Contacts of the helix formed by residues 159 - 171 (chain C) in PDB entry 2GH0
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 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157C ALA 3.5 2.7 + - - -
158C ARG* 1.3 73.8 - - - +
160C PRO* 1.4 70.4 - - - +
161C HIS* 3.4 10.4 + - - +
162C ASP* 3.1 30.9 + - - -
163C LEU* 2.8 34.4 + - - +
189D ARG* 5.0 0.7 + - - -
193D TYR* 4.4 11.4 + - - -
210D ARG* 4.1 13.7 - - - -
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Residues in contact with PRO 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ARG 4.7 0.7 - - - +
159C SER* 1.4 85.8 - - - +
161C HIS* 1.3 61.7 + - - +
163C LEU* 3.4 12.0 + - + +
164C SER* 3.1 18.9 + - - -
208D VAL* 5.4 3.4 - - + -
209D ASP 4.6 9.2 - - - +
210D ARG* 4.0 24.5 - - - +
211D LEU* 3.4 23.5 - - + +
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Residues in contact with HIS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C SER* 3.2 6.5 + - - +
160C PRO* 1.3 77.4 - - - +
162C ASP* 1.3 61.8 + - - +
164C SER* 3.3 2.8 + - - -
165C LEU* 2.8 57.8 + - + +
147D PHE* 3.5 16.0 - + - -
148D ARG 3.3 17.6 + - - -
149D PHE* 3.9 7.8 - - + -
150D CYS 5.0 0.7 - - - -
190D PRO* 3.5 29.2 - - + +
193D TYR* 3.5 26.0 - + + -
210D ARG 3.9 5.8 + - - +
211D LEU* 2.8 35.9 - - - +
213D ALA 3.8 12.0 + - - -
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Residues in contact with ASP 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ALA 4.3 0.7 - - - +
158C ARG* 3.6 13.7 - - + -
159C SER* 3.1 33.9 + - - +
161C HIS* 1.3 87.9 + - - +
163C LEU* 1.3 55.1 + - - +
165C LEU* 3.3 4.6 + - - +
166C ALA* 2.7 35.5 + - - +
184C SER* 3.4 22.6 - - - +
186C PRO* 3.6 6.8 - - - +
189D ARG* 2.8 45.1 + - - -
190D PRO* 5.2 0.5 - - - +
193D TYR* 5.6 0.5 + - - -
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ARG* 3.6 47.3 - - + +
159C SER 2.8 27.3 + - - +
160C PRO* 3.7 9.0 - - + +
162C ASP* 1.3 74.2 - - - +
164C SER* 1.3 56.6 + - - +
166C ALA* 3.5 5.1 + - + +
167C SER* 3.0 27.0 + - - -
135D LEU 4.8 0.7 - - - -
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Residues in contact with SER 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C PRO 3.1 13.0 + - - -
161C HIS 3.8 3.4 - - - -
163C LEU* 1.3 73.1 - - - +
165C LEU* 1.3 61.1 + - - +
167C SER* 3.3 2.1 + - - -
168C LEU* 3.0 35.3 + - - +
135D LEU* 2.9 38.1 + - - +
137D LEU* 3.8 6.1 - - - +
147D PHE* 4.2 6.5 - - - -
211D LEU* 3.2 31.1 - - - +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C HIS* 2.8 38.0 + - + +
162C ASP* 3.7 5.6 - - - +
164C SER* 1.3 76.5 - - - +
166C ALA* 1.3 62.4 + - - +
168C LEU* 3.2 3.7 + - - +
169C LEU* 3.1 36.2 + - + +
174C LEU* 3.7 26.0 - - + -
182C PRO* 4.3 13.9 - - + -
183C VAL 3.4 26.5 - - - +
184C SER* 4.1 9.9 - - - -
147D PHE* 4.2 13.8 - - + -
149D PHE* 4.2 20.9 - - + -
150D CYS 5.3 1.8 - - - +
189D ARG* 5.4 0.4 - - - +
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ARG* 4.1 20.6 - - - +
162C ASP 2.7 20.5 + - - +
163C LEU* 3.7 6.3 - - + +
165C LEU* 1.3 71.9 - - - +
167C SER* 1.3 57.0 + - - +
169C LEU* 3.5 5.4 + - - +
170C GLY* 2.8 27.2 + - - -
184C SER* 3.6 20.6 - - - +
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Residues in contact with SER 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LEU 3.0 18.2 + - - -
164C SER 3.6 4.3 - - - -
165C LEU 3.3 0.2 - - - -
166C ALA* 1.3 77.6 - - - +
168C LEU* 1.3 51.3 + - - +
170C GLY* 3.3 1.4 + - - -
171C ALA* 2.8 39.0 + - - +
134D ALA 2.7 21.9 + - - -
135D LEU 3.7 10.1 - - - -
136D GLY* 3.2 16.4 + - - -
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C SER 3.0 19.4 + - - +
165C LEU* 3.2 4.7 + - - +
167C SER* 1.3 75.1 - - - +
169C LEU* 1.3 61.1 + - - +
171C ALA* 3.3 2.0 + - - -
172C GLY 3.2 3.1 + - - -
173C ALA* 2.9 40.1 + - + +
174C LEU* 3.9 22.3 + - + -
130D VAL* 3.9 18.6 - - + -
134D ALA* 3.5 34.8 - - + +
135D LEU* 3.8 18.4 - - + +
147D PHE* 3.5 39.0 - - + -
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 3.1 34.3 + - + +
166C ALA* 3.8 4.5 - - - +
168C LEU* 1.3 71.2 - - - +
170C GLY* 1.3 66.6 + - - +
172C GLY* 3.2 12.9 + - - +
173C ALA 5.1 0.4 - - - +
174C LEU* 3.9 26.7 - - + +
181C ARG* 3.6 41.0 + - - +
182C PRO* 4.1 33.0 - - + +
184C SER* 4.3 12.1 - - - +
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Residues in contact with GLY 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ALA 2.8 17.9 + - - -
167C SER* 3.7 1.6 - - - -
169C LEU* 1.3 78.1 - - - +
171C ALA* 1.3 59.0 + - - +
172C GLY 3.6 0.7 + - - -
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Residues in contact with ALA 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C SER* 2.8 19.6 + - - +
168C LEU 3.7 4.9 - - - +
169C LEU 3.1 0.2 - - - -
170C GLY* 1.3 78.6 - - - +
172C GLY* 1.4 59.9 + - - +
173C ALA* 3.4 3.0 + - + +
134D ALA* 4.0 26.0 - - + +
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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