Contacts of the helix formed by residues 167 - 182 (chain B) in PDB entry 3GGS
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 ASP 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B ASP 4.7 5.6 - - - -
165B ALA 3.3 4.6 + - - -
166B TYR* 1.3 76.5 - - - +
168B ARG* 1.3 63.9 + - - +
169B THR* 3.4 12.6 + - - -
170B MET* 3.2 35.5 + - + +
171B ARG* 3.4 20.8 + - - +
234B ARG* 3.6 32.8 + - + +
235B VAL 3.0 20.2 + - - +
236B PHE* 5.3 0.2 - - - +
291B SO4 4.4 10.9 + - - -
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR 3.4 1.6 + - - -
167B ASP* 1.3 74.1 + - - +
169B THR* 1.3 66.0 + - - +
171B ARG* 3.2 19.4 + - - +
172B GLN* 3.1 54.9 + - + +
294B SO4 3.2 21.8 + - - +
253C GLU* 3.0 43.4 + - - +
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Residues in contact with THR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 3.4 12.2 + - - -
168B ARG* 1.3 80.1 - - - +
170B MET* 1.3 65.7 + - - +
172B GLN* 3.3 14.4 + - - +
173B ARG* 3.1 61.8 + - - +
234B ARG* 6.1 0.9 - - - -
283B PRO* 5.2 6.7 - - + -
297B SO4 5.2 0.7 - - - +
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Residues in contact with MET 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 5.7 0.2 - - - -
167B ASP* 3.2 20.2 + - + +
168B ARG 3.3 0.2 - - - -
169B THR* 1.3 75.9 - - - +
171B ARG* 1.3 60.9 + - - +
173B ARG* 3.8 5.5 - - + +
174B ALA* 2.8 31.5 + - - +
234B ARG* 3.9 9.9 - - - -
236B PHE* 3.7 60.2 - - + -
278B LEU* 4.2 6.1 - - + +
281B SER* 3.7 29.2 - - - +
282B ILE* 3.8 28.9 - - + +
283B PRO* 3.9 10.3 - - - -
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.5 42.8 - - + +
132B ILE 3.8 18.8 - - - +
133B ARG* 4.0 17.1 + - - +
166B TYR* 2.7 41.7 + - + -
167B ASP 3.4 5.0 + - - +
168B ARG* 3.2 28.7 + - - +
170B MET* 1.3 77.8 - - - +
172B GLN* 1.3 61.2 + - + +
174B ALA* 4.3 0.2 - - - -
175B LEU* 3.2 24.8 + - + +
189B GLU* 3.5 12.1 + - - +
236B PHE* 5.4 4.5 - - + -
294B SO4 3.1 46.7 + - - -
249C TYR* 5.7 0.8 - - - -
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 3.1 52.5 + - + +
169B THR* 3.5 14.7 + - - +
170B MET 3.3 0.2 - - - -
171B ARG* 1.3 78.0 - - + +
173B ARG* 1.3 59.4 + - + +
175B LEU* 3.6 8.6 + - - +
176B SER* 2.9 27.4 + - - -
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B THR* 3.1 39.5 + - - +
170B MET* 3.3 8.0 + - + +
172B GLN* 1.3 76.1 - - + +
174B ALA* 1.3 60.2 + - - +
176B SER* 3.5 7.0 - - - -
177B THR* 2.8 36.2 + - - -
278B LEU* 4.2 1.3 - - - -
281B SER* 2.7 60.0 + - - +
283B PRO* 4.2 3.0 - - - +
297B SO4 3.4 41.2 + - - -
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 4.0 22.7 - - + -
170B MET 2.8 21.8 + - - +
171B ARG* 3.7 5.8 - - - +
173B ARG* 1.3 71.7 - - - +
175B LEU* 1.3 62.4 + - - +
177B THR* 3.8 0.2 - - - -
178B TRP* 3.0 21.7 + - - +
187B LEU* 4.1 2.9 - - + -
236B PHE* 5.8 1.3 - - + -
238B PHE* 4.3 4.7 - - + -
274B PHE* 3.5 15.8 - - + -
278B LEU* 3.8 28.1 - - + +
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 4.3 7.0 - - + -
171B ARG 3.2 19.6 + - - +
172B GLN* 3.9 7.0 - - - +
174B ALA* 1.3 79.4 - - - +
176B SER* 1.3 60.9 + - - +
178B TRP* 3.9 2.4 + - - +
179B LYS* 3.2 48.8 + - - +
186B GLU* 4.2 9.4 - - - +
187B LEU* 4.0 36.8 - - + +
189B GLU* 3.4 31.4 - - + +
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN 2.9 18.9 + - - -
173B ARG* 3.5 9.6 - - - -
174B ALA 3.1 0.2 - - - -
175B LEU* 1.3 74.9 - - - +
177B THR* 1.3 67.1 + - - +
179B LYS* 3.0 20.1 + - - +
180B GLN* 3.3 23.3 + - - +
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 2.8 25.4 + - - +
174B ALA 3.8 3.1 - - - -
176B SER* 1.3 72.9 + - - +
178B TRP* 1.3 62.8 + - - +
180B GLN* 3.3 17.5 + - + +
181B MET* 3.0 33.5 + - + +
274B PHE* 4.0 5.6 - - + -
277B ILE* 3.4 33.4 + - + +
278B LEU* 3.5 16.3 - - + +
281B SER* 3.9 10.2 + - - -
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Residues in contact with TRP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 3.8 34.8 - - + -
174B ALA 3.0 16.4 + - - +
175B LEU* 4.0 4.7 - - + +
177B THR* 1.3 78.0 - - - +
179B LYS* 1.3 68.0 + - + +
181B MET* 3.2 28.7 + - + +
182B GLY 3.4 8.3 + - - -
183B GLU* 3.5 34.7 + - + +
185B ARG* 2.8 35.7 + - + -
186B GLU* 4.0 6.2 - - - +
187B LEU* 3.3 40.2 - - + +
270B LYS* 4.4 13.0 - - + -
274B PHE* 3.8 35.6 - + + -
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 3.2 46.3 + - - +
176B SER* 3.0 12.2 + - - +
178B TRP* 1.3 84.5 - - + +
180B GLN* 1.3 57.9 + - - +
182B GLY* 3.3 16.8 + - - -
186B GLU* 4.8 11.4 - - - +
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Residues in contact with GLN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 3.3 16.7 + - - +
177B THR* 3.6 23.8 + - + +
179B LYS* 1.3 75.2 - - - +
181B MET* 1.3 63.0 + - + +
182B GLY* 3.3 1.6 - - - -
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Residues in contact with MET 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B THR* 3.0 29.4 + - + +
178B TRP* 3.2 17.9 + - + +
180B GLN* 1.3 77.8 - - + +
182B GLY* 1.3 63.6 + - - +
183B GLU* 3.5 33.5 - - + +
270B LYS* 5.7 3.1 - - + +
273B GLN* 5.7 6.7 - - + +
274B PHE* 3.5 41.5 - - + +
277B ILE* 4.3 23.3 - - + -
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Residues in contact with GLY 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TRP 3.4 1.4 + - - -
179B LYS 3.3 13.6 + - - -
180B GLN 3.3 3.2 - - - -
181B MET* 1.3 81.7 - - - +
183B GLU* 1.3 64.3 + - - +
184B GLN 4.1 0.3 + - - -
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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