Contacts of the helix formed by residues 177 - 193 (chain C) in PDB entry 2Y0N
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 177 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C GLU 3.7 8.3 - - - +
176C ILE* 1.3 86.1 - - + +
178C GLU* 1.3 56.0 + - - +
179C VAL* 3.2 4.3 - - + +
180C LEU* 2.8 31.1 + - + -
181C LYS 2.9 9.0 + - - -
488C LEU* 3.8 41.1 - - + +
489C ARG* 4.4 8.3 - - + +
492C ALA* 3.9 21.5 - - + -
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Residues in contact with GLU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ILE 3.3 4.2 + - - +
177C PRO* 1.3 70.8 - - - +
179C VAL* 1.3 62.2 + - + +
181C LYS* 3.5 29.8 + - + +
182C LYS* 3.0 39.8 + - - +
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C PRO* 5.2 2.0 - - + -
178C GLU* 1.3 77.2 - - - +
180C LEU* 1.3 57.3 + - - +
182C LYS* 3.7 20.3 - - + +
183C GLN* 3.2 22.3 + - - +
492C ALA* 4.5 22.2 - - + +
495C HIS* 4.1 36.4 + - + +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ILE* 3.8 8.5 - - + -
177C PRO* 2.8 21.6 + - + +
179C VAL* 1.3 72.7 - - - +
181C LYS* 1.3 60.8 + - - +
182C LYS 3.3 0.4 - - - -
183C GLN* 3.3 6.5 + - + +
184C LEU* 2.9 32.6 + - - +
457C LEU* 3.8 15.8 - - + +
488C LEU* 3.3 50.3 - - + +
491C LEU* 3.9 25.4 - - + +
492C ALA* 3.9 13.0 - - + +
495C HIS* 4.6 8.3 - - + -
499C PHE* 4.0 21.5 - - + -
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Residues in contact with LYS 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ILE* 3.5 45.7 - - + +
177C PRO 2.9 4.9 + - - -
178C GLU* 3.5 33.2 + - + +
180C LEU* 1.3 73.6 - - - +
182C LYS* 1.3 64.5 + - + +
184C LEU* 3.2 11.2 + - + +
185C GLU* 3.1 30.5 + - - +
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Residues in contact with LYS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C GLU* 3.0 32.0 + - + +
179C VAL* 3.7 19.7 - - + +
181C LYS* 1.3 71.2 - - + +
183C GLN* 1.3 59.3 + - - +
185C GLU* 2.8 38.1 + - - +
186C ASP* 2.8 21.7 + - - +
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Residues in contact with GLN 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C VAL 3.2 13.3 + - - +
180C LEU* 3.3 13.0 + - + +
182C LYS* 1.3 78.1 - - - +
184C LEU* 1.3 57.1 + - - +
186C ASP* 3.3 16.4 + - - +
187C ASP* 2.9 31.9 + - + +
190C TYR* 5.8 1.8 - - - -
454C GLN* 5.0 1.0 - - - +
457C LEU* 4.0 9.0 - - + -
495C HIS* 3.4 24.0 + - + +
499C PHE* 3.5 48.9 - - + +
501C GLU* 5.4 3.8 - - - +
504C TYR* 4.0 21.4 + - - -
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ILE* 4.0 18.2 - - + -
180C LEU 2.9 16.3 + - - +
181C LYS* 3.5 10.8 - - + +
182C LYS 3.1 0.4 - - - -
183C GLN* 1.3 73.1 - - - +
185C GLU* 1.3 61.4 + - + +
187C ASP* 3.4 10.2 - - + +
188C CYS* 3.1 26.5 + - - +
275C TYR* 5.1 1.0 + - - -
454C GLN 5.1 0.7 - - - +
457C LEU* 3.8 30.3 - - + +
458C ARG* 4.1 32.3 - - + +
461C VAL* 3.8 25.4 - - + -
589G PHE* 4.7 9.0 - - + -
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Residues in contact with GLU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C LYS* 3.1 19.9 + - - +
182C LYS* 2.8 23.7 + - - +
184C LEU* 1.3 70.5 - - + +
186C ASP* 1.3 64.2 + - - +
188C CYS* 3.4 8.1 + - - +
189C TYR* 3.1 22.7 + - - +
