Contacts of the helix formed by residues 168 - 185 (chain A) in PDB entry 1Y88
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 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ARG* 4.4 0.7 - - - -
166A GLY 3.7 2.6 + - - -
167A LEU* 1.3 74.8 - - - +
169A ALA* 1.3 57.3 + - - +
170A LYS* 3.4 10.1 + - - +
171A LYS* 2.9 28.1 + - - +
172A ALA* 2.8 27.5 + - - +
307A SO4 3.4 25.1 - - - -
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Residues in contact with ALA 169 (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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159A GLU* 4.2 6.0 - - - +
163A ARG* 3.7 32.7 - - - +
168A SER* 1.3 71.3 - - - +
170A LYS* 1.3 58.0 + - - +
172A ALA* 3.4 3.1 + - - +
173A ARG* 3.0 47.4 + - - +
307A SO4 2.7 23.4 + - - +
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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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168A SER* 3.2 8.8 + - - +
169A ALA* 1.3 78.9 - - - +
171A LYS* 1.3 62.1 + - - +
173A ARG* 3.3 30.4 + - - +
174A GLU* 2.8 58.1 + - + +
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Residues in contact with LYS 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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134A ARG 3.6 20.8 + - - -
135A ILE* 4.3 7.7 - - - +
136A ASP* 5.0 4.4 + - - +
139A VAL* 4.1 23.3 - - + +
167A LEU* 3.9 17.7 - - + -
168A SER* 2.9 26.0 + - - +
170A LYS* 1.3 76.4 - - - +
172A ALA* 1.3 57.8 + - - +
174A GLU* 3.2 20.2 + - + +
175A VAL* 2.9 47.1 + - + +
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Residues in contact with ALA 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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159A GLU* 4.0 17.7 - - + +
162A LEU* 3.8 27.9 - - + +
163A ARG* 4.4 4.7 - - + -
167A LEU* 3.9 14.5 - - + +
168A SER 2.8 17.2 + - - +
169A ALA 3.6 5.4 - - - +
171A LYS* 1.3 76.9 - - - +
173A ARG* 1.3 62.2 + - - +
175A VAL 3.4 0.2 + - - -
176A ILE* 3.0 31.4 + - - +
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Residues in contact with ARG 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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159A GLU* 4.5 16.4 + - + +
169A ALA* 3.0 36.7 + - - +
170A LYS* 3.3 38.5 + - - +
172A ALA* 1.3 75.0 - - - +
174A GLU* 1.3 58.1 + - + +
176A ILE* 3.6 7.3 + - - +
177A ALA* 3.0 30.0 + - - +
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Residues in contact with GLU 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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170A LYS* 2.8 50.3 + - + +
171A LYS* 3.2 29.1 + - + +
173A ARG* 1.3 75.5 - - + +
175A VAL* 1.3 60.5 + - + +
177A ALA* 3.3 7.1 + - - +
178A GLU* 2.9 38.3 + - + +
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Residues in contact with VAL 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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133A LEU* 4.0 17.8 - - + +
135A ILE* 3.7 24.2 - - + -
139A VAL* 4.7 0.2 - - + -
143A LEU* 4.5 11.4 - - + -
154A VAL* 3.6 23.8 - - + -
162A LEU* 4.9 2.0 - - + -
167A LEU* 4.1 16.2 - - + -
171A LYS* 2.9 36.0 + - + +
172A ALA 4.0 2.7 - - - +
174A GLU* 1.3 75.0 - - + +
176A ILE* 1.3 58.4 - - - +
178A GLU* 3.3 9.4 + - - +
179A ALA* 2.9 27.5 + - - +
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Residues in contact with ILE 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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154A VAL* 4.0 17.7 - - + +
155A VAL* 5.0 8.7 - - + +
158A GLY* 3.8 4.0 - - - -
159A GLU* 3.2 48.7 - - + +
162A LEU* 3.6 15.5 - - + -
172A ALA 3.0 18.5 + - - +
