Contacts of the helix formed by residues 155 - 168 (chain A) in PDB entry 2PHG
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 ALA 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ARG* 1.3 80.9 - - + +
156A ASN* 1.3 65.8 + - - +
157A ASP* 3.3 4.9 - - - +
158A ALA* 3.5 21.3 - - + +
159A ILE* 3.0 30.6 + - - +
187A SER* 4.0 17.3 - - - +
190A GLU* 4.2 13.2 - - + +
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Residues in contact with ASN 156 (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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113A ALA* 2.8 47.5 - - + +
116A ASN* 3.2 30.1 - - - +
117A ALA* 3.1 20.1 + - - +
120A GLU* 4.2 10.7 + - - +
142A PHE* 6.0 0.9 - - - -
153A GLY 4.4 3.4 + - - +
154A ARG 4.0 1.8 + - - -
155A ALA* 1.3 71.9 - - - +
157A ASP* 1.3 67.7 + - - +
159A ILE* 3.9 6.3 - - - +
160A ALA* 2.9 31.7 + - - +
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Residues in contact with ASP 157 (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* 5.8 6.7 - - - +
155A ALA* 4.2 3.3 - - - +
156A ASN* 1.3 89.0 + - - +
158A ALA* 1.3 57.0 + - - +
160A ALA* 3.7 5.3 - - - +
161A SER* 2.7 33.7 + - - -
183A VAL* 4.6 9.1 - - + +
186A ILE* 3.3 37.9 - - + +
187A SER* 2.6 35.0 + - - -
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Residues in contact with ALA 158 (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 ALA* 3.2 15.8 + - + +
157A ASP* 1.3 80.6 - - - +
159A ILE* 1.3 60.3 + - + +
161A SER 3.2 1.7 + - - -
162A ALA* 2.9 27.0 + - - +
187A SER* 3.2 26.7 - - - +
190A GLU* 3.4 23.8 - - + -
191A ILE* 3.4 22.7 - - + +
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Residues in contact with ILE 159 (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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113A ALA* 6.2 0.7 - - + -
142A PHE* 3.5 24.7 - - + -
145A VAL* 3.6 31.6 - - + +
146A TYR* 5.5 3.8 - - + -
151A LEU* 4.8 13.0 - - + -
153A GLY* 3.8 30.3 - - - +
154A ARG* 4.2 5.2 - - + +
155A ALA 3.0 19.8 + - - +
156A ASN* 4.0 4.7 - - - +
158A ALA* 1.3 75.3 - - + +
160A ALA* 1.3 63.7 + - - +
162A ALA* 3.3 6.3 + - - +
163A CYS* 3.1 31.2 + - - -
190A GLU* 5.9 0.7 - - + -
194A CYS* 3.8 22.2 - - + -
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Residues in contact with ALA 160 (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 ALA* 3.7 24.2 - - + +
120A GLU* 4.9 6.5 - - + -
121A ILE* 3.8 28.8 - - + +
142A PHE* 4.5 2.6 - - - -
156A ASN 2.9 18.7 + - - +
157A ASP* 3.7 7.4 - - - +
159A ILE* 1.3 79.6 - - - +
161A SER* 1.3 57.1 + - - +
163A CYS* 3.5 0.9 + - - +
164A LEU* 3.1 27.8 + - - +
183A VAL* 6.1 2.0 - - + -
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Residues in contact with SER 161 (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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157A ASP 2.7 23.5 + - - -
158A ALA 3.7 0.2 - - - -
160A ALA* 1.3 73.2 - - - +
162A ALA* 1.3 61.0 + - - +
164A LEU* 3.5 12.5 - - - +
165A TYR* 2.9 30.8 + - - +
177A PHE* 4.9 3.0 - - - -
183A VAL* 3.2 33.3 + - - +
184A SER* 4.9 6.1 - - - -
191A ILE* 3.7 30.6 - - - +
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Residues in contact with ALA 162 (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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158A ALA 2.9 11.9 + - - +
159A ILE 3.4 11.0 - - - +
160A ALA 3.2 0.2 - - - -
161A SER* 1.3 79.0 - - - +
