Contacts of the helix formed by residues 160 - 178 (chain A) in PDB entry 2G5W
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 GLU 160 (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* 3.0 40.2 + - - -
156A LEU* 3.6 13.7 - - + +
157A GLU* 2.7 49.5 + - + +
159A SER* 1.3 79.7 - - - +
161A ILE* 1.3 63.3 + - - +
162A PRO 3.5 0.2 - - - -
163A ARG* 3.2 37.2 + - - +
164A VAL* 3.5 10.8 + - + +
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Residues in contact with ILE 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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156A LEU* 4.2 18.4 - - + -
157A GLU 3.8 18.4 - - - +
158A ALA* 3.2 6.9 + - - +
160A GLU* 1.3 71.4 - - - +
162A PRO* 1.4 70.9 - - + +
163A ARG 3.0 2.5 - - - -
164A VAL* 2.9 19.0 + - - +
165A VAL* 3.0 11.6 + - + +
196A PHE* 4.4 14.1 - - + -
204A ARG* 4.6 7.2 - - - +
208A TYR* 3.5 55.4 - - + +
218A PHE* 3.9 21.5 - - + -
221A GLN* 3.5 14.4 - - - +
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Residues in contact with PRO 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 3.3 14.6 - - - +
159A SER* 3.5 14.8 - - - +
161A ILE* 1.4 93.4 - - + +
163A ARG* 1.3 55.8 + - + +
165A VAL* 3.6 11.5 + - + +
166A GLU* 3.1 24.6 + - - +
208A TYR* 5.0 3.4 - - - +
221A GLN* 5.3 4.3 - - - +
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Residues in contact with ARG 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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159A SER* 4.1 22.7 + - - +
160A GLU* 3.2 28.0 + - - +
161A ILE 3.0 0.6 - - - -
162A PRO* 1.3 77.0 - - + +
164A VAL* 1.3 62.5 + - + +
166A GLU* 3.1 9.7 + - - +
167A ASP* 3.0 31.2 + - - +
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Residues in contact with VAL 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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109A HIS* 4.6 10.5 - - + -
126A ILE* 4.2 20.0 - - + -
156A LEU* 4.4 14.6 - - + -
160A GLU* 3.7 14.4 - - + +
161A ILE* 2.9 7.8 + - - +
163A ARG* 1.3 77.6 - - + +
165A VAL* 1.3 61.5 + - - +
167A ASP* 3.3 22.3 - - + +
168A TYR* 3.2 25.0 - - + -
192A LEU* 3.9 27.4 - - + -
218A PHE* 4.4 9.4 - - + -
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Residues in contact with VAL 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 ILE* 3.0 21.7 + - + +
162A PRO* 3.6 11.2 - - + +
163A ARG 3.2 0.2 - - - -
164A VAL* 1.3 76.2 - - - +
166A GLU* 1.3 62.4 + - - +
168A TYR* 3.1 19.1 + - - +
169A CYS* 3.1 22.0 + - - -
218A PHE* 4.6 1.6 - - + -
221A GLN* 3.9 46.2 - - + +
222A VAL* 4.0 24.2 - - + +
225A GLY* 4.7 4.5 - - - -
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Residues in contact with GLU 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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162A PRO 3.1 13.9 + - - +
163A ARG* 3.1 13.2 + - - +
165A VAL* 1.3 73.3 - - - +
167A ASP* 1.3 59.7 + - - +
169A CYS* 3.2 17.8 + - - +
170A LEU* 3.0 58.9 + - + +
173A LEU* 6.1 0.5 - - - +
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Residues in contact with ASP 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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67A VAL* 3.6 18.1 - - + +
68A SER* 3.1 29.9 + - - +
163A ARG 3.0 16.7 + - - +
164A VAL* 3.3 20.8 - - + +
166A GLU* 1.3 78.2 - - - +
168A TYR* 1.3 56.2 + - - +
170A LEU* 3.7 13.2 + - - +
171A SER* 2.7 34.5 + - - -
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Residues in contact with TYR 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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67A VAL* 4.2 15.3 - - + -
107A LEU* 3.5 36.7 + - + +
109A HIS* 3.3 31.4 + - + +
164A VAL* 3.2 37.0 + - + -
165A VAL* 3.1 9.0 + - - +
167A ASP* 1.3 77.8 - - - +
169A CYS* 1.3 59.5 + - - +
171A SER* 3.4 3.0 + - - -
172A ALA* 2.9 29.6 + - - +
185A ILE* 4.0 14.1 - - + -
186A HIS 4.8 1.2 + - - -
192A LEU* 4.4 4.5 - - + +
193A ILE* 3.9 25.1 - - + +
218A PHE* 4.7 1.1 - + - -
222A VAL* 3.7 36.1 - - + +
226A VAL* 3.9 14.3 - - + +
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Residues in contact with CYS 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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165A VAL* 3.1 21.7 + - - -
166A GLU* 3.2 27.1 + - - +
168A TYR* 1.3 75.2 - - - +
170A LEU* 1.3 52.1 + - - +
