Contacts of the helix formed by residues 169 - 184 (chain A) in PDB entry 2LV9
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 ASP 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A CYS 4.1 4.8 - - - +
167A ASN* 5.1 2.1 - - - +
168A LEU* 1.3 70.4 - - - +
170A LYS* 1.3 59.7 + - - +
171A GLU* 3.4 2.5 - - - +
172A ARG* 3.5 24.6 - - + +
173A ALA* 3.1 24.9 + - - +
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Residues in contact with LYS 170 (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* 3.7 45.0 - - + +
147A MET* 5.7 1.1 - - - -
161A GLU* 3.0 31.0 + - + +
162A ARG* 3.1 32.9 - - - +
167A ASN* 5.5 0.7 - - - +
168A LEU* 2.8 13.9 + - - +
169A ASP* 1.3 69.0 - - - +
171A GLU* 1.3 61.3 + - - +
173A ALA* 3.3 4.2 + - - +
174A VAL* 3.0 33.8 + - + +
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Residues in contact with GLU 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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169A ASP* 3.4 0.9 - - - -
170A LYS* 1.3 79.8 - - - +
172A ARG* 1.3 56.8 + - - +
174A VAL* 3.1 12.8 + - + +
175A LEU* 2.9 47.6 + - + +
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Residues in contact with ARG 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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169A ASP* 3.5 30.7 + - + +
170A LYS 3.3 0.4 - - - -
171A GLU* 1.3 76.1 - - - +
173A ALA* 1.3 60.5 - - - +
175A LEU* 3.3 31.7 + - - +
176A LEU* 3.1 28.8 + - + +
179A ARG* 6.3 0.8 - - - +
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Residues in contact with ALA 173 (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* 3.7 23.6 - - + -
123A CYS* 3.3 11.7 - - - +
145A ASP 5.6 0.4 - - - -
146A CYS* 3.2 36.3 - - + +
169A ASP 3.1 10.3 + - - +
170A LYS 3.3 10.8 - - - +
172A ARG* 1.3 74.5 - - - +
174A VAL* 1.4 62.3 + - - +
176A LEU* 3.6 5.3 + - - +
177A GLN* 3.3 21.7 + - - +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE 3.5 22.4 - - - +
123A CYS* 3.8 20.0 - - - +
170A LYS* 3.0 25.0 + - + +
171A GLU* 3.1 12.3 + - + +
173A ALA* 1.4 73.8 - - - +
175A LEU* 1.4 56.7 + - + +
176A LEU 3.3 0.2 + - - -
177A GLN* 3.4 1.2 + - - +
178A ARG* 2.8 54.9 + - + +
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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
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171A GLU* 2.9 36.5 + - + +
172A ARG* 3.3 43.7 + - - +
174A VAL* 1.4 79.3 - - + +
176A LEU* 1.3 55.8 + - - +
178A ARG* 4.0 9.8 - - - +
179A ARG* 3.0 36.8 + - - +
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Residues in contact with LEU 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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145A ASP* 3.6 41.7 - - + +
146A CYS* 4.6 3.8 - - - +
172A ARG* 3.1 17.0 + - + +
173A ALA* 3.8 6.3 - - - +
174A VAL 3.3 0.2 - - - -
175A LEU* 1.3 75.5 - - - +
177A GLN* 1.3 69.0 + - + +
179A ARG* 3.2 19.9 - - + +
180A LYS* 3.0 28.4 + - + +
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Residues in contact with GLN 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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123A CYS* 3.4 25.1 - - + -
125A PHE* 3.2 28.4 - - + -
129A ASP* 3.1 33.3 + - - +
143A HIS* 3.4 17.6 + - - +
145A ASP* 5.2 4.0 + - - +
146A CYS* 3.2 29.9 - - - -
173A ALA 3.3 4.2 + - - +
176A LEU* 1.3 86.7 - - + +
178A ARG* 1.3 63.2 + - - +
180A LYS* 3.2 22.6 - - - +
181A ARG* 3.3 21.0 + - - +
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Residues in contact with ARG 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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123A CYS 5.6 1.7 + - - +
125A PHE* 6.1 0.2 - - - -
174A VAL* 2.8 34.5 + - + +
175A LEU* 4.0 10.2 - - - +
177A GLN* 1.3 74.2 - - - +
179A ARG* 1.4 58.3 + - - +
180A LYS 3.1 1.1 - - - -
181A ARG* 3.0 51.2 + - - +
182A GLU* 3.0 33.4 + - + +
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Residues in contact with ARG 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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172A ARG* 6.3 0.9 - - - +
175A LEU* 3.0 26.6 + - - +
176A LEU* 3.2 26.3 - - + +
178A ARG* 1.4 75.5 - - - +
180A LYS* 1.3 56.6 + - - +
182A GLU* 3.7 13.0 - - - +
183A ASN* 2.9 31.7 + - - +
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Residues in contact with LYS 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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125A PHE* 3.8 16.2 - - + -
128A ASP* 3.0 28.7 + - - -
129A ASP* 3.0 36.7 + - - +
176A LEU* 3.0 20.9 + - + +
177A GLN* 3.2 32.1 - - - +
179A ARG* 1.3 77.4 - - - +
181A ARG* 1.4 57.7 + - - +
183A ASN* 3.3 7.1 + - - +
184A MET* 3.1 38.8 + - + +
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Residues in contact with ARG 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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124A GLY 4.6 12.7 + - - -
125A PHE* 3.7 40.6 - - + +
177A GLN 3.3 6.0 + - - +
178A ARG* 3.0 49.8 + - - +
180A LYS* 1.4 76.2 - - - +
182A GLU* 1.4 78.8 + - - +
184A MET* 3.3 30.4 + - + +
185A SER* 3.9 2.6 + - - -
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Residues in contact with GLU 182 (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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178A ARG* 3.0 37.4 + - + +
179A ARG* 3.7 11.0 - - - +
181A ARG* 1.4 108.8 + - - +
183A ASN* 1.3 58.6 + - - +
185A SER* 3.1 22.3 + - - -
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Residues in contact with ASN 183 (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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179A ARG 2.9 19.3 + - - +
180A LYS* 3.5 8.2 + - - +
181A ARG 3.3 0.2 - - - -
182A GLU* 1.3 73.9 - - - +
184A MET* 1.3 59.7 + - - +
185A SER* 2.9 13.7 + - - +
186A ASP* 4.8 0.5 + - - -
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Residues in contact with MET 184 (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 PHE* 3.9 16.4 - - + -
128A ASP* 3.6 32.1 - - - +
180A LYS* 3.1 29.3 + - + +
181A ARG* 3.5 31.3 - - + +
182A GLU 3.3 1.2 - - - -
183A ASN* 1.3 75.9 - - - +
185A SER* 1.3 63.4 + - - +
186A ASP* 4.1 2.0 - - - -
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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