163A CYS* 1.3 63.9 + - - +
165A TYR 3.3 0.5 + - - -
166A ILE* 3.2 28.4 + - - +
191A ILE* 3.2 32.3 - - - +
194A CYS* 4.0 11.2 - - + -
195A PHE* 3.5 20.5 - - - +
198A ILE* 5.3 0.9 - - + -
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Residues in contact with CYS 163 (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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138A THR* 3.6 21.7 + - + +
141A LEU* 3.6 17.7 - - + +
142A PHE* 3.8 19.3 - - - -
145A VAL* 3.7 29.2 - - - -
159A ILE* 3.1 18.3 + - - +
160A ALA 4.0 1.1 - - - +
162A ALA* 1.3 76.2 - - - +
164A LEU* 1.3 60.2 + - - +
166A ILE* 3.3 9.6 + - - -
167A ALA* 3.0 28.4 + - - +
198A ILE* 3.9 10.5 - - - -
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Residues in contact with LEU 164 (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* 3.9 25.4 - - + +
124A MET* 4.8 14.6 - - + -
125A ALA* 5.0 5.2 - - + +
130A LEU* 4.7 11.2 - - + -
134A ILE* 3.7 27.1 - - + -
138A THR* 3.9 7.8 - - - +
160A ALA 3.1 18.4 + - - +
161A SER* 3.5 7.9 - - - +
162A ALA 3.2 0.2 - - - -
163A CYS* 1.3 77.8 - - - +
165A TYR* 1.3 59.7 + - - +
167A ALA* 3.2 3.8 + - - +
168A CYS* 2.9 32.2 + - - +
177A PHE* 5.2 9.4 - - + -
180A ILE* 5.1 11.0 - - + +
183A VAL* 4.3 24.5 - - + -
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Residues in contact with TYR 165 (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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161A SER 2.9 17.8 + - - +
162A ALA* 3.6 1.1 - - - +
164A LEU* 1.3 76.7 - - - +
166A ILE* 1.3 58.3 + - - +
168A CYS* 3.4 8.6 + - - -
169A ARG* 3.0 29.7 + - + +
173A VAL* 5.8 2.0 - - + -
177A PHE* 3.6 53.8 - + + +
195A PHE* 3.4 24.9 - + + -
286A ARG* 6.1 0.9 - - - -
315A GLN* 3.8 16.8 - - - +
316A LEU* 3.8 24.0 - - + +
473B PHE* 3.5 25.9 - + - -
476B GLU 4.8 0.7 - - - -
477B GLN* 3.6 21.3 - - - +
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Residues in contact with ILE 166 (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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137A ARG* 4.4 5.8 - - - -
141A LEU* 3.7 17.7 - - + -
162A ALA 3.2 16.1 + - - +
163A CYS* 3.3 6.5 + - - +
165A TYR* 1.3 75.8 - - - +
167A ALA* 1.3 61.7 + - - +
169A ARG* 3.2 25.3 - - + +
170A GLN 4.8 0.3 + - - -
195A PHE* 3.3 36.1 - - + +
198A ILE* 3.5 46.0 - - + +
199A LEU* 4.2 17.0 - - + +
202A LEU* 5.6 6.7 - - + -
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Residues in contact with ALA 167 (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 ILE* 3.5 25.9 - - + +
137A ARG* 3.3 39.5 + - + +
138A THR* 3.2 28.5 - - - +
141A LEU* 4.2 0.6 - - - +
163A CYS 3.0 9.4 + - - +
164A LEU 3.2 7.4 + - - +
166A ILE* 1.3 79.1 - - - +
168A CYS* 1.3 58.2 + - - +
169A ARG 3.2 1.1 + - - -
170A GLN 4.5 2.6 + - - -
171A GLU 3.8 4.9 - - - +
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Residues in contact with CYS 168 (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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130A LEU* 5.4 2.5 - - + -
134A ILE* 3.6 22.7 - - + -
164A LEU* 2.9 29.0 + - - +
165A TYR* 3.4 20.9 - - - -
167A ALA* 1.3 73.5 - - - +
169A ARG* 1.3 63.5 + - - +
170A GLN 3.3 3.9 + - - -
171A GLU 4.0 3.4 - - - -
172A GLY 3.7 3.9 + - - +
173A VAL* 2.9 38.4 + - - +
177A PHE* 4.5 1.3 - - - -
180A ILE* 3.8 26.2 - - + -
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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