Contacts of the helix formed by residues 172 - 188 (chain B) in PDB entry 4OG2
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 PRO 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B THR* 3.4 15.7 - - - +
156B ALA 5.1 1.1 - - - +
157B LYS* 5.6 1.6 - - - +
168B ARG* 3.4 26.9 - - - +
170B SER 4.0 1.1 - - - +
171B ALA* 1.3 90.7 - - + +
173B VAL* 1.3 68.5 + - + +
174B SER* 3.1 17.7 - - - +
175B VAL* 3.0 25.0 + - + -
176B VAL* 3.0 11.9 + - - +
390B GLU* 3.8 22.9 - - + +
391B VAL* 4.5 3.8 - - + +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 3.0 39.0 + - - +
156B ALA* 4.7 0.4 - - - +
157B LYS* 4.5 4.7 - - + +
172B PRO* 1.3 72.3 - - + +
174B SER* 1.3 65.8 + - - +
176B VAL* 4.4 3.8 - - - +
177B ALA* 3.0 30.0 + - - +
204B PHE* 3.8 11.9 - - + +
207B SER* 3.5 27.1 - - - +
208B GLU* 3.7 36.3 - - + +
211B ILE* 3.6 19.0 - - + +
280B ASP* 6.0 0.2 - - + -
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO* 3.9 15.4 - - - +
173B VAL* 1.3 82.6 - - - +
175B VAL* 1.3 64.7 + - - +
178B PRO* 3.5 18.8 - - - +
211B ILE* 3.8 26.9 - - - +
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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
----------------------------------------------------------
171B ALA* 4.8 0.7 - - + -
172B PRO* 3.0 23.9 + - + +
174B SER* 1.3 91.2 - - - +
176B VAL* 1.3 59.9 + - + +
178B PRO* 3.8 5.4 - - - +
179B ASN* 3.0 18.7 + - - -
393B GLN 5.3 0.9 - - - +
396B PHE* 3.4 39.5 - - + -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 5.9 0.2 - - + -
171B ALA* 3.5 31.4 - - + +
172B PRO 3.0 15.9 + - - +
173B VAL* 4.5 2.5 - - - +
175B VAL* 1.3 77.9 - - - +
177B ALA* 1.3 67.8 + - - +
179B ASN* 3.0 27.1 + - - +
280B ASP* 5.4 10.1 - - + +
301B ALA* 3.4 30.8 - - + +
302B GLN 4.5 7.6 - - - +
303B ALA* 4.4 7.4 - - + +
330B GLN* 5.5 1.1 - - - +
396B PHE* 3.9 13.2 - - + -
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 3.0 16.3 + - - +
176B VAL* 1.3 80.9 - - - +
178B PRO* 1.4 65.9 - - + +
179B ASN 3.0 1.0 + - - -
180B SER* 3.1 21.3 + - - -
181B VAL 3.8 1.2 + - - -
208B GLU* 4.3 14.4 - - + +
211B ILE* 3.9 11.9 - - + -
212B PHE* 3.4 38.7 - - + -
301B ALA* 4.7 1.8 - - - -
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Residues in contact with PRO 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL 3.6 4.0 - - - +
174B SER 3.5 25.1 - - - +
175B VAL 3.8 4.7 - - - +
176B VAL 3.5 4.3 - - - -
177B ALA* 1.4 90.7 - - + +
179B ASN* 1.3 61.2 + - - +
181B VAL* 3.2 5.5 + - + +
182B LYS* 3.1 42.9 + - - +
211B ILE* 3.8 6.1 - - + -
215B THR* 3.7 33.9 - - + +
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Residues in contact with ASN 179 (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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175B VAL 3.0 27.1 + - - -
176B VAL* 3.0 15.7 + - - +
177B ALA 3.0 0.6 + - - -
178B PRO* 1.3 78.5 - - - +
180B SER* 1.3 59.5 + - - +
182B LYS* 3.4 11.7 + - - +
183B ALA* 2.9 22.9 + - - +
301B ALA* 4.2 4.0 - - + +
396B PHE* 3.7 31.3 - - - +
397B TYR* 4.4 2.6 - - - +
398B VAL* 3.4 22.4 - - + +
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA 3.1 14.5 + - - -
179B ASN* 1.3 77.1 - - - +
181B VAL* 1.3 61.2 + - - +
183B ALA* 3.7 2.8 - - - +
184B ALA* 2.9 24.1 + - - +
212B PHE* 3.5 6.4 - - - -
277B ILE* 3.3 41.0 - - - +
278B GLY 5.0 0.2 + - - -
299B LEU* 4.5 5.5 - - - +
301B ALA* 3.9 26.3 + - - +
398B VAL* 3.9 13.0 - - - +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA 4.2 2.7 - - - +
