* 3.5 25.4 - - + +
181A LEU* 1.3 73.5 - - - +
183A ASN* 1.3 63.6 + - - +
184A TRP* 3.3 46.7 + - + +
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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