Contacts of the helix formed by residues 185 - 192 (chain C) in PDB entry 4LXZ
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 GLY 185 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C HIS* 3.3 13.2 - - - -
177C TYR* 4.8 4.6 - - - -
179C ASP* 3.2 24.6 + - - -
183C HIS 3.5 2.0 + - - -
184C HIS* 1.3 73.2 + - - +
186C ASP* 1.3 56.9 + - - -
187C GLY 3.5 2.5 - - - -
188C VAL* 3.6 5.2 + - - +
189C GLU* 3.0 29.6 + - - +
202C SER* 3.3 14.3 + - - -
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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
----------------------------------------------------------
146C HIS* 2.7 34.3 + - - +
148C LYS* 2.7 28.5 + - - +
153C SER* 4.8 0.3 + - - -
184C HIS* 2.9 31.6 + - + +
185C GLY* 1.3 71.2 - - - +
187C GLY* 1.3 62.9 + - - -
189C GLU* 3.5 1.8 + - - +
190C GLU* 2.8 32.2 + - - +
211C PRO* 3.6 22.0 - - - +
213C THR* 3.5 12.7 + - + +
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Residues in contact with GLY 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 4.1 4.3 + - - -
145C HIS 3.1 13.0 + - - -
146C HIS 4.1 0.9 - - - -
147C ALA 3.8 16.0 - - - +
148C LYS* 3.9 15.3 - - - -
159C ASN* 3.8 5.6 - - - -
162C VAL* 4.1 2.1 - - - +
186C ASP* 1.3 84.7 + - - +
188C VAL* 1.3 57.7 + - - +
190C GLU* 3.9 2.0 - - - +
191C ALA* 3.1 27.0 + - - +
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Residues in contact with VAL 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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145C HIS* 3.9 12.1 - - + +
159C ASN* 3.9 6.5 - - - +
161C ILE* 3.8 37.5 - - + -
162C VAL* 3.9 8.3 - - + -
165C ILE* 4.0 19.1 - - + -
177C TYR* 3.6 42.2 - - + +
185C GLY 3.6 2.0 + - - +
186C ASP 3.3 0.4 - - - -
187C GLY* 1.3 71.9 - - - +
189C GLU* 1.3 66.7 + - - +
191C ALA* 3.3 1.7 + - - +
192C PHE* 3.2 34.1 + - + +
200C THR* 4.0 3.5 - - + +
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C HIS* 2.7 35.6 + - - +
185C GLY 3.0 19.0 + - - +
186C ASP* 3.7 3.4 - - - +
188C VAL* 1.3 78.1 - - - +
190C GLU* 1.3 57.5 + - - +
192C PHE 3.5 1.0 - - - -
193C TYR* 2.9 58.7 + - + -
200C THR* 3.8 27.0 + - - +
202C SER* 5.5 0.3 - - - -
213C THR* 5.6 0.3 - - - -
218C ASP* 4.4 7.4 - - - +
228C ALA* 4.2 4.7 - - + +
229C VAL 4.9 1.0 - - - +
230C ASN* 2.8 24.9 + - - +
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Residues in contact with GLU 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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365A GLU* 3.8 20.4 - - - +
368A LYS* 5.3 0.7 + - - -
369A GLN* 3.0 38.2 + - - +
372A PHE* 5.8 0.3 - - - -
72C TYR* 4.2 8.8 + - - -
148C LYS* 3.4 37.0 - - + +
149C LYS* 4.7 11.8 + - - +
186C ASP 2.8 21.9 + - - +
187C GLY 3.9 2.8 - - - +
189C GLU* 1.3 75.3 - - - +
191C ALA* 1.3 62.1 + - - +
192C PHE 3.3 0.5 + - - -
193C TYR* 3.3 20.0 + - - +
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Residues in contact with ALA 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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72C TYR* 3.2 38.0 + - + +
149C LYS* 4.4 4.8 + - - +
162C VAL* 3.7 20.0 - - + -
187C GLY 3.1 16.0 + - - +
188C VAL 3.3 6.5 + - - +
190C GLU* 1.3 75.1 - - - +
192C PHE* 1.4 65.1 + - + +
193C TYR 3.5 0.8 + - - -
194C THR* 5.3 1.0 + - - -
404C PG4 3.6 22.9 - - - +
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Residues in contact with PHE 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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162C VAL* 4.0 28.5 - - + -
165C ILE* 3.5 39.3 - - + -
166C LEU* 4.0 13.2 - - + -
169C LEU* 4.1 3.1 - - + -
188C VAL* 3.2 28.1 + - + +
189C GLU 3.5 2.5 - - - -
191C ALA* 1.4 84.2 - - + +
193C TYR* 1.3 58.3 + - - +
194C THR 3.2 2.7 - - - -
195C THR* 3.2 15.9 + - + +
198C VAL* 3.6 42.6 - - + -
200C THR* 4.5 4.0 - - + -
403C NA 2.3 31.4 - - - -
404C PG4 3.8 30.1 - - - -
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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