Contacts of the helix formed by residues 163 - 177 (chain B) in PDB entry 3G1I
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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SO4 3.3 31.0 - - - -
161B SER 3.5 4.9 + - - -
162B GLU* 1.3 78.5 - - - +
164B PHE* 1.3 64.5 + - - +
165B VAL* 3.3 11.1 - - - +
166B ASP* 3.1 33.5 + - - +
167B PHE* 3.0 19.9 + - - +
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Residues in contact with PHE 164 (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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1B SO4 2.9 17.6 + - - +
158B GLN* 3.6 20.6 - - - +
162B GLU 3.6 0.8 + - - -
163B SER* 1.3 71.5 - - - +
165B VAL* 1.3 53.9 + - - +
167B PHE* 3.2 14.6 + + - +
168B ALA* 2.8 33.2 + - + +
193B PHE* 3.9 26.0 - + - -
197B SER* 3.7 21.5 - - - -
201B ILE* 3.8 19.1 - - + -
205B ILE* 4.8 2.0 - - + -
218B ILE* 4.9 0.4 - - + -
219B ILE* 3.7 31.0 - - + -
222B VAL* 3.5 40.4 - - + -
223B LEU* 4.2 12.3 - - + -
226B GLN* 4.4 9.6 - - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SO4 5.1 2.9 - - - +
163B SER* 3.3 19.5 - - - +
164B PHE* 1.3 81.1 - - - +
166B ASP* 1.3 61.0 + - - +
168B ALA* 3.3 6.5 + - - +
169B ASN* 2.9 45.8 + - - +
219B ILE* 5.6 4.0 - - + -
223B LEU* 4.5 23.6 - - + +
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Residues in contact with ASP 166 (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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162B GLU* 3.8 15.4 - - + +
163B SER* 3.1 29.0 + - - +
165B VAL* 1.3 80.1 - - - +
167B PHE* 1.3 60.6 + - - +
169B ASN* 3.4 8.8 + - - +
170B ARG* 2.9 31.5 + - - +
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Residues in contact with PHE 167 (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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156B ILE* 3.8 18.4 - - + -
157B MET* 3.6 6.7 - - - -
158B GLN* 3.3 54.5 - - + -
162B GLU* 3.5 14.4 + - - -
163B SER 3.0 12.6 + - - +
164B PHE* 3.4 22.7 - + - +
166B ASP* 1.3 76.0 - - - +
168B ALA* 1.3 57.4 + - - +
170B ARG* 3.3 13.5 + - - +
171B LEU* 2.8 40.6 + - + +
192B CYS* 4.2 12.6 - - + -
193B PHE* 3.7 16.6 - + - -
196B LYS* 4.1 7.2 - - + -
197B SER* 3.3 24.2 - - - -
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 2.8 22.8 + - + +
165B VAL* 3.6 9.2 - - + +
166B ASP 3.3 0.2 - - - -
167B PHE* 1.3 73.8 - - - +
169B ASN* 1.3 60.3 + - - +
171B LEU* 3.2 1.0 + - - +
172B ILE* 2.9 36.7 + - - +
193B PHE* 3.8 31.6 - - + -
219B ILE* 3.9 21.3 - - + -
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Residues in contact with ASN 169 (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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165B VAL* 2.9 39.3 + - - +
166B ASP* 3.9 8.8 + - - +
168B ALA* 1.3 77.2 - - - +
170B ARG* 1.3 61.4 + - - +
172B ILE* 4.0 7.1 - - - +
173B LYS* 2.9 52.2 + - - +
219B ILE* 6.0 0.9 - - - +
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Residues in contact with ARG 170 (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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156B ILE* 3.6 31.3 - - + +
157B MET 2.8 31.7 + - - +
159B GLY 4.6 0.4 - - - +
162B GLU* 2.8 35.1 + - - +
166B ASP 2.9 20.8 + - - +
167B PHE* 3.6 9.5 - - - +
169B ASN* 1.3 72.4 - - - +
171B LEU* 1.3 61.8 + - - +
173B LYS* 3.8 8.7 - - - +
174B ALA* 3.1 23.4 + - + +
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Residues in contact with LEU 171 (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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153B TRP 4.8 1.8 - - - +
156B ILE* 4.3 32.3 - - + +
167B PHE* 2.8 26.9 + - + +
168B ALA 3.8 2.2 - - - +
170B ARG* 1.3 71.1 - - - +
172B ILE* 1.3 66.4 + - - +
174B ALA* 3.3 2.1 + - - +
175B VAL* 3.0 37.5 + - + +
189B ILE* 3.7 20.4 - - + +
192B CYS* 3.6 42.6 - - + -
193B PHE* 3.5 30.5 - - + -
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Residues in contact with ILE 172 (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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168B ALA 2.9 23.3 + - - +
169B ASN* 4.1 7.0 - - - +
171B LEU* 1.3 75.7 - - - +
173B LYS* 1.3 56.7 + - + +
175B VAL* 3.4 1.4 + - - +
176B GLU* 2.9 55.2 + - + +
189B ILE* 3.8 39.7 - - + -
193B PHE* 4.6 0.7 - - + -
215B PRO* 4.7 7.0 - - + -
219B ILE* 3.8 27.8 - - + -
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Residues in contact with LYS 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 ASN* 2.9 42.3 + - - +
170B ARG* 3.8 7.8 - - - +
172B ILE* 1.3 74.5 - - + +
174B ALA* 1.3 66.0 + - - +
176B GLU* 3.4 9.2 + - - +
177B GLY* 3.0 21.0 + - - -
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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
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152B PRO* 5.8 0.4 - - + -
153B TRP* 4.6 9.8 - - + +
156B ILE* 3.4 32.5 - - + -
170B ARG* 3.1 10.9 + - + +
171B LEU 3.3 1.5 + - - +
173B LYS* 1.3 77.7 - - - +
175B VAL* 1.3 58.1 + - - +
177B GLY* 3.5 2.2 + - - -
178B SER* 3.1 27.5 + - - -
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Residues in contact with VAL 175 (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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153B TRP* 4.0 13.2 - - + -
171B LEU* 3.0 35.1 + - + +
172B ILE 3.9 2.9 - - - +
173B LYS 3.2 0.2 - - - -
174B ALA* 1.3 73.9 - - - +
176B GLU* 1.3 65.6 + - + +
178B SER* 2.5 26.9 + - - -
180B LEU* 4.0 9.4 - - + -
185B ARG* 3.8 42.6 + - + +
188B VAL* 3.9 21.1 - - + -
189B ILE* 3.9 18.2 - - + -
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Residues in contact with GLU 176 (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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172B ILE* 2.9 42.0 + - + +
173B LYS* 3.9 8.1 - - - +
175B VAL* 1.3 79.3 - - + +
177B GLY* 1.3 58.6 + - - +
178B SER 3.5 1.6 + - - +
185B ARG* 3.9 42.1 + - + +
189B ILE* 5.7 2.6 - - + +
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Residues in contact with GLY 177 (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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173B LYS 3.0 17.5 + - - -
174B ALA* 3.7 3.4 - - - -
176B GLU* 1.3 72.4 - - - +
178B SER* 1.3 63.0 - - - +
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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