172A ALA* 3.1 8.4 + - - +
173A LEU* 2.8 43.5 + - + +
225A GLY* 3.5 37.7 - - - -
226A VAL* 4.1 3.6 - - - -
229A ALA* 4.5 10.9 - - + +
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Residues in contact with LEU 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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67A VAL 6.0 0.2 - - - +
81A TYR* 5.8 4.9 - - + +
166A GLU* 3.0 45.7 + - + +
167A ASP* 4.0 12.6 - - - +
169A CYS* 1.3 75.7 - - - +
171A SER* 1.3 53.3 + - - +
173A LEU* 3.3 16.4 + - + +
174A ASN* 2.8 46.9 + - - +
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Residues in contact with SER 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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67A VAL* 3.2 37.6 + - - -
80A ILE* 3.6 32.6 + - - +
81A TYR* 4.7 0.9 - - - +
107A LEU* 3.9 6.3 - - - -
167A ASP 2.7 23.4 + - - -
168A TYR 3.5 5.2 - - - -
169A CYS 3.2 0.2 - - - -
170A LEU* 1.3 74.5 - - - +
172A ALA* 1.3 60.0 + - - +
174A ASN* 3.4 2.6 + - - +
175A ALA* 2.9 28.9 + - - +
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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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107A LEU* 3.8 6.8 - - + +
168A TYR 2.9 13.8 + - - +
169A CYS* 3.4 8.7 - - - +
171A SER* 1.3 74.8 - - - +
173A LEU* 1.3 62.2 + - - +
175A ALA* 3.2 3.3 + - - +
176A ILE* 3.1 27.5 + - - +
183A ILE* 4.0 17.7 - - + +
226A VAL* 4.1 27.6 - - + -
229A ALA* 5.1 0.2 - - + -
230A ILE* 3.9 14.1 - - + -
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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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166A GLU* 6.1 0.4 - - - +
169A CYS* 2.8 29.6 + - + +
170A LEU* 3.7 17.0 - - + +
172A ALA* 1.3 69.9 - - - +
174A ASN* 1.3 66.1 + - - +
176A ILE* 3.7 3.1 + - + +
177A ARG* 3.2 25.2 + - - +
229A ALA* 4.0 33.4 - - + +
230A ILE* 4.2 7.6 - - + -
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Residues in contact with ASN 174 (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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80A ILE* 2.7 32.9 + - + +
81A TYR* 3.3 24.2 + - - +
82A SER 4.4 0.8 + - - -
83A ASP* 5.3 0.4 + - - -
86A VAL* 3.5 15.1 - - + +
170A LEU* 2.8 25.5 + - - +
171A SER 3.6 0.9 - - - +
173A LEU* 1.3 73.2 - - - +
175A ALA* 1.3 53.5 + - - +
177A ARG* 2.8 35.3 + - - +
178A ALA* 2.7 36.7 + - - +
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Residues in contact with ALA 175 (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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80A ILE* 3.8 8.9 - - + +
105A CYS* 4.3 7.2 - - + -
107A LEU* 5.1 0.2 - - + -
171A SER 2.9 17.6 + - - +
172A ALA 3.2 6.7 + - - +
174A ASN* 1.3 74.9 - - - +
176A ILE* 1.3 63.8 + - + +
178A ALA 3.1 7.1 + - - -
180A PHE* 3.0 48.3 + - + -
183A ILE* 3.5 24.5 - - + -
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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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172A ALA 3.1 14.4 + - - +
173A LEU* 4.1 4.5 - - + +
175A ALA* 1.3 75.0 - - - +
177A ARG* 1.3 56.5 + - - +
179A GLY* 2.8 24.8 + - - -
180A PHE 3.4 20.4 - - - +
181A ASP 4.3 0.2 - - - -
182A GLY* 4.1 18.4 - - - -
230A ILE* 3.7 26.5 - - + -
234A LYS* 3.9 36.1 - - + +
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Residues in contact with ARG 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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83A ASP* 3.6 26.0 + - - +
86A VAL* 3.4 32.1 - - + +
87A GLU* 4.9 6.3 + - - -
90A LYS* 3.7 18.0 - - - +
173A LEU 3.2 15.9 + - - +
174A ASN* 2.8 33.8 + - - +
176A ILE* 1.3 78.8 - - - +
178A ALA* 1.3 58.3 + - - +
179A GLY* 3.2 0.6 + - - -
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Residues in contact with ALA 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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80A ILE* 4.3 3.4 - - + -
86A VAL* 3.6 31.0 - - + +
89A TRP* 4.1 13.9 - - + -
90A LYS* 3.4 30.8 - - - +
93A VAL* 4.0 7.5 - - - +
174A ASN 2.7 19.6 + - - +
175A ALA 3.5 6.7 - - - +
176A ILE 3.1 0.4 - - - -
177A ARG* 1.3 72.2 - - - +
179A GLY* 1.3 57.8 + - - +
180A PHE* 3.6 7.4 + - + -
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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