178B PRO 3.2 6.6 + - - +
180B SER* 1.3 76.8 + - - +
182B LYS* 1.3 63.7 + - - +
184B ALA* 3.2 4.0 + - - +
185B LEU* 3.1 41.6 + - + +
212B PHE* 3.7 32.8 - - + +
215B THR* 3.8 29.2 - - + -
216B VAL* 4.8 6.7 - - + +
219B GLN* 4.5 6.3 - - + -
221B LEU* 4.5 11.2 - - + -
250B LEU* 5.0 6.1 - - + -
252B ILE* 4.1 13.9 - - + -
277B ILE* 3.7 7.0 - - + -
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Residues in contact with LYS 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 PRO* 3.1 32.0 + - - +
179B ASN* 3.7 13.0 + - - +
181B VAL* 1.3 76.3 - - + +
183B ALA* 1.3 58.0 + - - +
185B LEU* 3.4 9.2 + - - +
186B LYS* 3.0 28.1 + - - +
215B THR* 5.4 2.5 - - + -
219B GLN* 4.0 28.3 - - - +
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Residues in contact with ALA 183 (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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179B ASN 2.9 18.1 + - - +
180B SER 3.7 4.3 - - - +
182B LYS* 1.3 74.9 - - - +
184B ALA* 1.3 59.3 + - - +
186B LYS* 3.3 9.0 + - - +
187B GLN* 2.9 33.1 + - - +
299B LEU* 4.6 3.6 - - + -
398B VAL* 3.8 29.4 - - + -
415B LEU* 4.1 12.1 - - + +
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Residues in contact with ALA 184 (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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180B SER 2.9 16.9 + - - +
181B VAL 3.2 5.4 + - - +
183B ALA* 1.3 75.5 - - - +
185B LEU* 1.3 58.6 + - + +
187B GLN* 3.3 4.6 + - - +
188B ASN* 2.9 24.4 + - - +
191B ILE* 3.5 22.4 - - + +
250B LEU* 4.2 11.9 - - + -
275B ALA* 5.2 1.3 - - + -
277B ILE* 4.0 13.0 - - + -
299B LEU* 3.7 23.5 - - + +
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Residues in contact with LEU 185 (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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181B VAL* 3.1 19.5 + - + +
182B LYS* 3.7 6.7 - - - +
184B ALA* 1.3 72.9 - - + +
186B LYS* 1.3 65.5 + - - +
188B ASN 3.9 4.0 - - - +
189B PRO* 3.1 29.9 - - + +
191B ILE* 3.7 37.2 - - + +
219B GLN* 3.2 35.4 - - + +
221B LEU* 3.8 30.7 - - + -
250B LEU* 5.2 1.1 - - + -
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Residues in contact with LYS 186 (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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182B LYS 3.0 16.8 + - - +
183B ALA* 3.3 9.4 + - - +
185B LEU* 1.3 77.6 - - - +
187B GLN* 1.3 62.9 - - + +
189B PRO* 4.0 9.5 - - - +
416B LYS* 4.2 19.7 + - - +
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Residues in contact with GLN 187 (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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183B ALA 2.9 18.6 + - - +
184B ALA* 3.6 5.4 - - - +
186B LYS* 1.3 81.1 - - + +
188B ASN* 1.3 59.3 + - + +
189B PRO* 3.8 4.3 - - - +
299B LEU* 4.0 16.0 - - - +
400B GLN* 2.8 41.7 + - - -
415B LEU* 3.8 22.4 - - + +
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Residues in contact with ASN 188 (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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184B ALA 2.9 10.2 + - - +
185B LEU* 3.2 6.7 - - - +
187B GLN* 1.3 79.6 - - + +
189B PRO* 1.3 67.4 - - - +
190B ASN* 3.0 31.4 + - - +
191B ILE* 3.1 42.3 + - + +
249B ASP* 5.3 4.8 + - - +
275B ALA* 5.9 1.8 - - - +
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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