Contacts of the helix formed by residues 162 - 174 (chain C) in PDB entry 1RZR
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 GLU 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C ASP* 2.5 24.5 + - - +
161C TYR* 1.3 73.5 - - - +
163C GLN* 1.3 69.0 + - - +
165C ALA* 2.8 13.3 + - - +
166C PHE* 2.8 11.3 + - - +
195C LYS* 3.4 23.8 - - + +
198C LYS* 3.2 30.8 - - - +
199C GLY* 2.7 31.9 + - - -
202C ARG* 3.8 29.5 + - - +
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Residues in contact with GLN 163 (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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160C ASP* 2.7 41.6 + - + +
162C GLU* 1.3 72.5 + - - +
164C ALA* 1.3 55.1 + - - +
165C ALA 2.7 1.4 + - - -
166C PHE* 2.6 42.0 + - - -
167C ASP* 2.7 35.7 + - - -
202C ARG* 3.7 17.7 + - - +
323C HIS* 3.8 15.5 - - + +
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Residues in contact with ALA 164 (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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159C ILE* 4.3 3.1 - - + -
160C ASP 2.8 17.0 + - - +
161C TYR* 4.3 0.2 - - - -
163C GLN* 1.3 73.7 - - - +
165C ALA* 1.3 61.2 + - - +
167C ASP* 4.5 1.6 - - - -
168C ALA* 3.2 24.4 + - - +
274C PHE* 3.7 29.1 - - + -
290C VAL* 3.8 12.7 - - + +
323C HIS* 3.5 37.5 - - + +
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Residues in contact with ALA 165 (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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161C TYR 3.2 17.6 + - - +
162C GLU 2.8 13.2 + - - +
163C GLN 2.7 4.9 + - - -
164C ALA* 1.3 75.8 - - - +
166C PHE* 1.3 62.8 + - - +
168C ALA* 3.5 2.3 - - - +
169C VAL* 3.0 24.4 + - - +
195C LYS 3.8 0.4 - - - +
196C LYS* 3.5 17.9 - - + +
199C GLY* 3.4 18.4 - - - -
200C TYR* 3.8 2.4 - - - +
244C PHE* 4.2 15.8 - - + -
274C PHE* 4.7 2.5 - - + -
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Residues in contact with PHE 166 (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 GLU 2.8 10.2 + - - +
163C GLN* 2.6 33.0 + - - +
165C ALA* 1.3 71.3 - - - +
167C ASP* 1.3 71.3 + - - +
169C VAL* 2.8 10.1 - - - +
170C GLN* 2.8 60.2 + - + +
199C GLY* 3.8 8.4 - - - +
202C ARG* 3.4 41.5 - - - +
203C ALA* 3.5 28.7 - - + -
206C GLU* 4.2 14.8 - - + -
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Residues in contact with ASP 167 (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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163C GLN* 2.7 36.8 + - - +
164C ALA 4.5 1.1 - - - +
166C PHE* 1.3 81.5 - - - +
168C ALA* 1.3 64.4 + - - +
170C GLN* 3.6 8.1 + - - +
171C SER* 3.3 17.5 + - - -
290C VAL* 6.1 1.3 - - + -
323C HIS* 3.0 30.6 + - + +
325C ILE* 5.0 12.1 - - + +
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Residues in contact with ALA 168 (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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164C ALA 3.2 17.5 + - - +
165C ALA 3.3 1.0 + - - +
166C PHE 3.1 0.6 - - - -
167C ASP* 1.3 78.4 - - - +
169C VAL* 1.3 64.4 + - - +
171C SER* 3.0 21.5 - - - -
172C LEU* 3.8 2.6 + - - +
244C PHE* 3.2 29.2 - - + -
272C ILE* 4.2 10.9 - - + +
290C VAL* 3.2 23.3 - - + +
325C ILE* 4.5 8.7 - - - -
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Residues in contact with VAL 169 (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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165C ALA 3.0 12.8 - - - +
166C PHE* 2.8 20.2 - - - +
168C ALA* 1.3 71.9 - - - +
170C GLN* 1.3 55.2 + - - +
172C LEU* 2.5 43.5 + - + +
173C ILE* 3.3 6.8 + - + -
180C ILE* 3.6 28.9 - - + -
200C TYR* 4.2 20.0 - - + +
203C ALA* 3.1 34.3 - - + -
204C LEU* 4.6 1.6 - - + -
244C PHE* 4.2 14.3 - - + -
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Residues in contact with GLN 170 (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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166C PHE* 2.8 65.0 + - + +
167C ASP* 3.7 7.9 - - - +
169C VAL* 1.3 71.0 - - - +
171C SER* 1.3 66.3 + - - +
173C ILE* 2.6 40.0 + - + +
174C ASP* 2.9 37.5 + - - +
203C ALA 4.4 0.5 - - - +
206C GLU* 3.4 13.7 - - - +
207C SER* 4.2 5.7 + - - -
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Residues in contact with SER 171 (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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167C ASP 3.3 9.0 + - - -
168C ALA* 3.0 18.5 + - - -
170C GLN* 1.3 78.4 - - - +
172C LEU* 1.3 58.0 + - - +
174C ASP* 3.5 19.2 + - - +
175C SER* 3.6 10.9 + - - -
272C ILE* 5.1 5.9 - - - +
325C ILE* 5.4 1.6 - - - -
327C PHE* 3.1 35.8 - - - -
331C THR* 5.0 8.2 - - - +
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Residues in contact with LEU 172 (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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168C ALA 4.8 2.0 - - - +
169C VAL* 2.5 27.7 + - + +
171C SER* 1.3 74.8 + - - +
173C ILE* 1.3 62.2 + - - +
175C SER* 3.3 9.8 + - - +
176C GLY 3.7 0.5 + - - -
177C HIS* 3.3 34.6 + - + +
180C ILE* 3.8 31.6 - - + -
242C ALA* 3.5 21.3 - - + -
243C ILE 3.8 22.0 - - - +
244C PHE* 4.8 4.9 - - + -
270C GLU* 4.3 19.1 - - + +
272C ILE* 4.4 16.6 - - + -
331C THR* 4.8 10.5 - - + +
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Residues in contact with ILE 173 (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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169C VAL* 4.1 13.9 - - + +
170C GLN* 2.6 34.6 + - - +
172C LEU* 1.3 71.9 - - - +
174C ASP* 1.3 65.0 + - - +
175C SER 3.0 2.2 + - - -
176C GLY* 3.2 11.6 + - - -
177C HIS 4.0 15.0 + - - +
180C ILE* 4.3 9.6 - - + -
203C ALA 3.1 25.6 - - - +
204C LEU* 4.3 8.3 - - + -
207C SER* 3.0 44.9 - - - +
209C LEU* 5.3 2.9 - - + -
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Residues in contact with ASP 174 (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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170C GLN* 2.9 33.2 + - - +
171C SER* 3.5 12.6 - - - +
173C ILE* 1.3 78.6 - - - +
175C SER* 1.3 58.0 + - - +
176C GLY 3.6 0.4 - - - -
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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