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Residues in contact with ASP 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LYS* 2.8 20.7 + - - +
183C GLN* 3.4 23.3 - - - +
185C GLU* 1.3 74.3 - - - +
187C ASP* 1.3 65.1 + - - +
189C TYR* 3.0 9.9 + - - +
190C TYR* 3.0 44.9 + - + -
501C GLU* 5.7 2.6 - - - +
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Residues in contact with ASP 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C GLN* 2.9 21.5 + - - +
184C LEU* 3.4 14.1 - - + +
186C ASP* 1.3 76.1 - - - +
188C CYS* 1.3 62.8 + - - +
190C TYR* 3.4 17.4 + - - +
191C ILE* 3.4 26.4 + - - +
198C VAL* 5.0 0.3 - - - +
275C TYR* 5.0 0.3 - - - -
454C GLN* 3.9 15.5 - - - +
458C ARG* 2.6 37.2 + - - +
504C TYR* 2.7 27.7 + - - +
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Residues in contact with CYS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU 3.1 10.6 + - - +
185C GLU* 3.5 10.8 - - - +
187C ASP* 1.3 79.0 - - - +
189C TYR* 1.3 62.5 + - - +
191C ILE* 3.1 11.1 + - - -
192C ASN* 2.8 39.8 + - - +
193C ARG* 6.2 1.6 - - - -
275C TYR* 3.5 33.6 + - - +
590G GLU 6.1 0.7 - - - -
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Residues in contact with TYR 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C GLU 3.1 9.7 + - - +
186C ASP* 3.0 12.0 + - - +
188C CYS* 1.3 79.1 - - - +
190C TYR* 1.3 64.9 + + - +
192C ASN* 4.7 0.4 - - - -
193C ARG* 3.2 45.1 + - + +
194C ARG* 3.0 69.2 + - + +
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Residues in contact with TYR 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C GLN* 5.8 2.0 - - - -
186C ASP* 3.0 43.1 + - + +
187C ASP* 3.5 11.9 - - - +
188C CYS 3.2 0.2 - - - -
189C TYR* 1.3 77.8 - + + +
191C ILE* 1.3 52.0 + - - +
194C ARG* 3.4 33.3 + - - -
195C LYS 3.2 9.7 + - - -
196C ARG* 2.8 60.2 + - + +
501C GLU* 2.8 40.6 + - + +
504C TYR* 4.1 40.4 - + + -
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Residues in contact with ILE 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ASP* 3.4 33.4 - - - +
188C CYS 3.1 4.2 + - - +
190C TYR* 1.3 82.2 - - + +
192C ASN* 1.3 60.3 + - - +
193C ARG 3.5 0.2 - - - -
195C LYS* 3.4 18.4 - - - +
196C ARG 3.3 22.6 + - - +
197C LEU* 4.6 3.0 - - + +
198C VAL* 5.1 3.6 - - + -
275C TYR* 4.3 19.3 - - + -
277C TYR* 4.3 19.0 - - + +
278C GLU* 3.4 43.3 - - + +
458C ARG* 3.5 12.8 - - - +
504C TYR* 4.4 8.1 - - + -
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Residues in contact with ASN 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C CYS* 2.8 33.9 + - - +
189C TYR* 4.7 0.2 - - - -
191C ILE* 1.3 74.8 - - + +
193C ARG* 1.3 69.8 + - - +
195C LYS* 4.7 5.5 - - - +
275C TYR* 3.1 46.9 - - - +
276C PRO* 5.6 0.6 - - + +
277C TYR* 3.9 34.4 + - + -
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Residues in contact with ARG 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C CYS* 6.2 1.2 - - - -
189C TYR* 3.2 49.8 + - + +
191C ILE 3.5 0.8 - - - -
192C ASN* 1.3 89.6 + - - +
194C ARG* 1.3 60.6 + - - +
195C LYS* 3.0 14.5 + - - +
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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