Contacts of the helix formed by residues 176 - 191 (chain L) in PDB entry 6E07
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 176 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175L ARG* 1.3 83.0 + - - +
177L LEU* 1.3 66.6 + - - +
178L GLN* 3.2 13.8 + - - +
179L SER* 3.0 38.1 + - - -
180L SER* 3.0 20.4 + - - -
257L ARG* 5.5 4.0 - - - +
462L TRP* 3.9 11.7 - - - -
466L THR* 4.2 3.4 - - - +
469L LEU* 5.6 2.5 - - + -
470L HIS* 3.9 30.4 + - + +
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Residues in contact with LEU 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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176L ASP* 1.3 71.5 - - - +
178L GLN* 1.3 57.3 + - - +
180L SER* 3.6 0.3 + - - -
181L ASP* 2.9 58.4 + - - +
459L LEU* 3.7 19.7 - - + +
462L TRP* 3.2 33.7 - - + -
463L ARG* 3.7 14.4 - - + +
466L THR* 3.2 27.9 + - + +
470L HIS* 6.1 0.7 - - + -
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Residues in contact with GLN 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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176L ASP* 3.1 11.6 + - - +
177L LEU* 1.3 80.1 - - - +
179L SER* 1.3 59.2 + - - +
181L ASP* 3.3 5.1 + - - +
182L ARG* 3.0 64.7 + - + +
470L HIS* 6.4 0.2 - - - -
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Residues in contact with SER 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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174L GLY* 4.1 4.0 - - - -
175L ARG* 3.1 44.6 + - - -
176L ASP* 3.0 29.2 + - - -
178L GLN* 1.3 76.1 - - - +
180L SER* 1.3 59.1 + - - +
182L ARG* 3.5 9.3 + - - +
183L LEU* 3.2 23.9 + - - +
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Residues in contact with SER 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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173L PHE* 2.9 26.9 + - - +
174L GLY* 3.7 3.7 - - - -
176L ASP 3.0 13.3 + - - -
177L LEU 3.9 1.1 - - - -
179L SER* 1.3 76.6 + - - +
181L ASP* 1.3 55.0 + - - +
183L LEU* 3.3 4.5 + - - +
184L SER* 2.8 35.6 + - - -
458L LEU* 4.2 13.2 - - - +
459L LEU* 5.9 0.2 - - - -
462L TRP* 2.9 37.1 + - - -
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Residues in contact with ASP 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 LEU* 2.9 41.9 + - - +
178L GLN* 3.3 6.6 + - - +
180L SER* 1.3 79.6 + - - +
182L ARG* 1.3 57.3 + - + +
184L SER* 3.5 6.3 + - - -
185L ASN* 3.0 41.2 + - - +
459L LEU* 3.5 35.5 - - - +
462L TRP* 5.5 0.5 - - - -
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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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178L GLN* 3.0 59.1 + - + +
179L SER* 4.0 7.4 - - - +
181L ASP* 1.3 72.0 - - + +
183L LEU* 1.3 61.3 + - - +
185L ASN* 3.4 8.0 + - - +
186L HIS* 2.9 29.2 + - - +
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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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144L PRO 5.8 0.9 - - - +
147L TYR* 4.5 26.2 - - + -
148L GLU* 4.9 11.4 - - + +
169L VAL* 5.7 0.2 - - + -
172L PRO 5.7 0.9 - - - +
173L PHE* 4.8 28.9 - - + -
174L GLY* 5.4 2.2 - - - +
179L SER 3.2 14.8 + - - +
180L SER* 3.3 10.3 + - - +
182L ARG* 1.3 77.0 - - - +
184L SER* 1.3 63.2 + - - +
186L HIS* 3.2 13.8 + - + +
187L ILE* 3.0 60.1 + - + +
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Residues in contact with SER 184 (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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180L SER* 2.8 21.5 + - - -
