Contacts of the helix formed by residues 183 - 193 (chain C) in PDB entry 5JHQ
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 LEU 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182C ALA* 1.3 73.7 - - - +
184C ARG* 1.3 65.6 + - + +
186C LEU* 3.0 23.1 + - + +
187C LEU* 3.1 42.8 + - + +
206C ASN* 5.2 8.3 - - + -
209C ALA* 3.6 35.2 - - + +
210C LYS 3.9 14.8 - - - +
211C ASP* 5.3 1.1 - - - +
212C MET 5.8 0.2 - - - +
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Residues in contact with ARG 184 (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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182C ALA* 4.4 3.9 - - - +
183C LEU* 1.3 79.6 - - + +
185C GLU* 1.3 60.3 + - - +
187C LEU* 3.5 11.1 + - + +
188C GLU* 3.1 25.1 + - - +
191C ARG* 5.2 0.9 + - - -
211C ASP* 5.8 3.1 - - - +
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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
----------------------------------------------------------
182C ALA* 3.5 23.1 + - - +
183C LEU 3.2 0.6 - - - -
184C ARG* 1.3 78.2 - - - +
186C LEU* 1.3 60.7 + - - +
188C GLU* 3.6 2.9 + - - +
189C ALA* 3.1 22.2 + - - +
197C ARG* 3.1 30.8 + - - +
200C ARG* 3.4 25.8 + - - -
201C LEU* 3.5 22.9 - - + +
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Residues in contact with LEU 186 (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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182C ALA 3.4 8.2 + - - +
183C LEU* 3.0 16.2 + - + +
185C GLU* 1.3 75.9 - - - +
187C LEU* 1.3 61.0 + - - +
189C ALA* 3.1 5.6 + - - +
190C CYS* 2.9 40.6 + - - -
198C VAL* 3.9 31.0 - - + -
201C LEU* 3.8 23.5 - - + +
202C VAL* 4.1 16.6 - - + -
206C ASN* 3.2 34.8 - - + +
219C PRO* 3.9 23.3 - - + -
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Residues in contact with LEU 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 LEU* 3.1 39.2 + - + +
184C ARG* 4.0 11.0 - - + +
186C LEU* 1.3 75.7 - - + +
188C GLU* 1.3 61.0 + - - +
190C CYS* 3.4 7.6 + - - +
191C ARG* 3.4 41.0 + - - +
211C ASP* 3.6 39.9 - - + +
217C SER 4.6 1.8 - - - +
218C SER 4.4 0.7 - - - -
219C PRO* 3.8 34.8 - - + -
222C PHE* 3.9 24.2 - - + -
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Residues in contact with GLU 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 ARG 3.1 17.9 + - - +
185C GLU* 3.9 5.6 - - - +
187C LEU* 1.3 74.3 - - - +
189C ALA* 1.3 63.5 - - - +
191C ARG* 2.7 39.6 + - - +
192C ASN* 3.2 47.1 + - - +
197C ARG* 3.8 13.0 - - - +
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Residues in contact with ALA 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 14.1 + - - +
186C LEU* 3.1 12.0 + - - +
188C GLU* 1.3 76.3 - - - +
190C CYS* 1.3 56.8 + - - +
192C ASN* 4.8 0.9 - - - -
193C GLY* 3.0 25.3 + - - -
194C ASP* 3.1 15.0 + - + +
197C ARG* 3.5 37.6 - - + +
198C VAL* 3.8 20.1 - - + +
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Residues in contact with CYS 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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186C LEU* 2.9 31.6 + - - -
187C LEU* 3.6 9.9 - - - +
188C GLU 3.2 0.2 - - - -
189C ALA* 1.3 77.2 - - - +
191C ARG* 1.3 61.4 + - - +
198C VAL* 4.1 8.7 - - - -
219C PRO* 3.9 42.6 - - - +
222C PHE* 4.3 3.4 - - + -
223C ALA* 3.6 25.2 - - + +
228C ARG* 3.7 13.3 - - - +
231C VAL* 4.2 15.8 - - - +
235C LEU* 4.2 3.8 - - - -
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Residues in contact with ARG 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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184C ARG 5.2 0.6 + - - -
187C LEU* 3.4 26.4 + - - +
188C GLU* 2.7 54.1 + - - +
190C CYS* 1.3 76.9 - - - +
192C ASN* 1.3 65.4 + - - +
211C ASP* 4.4 5.9 + - - -
222C PHE* 3.5 38.6 - - + -
226C PHE* 3.3 47.8 - - + +
228C ARG* 3.1 28.1 + - - -
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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 GLU* 3.2 41.5 + - - +
189C ALA* 4.1 3.4 - - - +
191C ARG* 1.3 80.7 - - - +
193C GLY* 1.3 62.2 + - - +
194C ASP* 4.3 8.8 - - + +
197C ARG* 4.2 9.3 - - - +
228C ARG* 3.0 20.0 + - - +
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Residues in contact with GLY 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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189C ALA 3.0 8.1 + - - -
191C ARG 3.4 3.6 + - - -
192C ASN* 1.3 78.7 - - - +
194C ASP* 1.3 59.6 + - - +
195C VAL* 3.0 16.7 + - - +
228C ARG* 3.3 26.2 - - - +
231C VAL* 3.7 9.0 - - - -
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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