Contacts of the helix formed by residues 168 - 183 (chain L) 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 ASN 168 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165L LEU 5.2 1.6 - - - +
166L ASP* 3.7 1.0 - - - -
167L LEU* 1.3 82.5 + - - +
169L GLU* 1.3 65.5 + - - +
170L ASP* 3.5 2.5 - - + +
171L GLU* 3.8 23.0 - - + +
172L ARG* 3.8 18.5 + - - +
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Residues in contact with GLU 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L ASN* 1.3 77.0 - - - +
170L ASP* 1.3 60.9 + - + +
172L ARG* 4.5 2.0 - - - +
173L GLU* 4.1 14.9 + - - +
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Residues in contact with ASP 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L ASN* 4.2 2.1 - - + +
169L GLU* 1.3 78.0 - - + +
171L GLU* 1.3 60.8 + - - +
172L ARG 3.3 0.4 - - - -
173L GLU* 3.4 7.4 + - - +
174L VAL* 2.9 29.6 + - - +
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Residues in contact with GLU 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L VAL* 5.5 1.2 - - - +
118L LEU* 5.6 11.2 - - + -
129L LEU* 5.0 13.5 - - + -
167L LEU* 4.3 11.2 - - + -
168L ASN* 3.8 26.6 - - + +
170L ASP* 1.3 77.4 - - - +
172L ARG* 1.3 59.0 + - - +
174L VAL* 3.4 5.6 + - - +
175L LEU* 2.9 30.0 + - - +
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Residues in contact with ARG 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L LEU* 4.2 22.9 - - + +
163L ASP* 5.9 1.1 - - - -
165L LEU* 4.8 13.7 - - + +
167L LEU* 5.3 2.8 - - + +
168L ASN 3.8 17.5 + - - +
169L GLU 4.8 2.5 - - - +
170L ASP 3.3 0.4 - - - -
171L GLU* 1.3 78.5 - - - +
173L GLU* 1.3 57.9 + - - +
175L LEU* 3.4 7.2 + - - +
176L ILE* 2.9 29.9 + - - +
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Residues in contact with GLU 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L GLU 4.1 12.4 + - - +
170L ASP* 3.4 10.6 + - - +
171L GLU 3.3 0.6 - - - -
172L ARG* 1.3 76.0 - - - +
174L VAL* 1.3 59.6 + - - +
176L ILE* 3.4 6.2 + - - +
177L ASN* 2.9 29.8 + - - +
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Residues in contact with VAL 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L VAL* 4.6 13.1 - - + +
117L VAL* 4.7 20.2 - - + -
118L LEU* 5.7 3.4 - - + +
170L ASP 2.9 17.2 + - - +
171L GLU* 3.8 7.2 - - - +
173L GLU* 1.3 76.3 - - - +
175L LEU* 1.3 57.8 + - - +
177L ASN* 3.4 5.9 + - - +
178L ASN* 2.9 29.3 + - - +
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Residues in contact with LEU 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L LEU* 6.4 2.7 - - + -
114L VAL* 4.4 16.7 - - + +
152L PHE* 6.2 4.3 - - + -
162L LEU* 6.3 1.6 - - + -
171L GLU 2.9 17.5 + - - +
172L ARG* 3.7 7.2 - - - +
174L VAL* 1.3 74.8 - - - +
176L ILE* 1.3 59.9 + - - +
178L ASN* 3.4 2.7 + - - +
179L ILE* 2.9 29.8 + - - +
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Residues in contact with ILE 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L ALA 6.0 1.6 - - - +
159L PRO* 5.5 9.0 - - + -
162L LEU* 4.9 16.0 - - + +
172L ARG 2.9 17.9 + - - +
173L GLU* 3.8 7.0 - - - +
174L VAL 3.3 0.2 - - - -
175L LEU* 1.3 75.5 - - - +
177L ASN* 1.3 57.4 + - - +
179L ILE* 3.4 5.6 + - - +
180L ASN* 2.9 30.8 + - - +
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Residues in contact with ASN 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173L GLU 2.9 17.9 + - - +
174L VAL* 3.8 7.6 - - - +
175L LEU 3.3 0.2 - - - -
176L ILE* 1.3 78.6 - - - +
178L ASN* 1.3 56.0 + - - +
180L ASN* 3.4 4.5 + - - +
181L ARG* 2.9 31.8 + - - +
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Residues in contact with ASN 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L ILE* 4.1 26.9 - - + +
113L HIS* 4.9 8.3 - - + -
114L VAL* 4.7 7.6 - - + +
174L VAL 2.9 18.5 + - - +
175L LEU* 3.8 6.7 - - - +
177L ASN* 1.3 76.5 - - - +
179L ILE* 1.3 56.6 + - - +
181L ARG* 3.8 5.0 - - - +
182L ARG* 2.9 34.7 + - - +
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Residues in contact with ILE 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L ILE* 5.4 6.2 - - + +
152L PHE* 4.7 29.6 - - + +
155L ALA* 5.6 4.3 - - + -
156L VAL* 4.3 9.7 - - + +
175L LEU 2.9 18.3 + - - +
176L ILE* 3.8 6.3 - - - +
178L ASN* 1.3 76.9 - - - +
180L ASN* 1.3 58.4 + - - +
182L ARG* 4.8 1.1 - - - -
183L LEU* 2.9 36.4 + - + +
184L THR* 3.7 2.3 + - - -
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Residues in contact with ASN 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L VAL* 4.9 11.6 - - - +
176L ILE 2.9 18.1 + - - +
177L ASN* 4.0 4.7 - - - +
178L ASN 3.4 0.2 - - - -
179L ILE* 1.3 77.1 - - - +
181L ARG* 1.3 60.2 + - - +
184L THR* 3.4 29.5 + - - +
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Residues in contact with ARG 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L ASN 2.9 18.9 + - - +
178L ASN* 4.0 4.9 - - - +
180L ASN* 1.3 78.8 - - - +
182L ARG* 1.3 58.6 + - - +
184L THR 4.9 1.7 - - - -
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Residues in contact with ARG 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L THR 5.9 0.7 - - - +
110L ILE* 4.9 14.6 - - + -
178L ASN 2.9 18.7 + - - +
179L ILE* 4.4 1.8 - - - +
181L ARG* 1.3 80.6 - - - +
183L LEU* 1.3 62.3 + - + +
184L THR 3.6 1.5 + - - -
185L PRO* 5.0 7.4 - - - +
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Residues in contact with LEU 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L TYR* 5.3 17.0 - - + -
152L PHE* 5.3 10.1 - - + +
153L LYS* 5.6 8.0 - - + +
156L VAL* 4.6 10.1 - - + +
179L ILE* 2.9 15.6 + - + +
182L ARG* 1.3 76.9 - - + +
184L THR* 1.3 59.2 + - - +
185L PRO* 3.6 3.9 - - - -
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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