Contacts of the helix formed by residues 166 - 180 (chain A) in PDB entry 5L9Y
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A TYR* 1.3 76.4 - - - +
167A ARG* 1.3 64.6 + - - +
168A SER* 3.4 11.3 - - - -
169A SER* 3.1 35.7 + - - -
170A VAL* 3.2 15.4 + - - +
104B PHE* 4.1 3.4 - - - -
105B ASP 4.1 6.7 - - - -
108B LYS* 3.9 35.1 - - - +
109B GLU* 4.0 9.4 + - - -
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER* 1.3 72.8 - - - +
168A SER* 1.3 62.5 + - - +
170A VAL* 3.3 4.5 + - - +
171A ASP* 3.0 29.5 + - - +
210A TYR* 3.5 45.8 + - + +
214A LYS* 5.8 1.8 - - - +
104B PHE* 3.6 28.2 - - + -
105B ASP 4.5 2.0 + - - -
106B PRO* 3.1 31.1 + - + +
107B LYS 5.2 1.8 + - - -
108B LYS 4.5 12.6 + - - +
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Residues in contact with SER 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER* 3.4 10.7 - - - -
167A ARG* 1.3 77.5 - - - +
169A SER* 1.3 55.8 + - - +
171A ASP* 3.1 13.8 + - - +
172A VAL* 3.0 31.2 + - - +
72B LEU* 4.4 17.8 - - - +
109B GLU* 4.0 15.3 - - - -
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 4.3 14.6 - - - +
166A SER* 3.1 27.1 + - - -
168A SER* 1.3 75.0 + - - +
170A VAL* 1.3 65.1 + - - +
172A VAL* 3.4 3.1 + - - -
173A LEU* 3.1 20.7 + - - +
66B ALA* 4.6 11.7 + - - -
71B PHE* 3.5 33.2 - - - +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 4.0 16.6 - - + -
166A SER 3.2 13.3 + - - +
167A ARG 3.4 7.9 - - - +
169A SER* 1.3 76.2 - - - +
171A ASP* 1.3 59.2 + - - +
173A LEU* 3.3 10.2 + - + +
174A TYR* 2.9 28.7 + - + +
184A LEU* 5.7 0.3 - - - +
186A PHE* 5.0 9.9 - - + -
207A LEU* 3.8 23.3 - - + -
210A TYR* 4.1 13.2 - - + -
211A CYS* 4.3 13.9 - - - -
216A TYR* 4.0 21.5 - - + -
218A ILE* 5.5 3.1 - - + -
104B PHE* 4.3 6.1 - - + -
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 3.0 19.7 + - - +
168A SER* 3.1 10.6 + - - +
170A VAL* 1.3 73.5 - - - +
172A VAL* 1.3 58.5 + - + +
174A TYR* 4.1 0.3 - - - +
175A THR* 2.5 39.7 + - - +
210A TYR* 2.6 26.5 + - - -
214A LYS* 4.2 8.0 + - - -
216A TYR* 2.5 32.3 + - - +
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A SER* 3.0 19.1 + - - +
169A SER* 3.7 7.9 - - - +
170A VAL 3.3 0.2 - - - -
171A ASP* 1.3 76.2 - - + +
173A LEU* 1.3 60.0 + - - +
175A THR* 3.6 4.5 - - - -
176A PHE* 2.9 30.0 + - - +
71B PHE* 3.9 27.4 - - + +
72B LEU* 3.8 38.4 - - + +
75B LEU* 3.6 27.3 - - + +
81B ARG* 4.8 2.7 + - - +
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Residues in contact with LEU 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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169A SER 3.1 11.3 + - - +
170A VAL* 3.5 11.4 - - + +
172A VAL* 1.3 81.2 - - - +
174A TYR* 1.3 61.5 + - - +
176A PHE* 3.4 2.9 + - - +
177A ALA* 3.1 22.3 + - - +
184A LEU* 4.0 22.7 - - + -
186A PHE* 3.9 16.8 - - + -
61B ILE* 5.4 4.9 - - + -
71B PHE* 4.4 5.6 - - + -
75B LEU* 4.1 20.2 - - + -
92B LEU* 4.6 9.9 - - + -
94B PHE* 3.4 59.0 - - + -
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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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170A VAL* 2.9 20.2 + - + +
171A ASP 4.1 2.7 - - - +
173A LEU* 1.3 73.2 - - - +
175A THR* 1.3 57.2 + - - +
177A ALA* 3.3 3.8 + - + +
178A ASN* 2.8 63.2 + - + +
184A LEU* 4.2 16.1 - - + +
215A GLY 4.3 3.1 + - - -
216A TYR* 3.4 67.7 - + + -
217A ASN* 3.2 36.5 + - - +
218A ILE* 4.0 11.4 - - + -
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Residues in contact with THR 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 ASP* 2.5 27.2 + - - +
172A VAL* 3.6 4.9 - - - -
174A TYR* 1.3 78.0 - - - +
176A PHE* 1.3 60.7 + - - +
178A ASN* 4.5 3.1 - - - +
179A CYS* 2.9 45.2 + - - +
216A TYR* 5.3 1.4 + - - -
81B ARG* 3.6 20.0 - - - +
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Residues in contact with PHE 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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172A VAL 2.9 17.1 + - - +
173A LEU 3.6 3.8 - - - +
175A THR* 1.3 77.5 - - - +
177A ALA* 1.3 63.8 + - - +
179A CYS* 3.9 0.9 - - - +
180A SER* 2.9 33.5 + - - -
182A LEU* 4.4 10.1 - - + -
385A PHE* 3.9 19.7 - + - -
61B ILE* 5.0 3.4 - - + -
75B LEU* 3.3 47.3 - - + +
80B LEU* 4.1 23.6 - - + -
81B ARG* 3.9 28.0 - - + +
84B ALA* 3.8 19.7 - - + -
92B LEU* 3.8 30.5 - - + -
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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 LEU 3.1 10.8 + - - +
174A TYR* 3.7 7.6 - - + +
176A PHE* 1.3 83.8 - - - +
178A ASN* 1.3 62.3 + - - +
180A SER* 3.2 7.2 + - - -
182A LEU* 3.0 46.2 + - + +
184A LEU* 4.1 20.4 - - + +
92B LEU* 3.9 17.9 - - + -
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Residues in contact with ASN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TYR* 2.8 51.9 + - + +
175A THR* 4.1 3.4 - - - +
177A ALA* 1.3 74.9 - - - +
179A CYS* 1.3 67.2 + - - +
180A SER 3.3 0.9 + - - -
181A GLY* 3.4 9.9 + - - -
182A LEU 4.3 3.6 + - - +
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Residues in contact with CYS 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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175A THR* 2.9 34.9 + - - +
176A PHE 4.2 1.8 - - - +
178A ASN* 1.3 78.9 - - - +
180A SER* 1.3 59.0 + - - +
181A GLY 3.5 0.4 + - - -
81B ARG* 3.7 26.9 - - - +
85B ARG* 3.1 28.6 + - - +
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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
----------------------------------------------------------
176A PHE* 2.9 21.7 + - - -
177A ALA 3.2 3.5 + - - -
179A CYS* 1.3 78.4 - - - +
181A GLY* 1.3 60.0 + - - +
182A LEU* 3.3 13.2 + - - +
81B ARG* 3.7 20.1 + - - +
84B ALA* 3.4 31.3 - - - +
85B ARG* 3.4 29.7 - - - +
88B SER* 3.7 6.6 - - - -
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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