Contacts of the helix formed by residues 159 - 172 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C ARG* 5.6 0.7 - - - -
193C TYR* 4.8 9.3 + - - -
157D ALA 3.3 6.5 + - - -
158D ARG* 1.3 75.7 - - - +
160D PRO* 1.4 68.4 - - - +
161D HIS* 3.5 7.8 + - - +
162D ASP* 3.1 35.0 + - - +
163D LEU* 2.8 31.3 + - - +
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Residues in contact with PRO 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C VAL* 5.1 9.4 - - + -
209C ASP 4.1 15.9 - - - +
210C ARG* 4.1 18.8 - - + +
211C LEU* 4.3 5.7 - - + +
158D ARG 4.4 2.2 - - - +
159D SER* 1.4 86.9 - - - +
161D HIS* 1.3 64.0 + - - +
163D LEU* 3.4 11.9 + - + +
164D SER* 3.0 26.3 + - - -
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Residues in contact with HIS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C PHE* 3.6 14.3 - + - -
148C ARG 3.3 18.0 + - - -
149C PHE* 3.9 8.9 - - + +
150C CYS 5.0 0.9 - - - -
189C ARG* 5.4 0.4 - - - -
190C PRO* 3.6 24.1 - - + +
193C TYR* 3.4 28.8 + + + -
210C ARG 3.7 6.4 + - - +
211C LEU* 2.8 33.7 - - - +
212C SER 4.2 0.4 - - - -
213C ALA 3.9 11.4 + - - -
159D SER* 3.3 5.4 + - - +
160D PRO* 1.3 78.7 - - - +
162D ASP* 1.3 62.5 + - - +
164D SER* 3.2 3.6 + - - -
165D LEU* 2.8 57.5 + - + +
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Residues in contact with ASP 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ARG* 2.7 46.3 + - - -
158D ARG* 4.0 10.5 + - - +
159D SER* 3.1 28.5 + - - +
161D HIS* 1.3 79.6 + - - +
163D LEU* 1.3 61.6 + - - +
165D LEU* 4.2 5.9 - - - +
166D ALA* 2.9 32.2 + - - +
183D VAL 4.3 0.2 - - - +
184D SER* 3.3 27.5 - - - +
185D GLN* 3.9 5.5 - - - -
186D PRO* 4.1 6.1 - - - +
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Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU 4.8 0.7 - - - -
158D ARG* 3.6 44.2 - - + +
159D SER 2.8 22.2 + - - +
160D PRO* 3.6 9.9 - - + +
162D ASP* 1.3 77.4 - - - +
164D SER* 1.3 58.1 + - - +
166D ALA* 3.5 4.9 + - + +
167D SER* 2.9 27.4 + - - -
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 2.5 39.9 + - - +
137C LEU* 3.9 8.7 - - - +
147C PHE* 4.3 1.1 - - - -
211C LEU* 3.4 34.3 - - - +
160D PRO 3.0 11.3 + - - -
161D HIS 3.8 1.3 - - - -
163D LEU* 1.3 74.7 - - - +
165D LEU* 1.3 55.1 + - - +
167D SER* 3.0 2.7 + - - -
168D LEU* 2.8 42.0 + - - +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C PHE* 4.1 8.1 - - + -
149C PHE* 4.0 20.4 - - + -
150C CYS 5.3 1.8 - - - +
189C ARG* 5.0 0.4 - - - +
161D HIS* 2.8 41.2 + - + +
162D ASP* 3.9 7.2 - - - +
164D SER* 1.3 71.6 - - - +
166D ALA* 1.3 57.1 + - - +
168D LEU* 3.3 6.5 + - - +
169D LEU* 2.9 44.6 + - + +
174D LEU* 3.5 30.5 - - + -
182D PRO* 4.1 20.0 - - + -
183D VAL 3.4 26.2 - - - +
184D SER* 4.2 4.3 - - - -
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ARG* 6.0 2.2 - - - +
158D ARG* 3.8 22.0 - - - +
162D ASP 2.9 19.7 + - - +
163D LEU* 3.7 6.1 - - + +
165D LEU* 1.3 76.7 - - - +
167D SER* 1.3 57.9 + - - +
169D LEU* 3.9 5.7 - - - +
170D GLY* 2.9 25.3 + - - -
184D SER* 3.9 11.8 - - - +
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ALA 3.1 18.7 + - - -
135C LEU 3.8 9.6 - - - -
136C GLY* 3.3 17.9 + - - -
163D LEU 2.9 15.4 + - - -
164D SER 3.3 8.1 - - - -
166D ALA* 1.3 77.2 - - - +
168D LEU* 1.3 52.4 + - - +
170D GLY* 3.1 2.9 + - - -
171D ALA* 2.7 37.6 + - - +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL* 3.9 23.1 - - + -
134C ALA* 3.6 34.3 - - + +
135C LEU* 3.8 13.2 - - + -
147C PHE* 3.5 39.0 - - + -
164D SER 2.8 23.1 + - - +
165D LEU* 3.7 3.1 - - - +
167D SER* 1.3 69.5 - - - +
169D LEU* 1.3 61.9 + - - +
171D ALA* 4.4 0.9 - - - +
172D GLY 2.9 7.4 + - - -
173D ALA* 2.8 41.4 + - + -
174D LEU* 3.9 21.8 + - + -
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D LEU* 2.9 40.6 + - + +
166D ALA* 4.0 4.7 - - - +
168D LEU* 1.3 76.2 - - - +
170D GLY* 1.3 61.9 + - - +
172D GLY* 3.3 12.7 + - - -
174D LEU* 4.1 28.5 - - + +
181D ARG* 5.8 6.3 - - + -
182D PRO* 4.0 32.3 - - + +
184D SER* 4.6 11.4 - - - +
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Residues in contact with GLY 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ALA 2.9 16.1 + - - -
167D SER* 3.1 4.9 + - - -
169D LEU* 1.3 78.5 - - - +
171D ALA* 1.3 56.7 + - - +
172D GLY 3.3 0.6 + - - -
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Residues in contact with ALA 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ALA* 4.2 26.2 - - + +
167D SER* 2.7 19.5 + - - +
168D LEU 4.1 3.4 - - - +
170D GLY* 1.3 71.9 - - - +
172D GLY* 1.3 62.2 + - - +
173D ALA* 3.3 2.8 + - + +
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Residues in contact with GLY 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D LEU 2.9 6.2 + - - -
169D LEU* 3.3 9.8 + - - -
170D GLY 3.3 4.4 + - - -
171D ALA* 1.3 77.8 - - - +
173D ALA* 1.3 60.7 + - - +
174D LEU 3.3 9.1 + - - +
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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