181L ASP* 3.7 9.4 - - - -
183L LEU* 1.3 75.9 - - - +
185L ASN* 1.3 61.1 + - - +
187L ILE* 3.4 6.4 + - - +
188L SER* 2.9 35.2 + - - -
198L ARG* 4.5 7.4 + - - +
455L SER* 4.4 16.9 + - - -
458L LEU* 4.1 21.1 - - - +
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Residues in contact with ASN 185 (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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181L ASP* 3.0 28.3 + - - +
182L ARG* 3.8 7.1 - - - +
183L LEU 3.3 0.2 - - - -
184L SER* 1.3 75.5 - - - +
186L HIS* 1.3 61.1 + - - +
188L SER* 3.8 5.7 - - - -
189L SER* 2.9 30.8 + - - -
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Residues in contact with HIS 186 (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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148L GLU* 3.1 49.9 + - + +
151L THR* 3.1 27.8 + - - -
152L LYS* 3.8 17.7 + - + -
182L ARG 2.9 14.1 + - - +
183L LEU* 3.2 13.2 + - + +
185L ASN* 1.3 74.1 - - - +
187L ILE* 1.3 72.7 + - + +
189L SER* 2.6 24.9 + - - -
190L LEU* 3.1 33.7 - - + +
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Residues in contact with ILE 187 (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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147L TYR* 5.3 4.5 - - + +
151L THR* 4.5 14.8 - - + +
167L ILE* 4.5 14.6 - - + -
169L VAL* 4.7 20.0 - - + -
173L PHE* 6.2 0.2 - - + -
183L LEU* 3.0 47.9 + - + +
184L SER* 4.0 5.2 - - - +
186L HIS* 1.3 83.5 - - + +
188L SER* 1.3 57.3 + - - +
190L LEU* 3.1 9.6 + - - +
191L PHE* 2.9 29.1 + - + +
196L ILE* 3.7 32.1 - - + -
198L ARG* 5.4 7.6 - - - +
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Residues in contact with SER 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L SER* 2.9 20.8 + - - -
185L ASN* 4.0 6.1 - - - -
187L ILE* 1.3 72.4 - - - +
189L SER* 1.3 62.7 + - - +
190L LEU 3.1 2.6 - - - -
191L PHE 3.2 20.0 + - - +
193L GLU* 4.8 2.1 + - - -
196L ILE* 4.6 9.0 - - - +
198L ARG* 4.7 1.9 + - - -
455L SER* 4.5 12.6 + - - -
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Residues in contact with SER 189 (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 HIS* 5.1 1.7 - - - -
185L ASN 2.9 15.6 + - - -
186L HIS* 2.6 25.6 + - - -
188L SER* 1.3 76.2 - - - +
190L LEU* 1.3 71.6 + - - +
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Residues in contact with LEU 190 (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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151L THR* 4.3 11.0 - - - +
152L LYS* 4.4 14.1 - - + +
155L HIS* 3.3 48.8 + - + +
186L HIS* 3.1 49.1 - - + +
187L ILE* 3.1 3.0 + - - +
188L SER 3.1 1.0 - - - -
189L SER* 1.3 99.4 - - - +
191L PHE* 1.3 74.7 + - + +
192L ARG 4.4 0.2 + - - -
195L GLN* 4.6 1.4 - - - +
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Residues in contact with PHE 191 (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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151L THR* 3.7 28.9 - - - -
154L ILE* 4.2 11.0 - - + -
155L HIS* 3.8 15.9 - - + -
159L MET* 3.9 22.0 - - + -
165L ASN* 5.5 2.7 - - + -
167L ILE* 3.7 45.5 - - + -
187L ILE* 2.9 16.0 + - + +
188L SER* 3.2 24.1 - - - +
190L LEU* 1.3 94.7 - - + +
192L ARG* 1.3 66.1 + - - +
193L GLU 3.9 0.3 + - - -
195L GLN* 3.5 23.1 - - + +
196L ILE* 3.9 19.7 - - + +
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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