173A ARG* 3.9 4.9 - - - +
175A VAL* 1.3 76.0 - - - +
177A ALA* 1.3 57.3 + - - +
179A ALA* 3.2 3.2 + - - +
180A LYS* 2.9 56.7 + - + +
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Residues in contact with ALA 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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173A ARG 3.0 18.7 + - - +
174A GLU* 3.3 6.5 + - - +
176A ILE* 1.3 78.4 - - - +
178A GLU* 1.3 62.5 + - + +
180A LYS* 3.4 10.3 + - - +
181A LYS* 3.0 24.8 + - - +
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Residues in contact with GLU 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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133A LEU* 3.6 18.1 - - + +
134A ARG* 3.0 78.2 + - - +
135A ILE* 4.7 2.4 - - - +
174A GLU* 2.9 26.2 + - + +
175A VAL* 3.6 9.4 - - - +
176A ILE 3.3 0.2 - - - -
177A ALA* 1.3 75.5 - - + +
179A ALA* 1.3 63.8 + - - +
181A LYS* 3.2 8.3 + - - +
182A VAL* 3.0 26.7 + - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LEU* 4.0 12.3 - - + +
151A CYS* 3.7 33.8 - - + +
154A VAL* 4.0 13.0 - - + -
155A VAL* 4.0 6.7 - - + -
175A VAL 2.9 16.3 + - - +
176A ILE 3.7 4.0 - - - +
178A GLU* 1.3 78.0 - - - +
180A LYS* 1.3 61.3 + - - +
182A VAL* 3.3 3.1 + - - +
183A ILE* 3.0 30.0 + - - +
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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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155A VAL* 4.0 24.9 - - + -
176A ILE* 2.9 40.9 + - + +
177A ALA* 3.7 8.9 - - - +
179A ALA* 1.3 78.0 - - - +
181A LYS* 1.3 56.5 + - - +
183A ILE* 3.3 5.7 + - - +
184A GLY* 2.9 26.7 + - - -
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Residues in contact with LYS 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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134A ARG* 5.4 11.0 - - - +
177A ALA 3.0 16.6 + - - +
178A GLU* 3.5 8.1 - - - +
179A ALA 3.2 0.2 - - - -
180A LYS* 1.3 74.3 - - - +
182A VAL* 1.3 65.1 + - + +
184A GLY* 3.8 1.4 - - - -
185A GLY* 3.0 23.2 + - - -
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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
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128A TYR* 3.6 45.6 - - + -
132A ILE* 3.7 30.3 - - + -
133A LEU* 4.1 13.9 - - + -
151A CYS* 4.1 8.1 - - - -
178A GLU* 3.0 19.1 + - + +
179A ALA 3.7 7.2 - - - +
181A LYS* 1.3 74.6 - - + +
183A ILE* 1.3 64.3 + - - +
185A GLY* 3.2 13.4 + - - -
186A SER* 4.0 4.7 + - - -
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Residues in contact with ILE 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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128A TYR* 4.2 21.8 + - + -
151A CYS* 3.7 16.2 - - + +
152A ARG* 3.6 36.6 - - + +
155A VAL* 4.2 12.3 - - + -
179A ALA 3.0 17.0 + - - +
180A LYS* 3.8 5.4 - - - +
182A VAL* 1.3 76.2 - - - +
184A GLY* 1.3 59.2 + - - +
185A GLY 3.6 0.5 + - - -
186A SER* 4.4 10.9 + - - -
201A CL 4.4 2.0 - - + -
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Residues in contact with GLY 184 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A LYS 2.9 16.2 + - - -
181A LYS* 3.8 2.2 - - - -
182A VAL 3.3 0.2 - - - -
183A ILE* 1.3 78.0 - - - +
185A GLY* 1.3 57.6 + - - +
186A SER* 3.5 2.9 + - - +
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Residues in contact with GLY 185 (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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181A LYS* 3.0 16.1 + - - -
182A VAL* 3.2 5.8 + - - -
184A GLY* 1.3 77.9 - - - +
186A SER* 1.3 64.2 + - - +
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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