Contacts of the helix formed by residues 161 - 175 (chain B) in PDB entry 6O81
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 ILE 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B LEU* 6.3 0.7 - - + -
82B PHE* 5.0 4.7 - - + -
86B THR* 3.7 18.5 - - + +
149B LEU* 3.7 30.1 - - + -
159B ILE* 3.7 27.1 - - + +
160B ASN* 1.3 77.8 + - - +
162B THR* 1.3 54.4 + - - +
163B ARG 3.2 2.7 - - - +
164B ALA* 3.3 16.1 + - + +
165B LEU* 2.8 35.6 + - + +
184B ILE* 3.7 26.7 - - + -
249B ILE* 4.7 8.3 - - + -
251B ILE* 3.8 20.1 - - + +
290B HIS* 5.3 3.6 - - + +
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Residues in contact with THR 162 (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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43B LEU* 6.3 2.2 - - + -
86B THR* 4.3 11.4 - - + +
160B ASN* 3.3 35.0 + - - +
161B ILE* 1.3 77.2 - - - +
163B ARG* 1.3 60.1 + - - +
165B LEU* 3.7 13.0 - - + +
166B GLU* 2.9 37.2 + - - +
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Residues in contact with ARG 163 (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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160B ASN 4.8 4.4 + - - +
161B ILE* 3.2 0.8 - - - +
162B THR* 1.3 82.5 + - - +
164B ALA* 1.3 57.4 + - - +
166B GLU* 3.4 5.6 + - - +
167B GLU* 2.9 50.3 + - + +
290B HIS* 4.4 18.8 + - + +
295B GLU* 5.9 0.6 + - - -
468F GLY* 4.7 18.0 + - - -
469F GLU* 4.8 20.9 - - - +
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Residues in contact with ALA 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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161B ILE* 3.3 19.2 + - + +
163B ARG* 1.3 76.4 - - - +
165B LEU* 1.3 60.6 + - - +
167B GLU* 3.4 12.1 + - - +
168B HIS* 2.9 30.0 + - - +
171B ARG* 4.7 2.1 + - - -
182B THR* 4.7 3.8 - - + +
184B ILE* 4.9 3.8 - - + -
251B ILE* 4.0 11.4 - - + +
290B HIS* 3.6 38.9 + - + +
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Residues in contact with LEU 165 (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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43B LEU* 3.8 35.2 - - + -
147B ASP* 4.3 20.6 - - + +
161B ILE* 2.8 24.1 + - + +
162B THR* 3.7 13.0 - - + +
164B ALA* 1.3 73.2 - - - +
166B GLU* 1.3 58.5 + - - +
168B HIS* 3.4 4.1 + - + +
169B ARG* 2.9 74.1 + - + +
251B ILE* 4.1 21.0 - - + +
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Residues in contact with GLU 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 THR* 2.9 24.7 + - - +
163B ARG* 3.8 5.6 - - - +
165B LEU* 1.3 75.7 - - - +
167B GLU* 1.3 60.1 + - + +
169B ARG* 2.9 40.0 + - - +
170B LEU* 2.9 37.2 + - + +
173B LYS* 5.5 3.6 + - - -
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Residues in contact with GLU 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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163B ARG* 2.9 36.7 + - + +
164B ALA* 3.6 6.4 - - - +
165B LEU 3.3 0.2 - - - -
166B GLU* 1.3 77.1 - - - +
168B HIS* 1.3 57.2 + - - +
170B LEU* 3.3 18.0 - - + +
171B ARG* 2.9 54.7 + - - +
182B THR* 6.1 0.2 - - - +
210B ASN* 5.3 6.7 + - - -
289B MET 5.5 0.9 - - - +
290B HIS* 3.5 27.8 - - - +
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Residues in contact with HIS 168 (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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147B ASP* 3.2 35.1 + - + -
164B ALA 2.9 17.1 + - - +
165B LEU* 3.7 5.8 - - + +
166B GLU 3.4 0.2 - - - -
167B GLU* 1.3 75.5 - - - +
169B ARG* 1.3 57.4 + - - +
171B ARG* 3.4 8.0 + - - +
172B ARG* 2.9 35.0 + - + +
179B SER* 3.6 35.6 + - - -
180B VAL 3.7 19.1 + - - -
181B MET 4.1 0.4 - - - -
182B THR* 2.8 30.7 + - - +
251B ILE* 4.5 9.4 - - + -
252B CYS* 4.1 9.0 - - - -
253B SER* 3.6 12.1 + - - -
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Residues in contact with ARG 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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41B PRO* 4.2 31.2 + - - +
42B PRO 4.4 9.5 + - - -
43B LEU* 4.6 6.1 - - - +
146B SER 5.5 1.2 + - - -
147B ASP* 3.4 28.5 + - - +
165B LEU* 2.9 51.7 + - - +
166B GLU* 2.9 35.7 + - - +
167B GLU 3.3 0.2 - - - -
168B HIS* 1.3 77.8 - - - +
170B LEU* 1.3 56.7 + - - +
172B ARG* 3.3 5.0 + - - +
173B LYS* 2.9 51.0 + - - +
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Residues in contact with LEU 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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166B GLU* 2.9 24.2 + - + +
167B GLU* 3.3 25.1 - - + +
169B ARG* 1.3 73.4 - - - +
171B ARG* 1.3 71.7 + - + +
173B LYS* 3.7 10.2 - - + -
174B LEU* 2.9 50.1 + - + +
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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
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167B GLU* 2.9 49.6 + - - +
168B HIS* 3.6 15.0 - - - +
170B LEU* 1.3 85.8 - - + +
172B ARG* 1.3 61.6 + - - +
174B LEU* 5.1 3.1 - - - -
175B GLU* 3.4 31.8 + - + +
179B SER* 3.9 15.8 + - - -
182B THR* 3.1 41.0 + - - +
209B THR* 4.9 6.1 - - - -
210B ASN* 3.8 16.3 + - - +
288B HIS* 3.3 47.4 + - + +
289B MET 5.0 1.8 + - - +
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Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASP* 3.3 26.1 + - - +
168B HIS* 2.9 26.6 + - + +
169B ARG* 3.7 5.4 - - - +
170B LEU 3.2 0.2 - - - -
171B ARG* 1.3 78.2 - - - +
173B LYS* 1.3 62.2 + - + +
176B LYS* 3.3 5.2 + - - -
177B ASN* 3.1 44.0 + - - +
179B SER* 3.3 30.6 + - - +
253B SER* 2.5 37.4 + - - -
254B PRO* 5.7 3.7 - - - +
255B GLN* 3.2 31.9 - - - +
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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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166B GLU* 5.5 3.2 + - - -
169B ARG* 2.9 38.2 + - - +
170B LEU* 3.2 9.4 + - + +
172B ARG* 1.3 79.3 - - + +
174B LEU* 1.3 69.1 + - + +
176B LYS* 4.1 4.3 + - - +
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Residues in contact with LEU 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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170B LEU* 2.9 35.6 + - + +
171B ARG* 4.8 2.5 - - - +
173B LYS* 1.3 84.4 - - + +
175B GLU* 1.3 65.1 + - + +
176B LYS* 3.3 5.7 + - - +
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Residues in contact with GLU 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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171B ARG* 3.4 21.7 + - - +
174B LEU* 1.3 81.1 - - + +
176B LYS* 1.3 71.3 + - - +
177B ASN 3.6 1.3 - - - -
178B VAL* 3.4 21.6 - - + +
179B SER 5.0 0.7 + - - -
286B GLN* 2.6 33.1 + - - -
288B HIS* 4.2 11.8 + - - -
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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