Contacts of the helix formed by residues 164 - 173 (chain C) in PDB entry 1PR1
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 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161C SER 4.6 3.0 + - - -
162C PRO 3.7 5.1 + - - -
163C ASP* 1.3 70.4 - - - +
165C GLU* 1.3 61.5 + - - +
166C MET 3.0 5.8 - - - -
167C PHE* 3.1 39.7 + - - +
168C ASP* 4.1 4.0 + - - +
207C ARG* 5.3 0.9 + - - -
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Residues in contact with GLU 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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163C ASP* 3.2 13.4 - - - +
164C GLY* 1.3 79.0 - - - +
166C MET* 1.3 61.0 + - - +
167C PHE 3.2 0.2 - - - -
168C ASP* 3.2 33.9 + - - +
169C VAL* 3.5 20.1 + - - +
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Residues in contact with MET 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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154C PHE* 3.9 30.5 - - + -
161C SER* 5.7 0.4 - - - +
163C ASP* 3.4 32.2 + - + +
164C GLY 3.0 0.4 - - - -
165C GLU* 1.3 78.3 - - - +
167C PHE* 1.3 59.5 + - + +
169C VAL* 3.1 33.8 + - + +
170C MET* 2.8 48.0 + - + +
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Residues in contact with PHE 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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94C VAL* 3.4 11.4 - - + +
159C PHE 5.7 4.3 - - - -
161C SER* 4.9 18.6 - - - -
163C ASP 4.9 2.5 - - - -
164C GLY* 3.1 32.9 + - - +
166C MET* 1.3 78.2 - - + +
168C ASP* 1.3 57.2 + - - +
170C MET* 3.3 31.5 + - + +
171C GLU* 2.8 31.5 + - - +
178C VAL* 4.6 10.5 - - + -
206C ILE* 3.6 42.4 - - + -
207C ARG* 3.5 22.7 - - - +
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Residues in contact with ASP 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 GLY 4.5 2.6 - - - +
165C GLU* 3.3 34.5 - - - +
166C MET 3.1 0.4 - - - -
167C PHE* 1.3 76.3 - - - +
169C VAL* 1.3 57.6 + - - +
171C GLU* 3.6 5.8 + - - +
172C LYS* 2.9 29.1 + - - +
207C ARG* 2.9 27.7 + - - +
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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
----------------------------------------------------------
165C GLU* 3.6 33.0 - - - +
166C MET* 3.1 32.9 + - + +
168C ASP* 1.3 75.4 - - - +
170C MET* 1.3 65.7 - - - +
172C LYS* 3.2 5.3 + - - +
173C TYR* 3.1 40.5 + - + +
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Residues in contact with MET 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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94C VAL* 4.5 3.4 - - + -
154C PHE* 3.7 42.2 - - + -
156C ALA* 6.0 0.7 - - + -
166C MET* 2.8 38.5 + - + +
167C PHE* 3.5 38.4 - - + +
169C VAL* 1.3 77.1 - - - +
171C GLU* 1.3 63.6 + - - +
173C TYR* 3.0 12.6 + - - -
174C GLY 3.1 8.7 + - - -
175C ILE* 3.2 31.5 + - + +
178C VAL* 3.6 28.9 - - + -
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Residues in contact with GLU 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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94C VAL* 3.5 28.3 - - + +
95C LEU* 3.6 21.3 - - + +
96C PRO* 3.3 26.0 - - - +
167C PHE 2.8 16.8 + - - +
168C ASP* 3.7 6.5 - - - +
170C MET* 1.3 76.2 - - - +
172C LYS* 1.3 65.0 + - - +
174C GLY* 2.8 16.2 + - - +
207C ARG* 3.0 20.8 + - - -
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Residues in contact with LYS 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 ASP 2.9 19.3 + - - +
169C VAL* 3.2 8.3 + - - +
171C GLU* 1.3 78.1 - - - +
173C TYR* 1.3 86.9 + - + +
174C GLY 3.4 1.9 + - - -
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Residues in contact with TYR 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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162B PRO* 4.9 13.2 - - - +
110C CYS* 6.5 0.4 - - - -
152C ASN* 5.5 5.2 + - - +
169C VAL* 3.1 31.2 + - + +
170C MET* 3.0 5.9 + - - +
172C LYS* 1.3 104.0 - - + +
174C GLY* 1.3 63.2 + - - +
175C ILE* 3.3 11.3 + - + +
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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