Contacts of the helix formed by residues 218 - 237 (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 GLN 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C ARG* 4.3 13.1 - - - +
211C GLN* 4.6 11.6 + - - +
214C ALA* 3.4 22.2 + - + +
217C ARG* 1.3 74.8 - - - +
219C THR* 1.3 57.8 + - - +
220C THR* 2.8 32.7 + - - +
221C PHE* 2.6 35.7 + - + +
222C ASN* 2.5 43.0 + - - +
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Residues in contact with THR 219 (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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101C ARG* 5.0 9.2 - - - +
218C GLN* 1.3 75.8 - - - +
220C THR* 1.3 53.4 + - - +
222C ASN* 2.8 21.2 + - + +
223C ASP* 2.6 44.9 + - - +
226C LYS* 5.4 5.8 - - - +
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Residues in contact with THR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ARG* 2.6 80.6 + - + +
103C VAL* 4.6 6.3 - - + +
201C THR* 3.6 10.8 + - + -
218C GLN* 2.8 22.2 + - - -
219C THR* 1.3 72.6 - - - +
221C PHE* 1.3 56.1 + - - +
222C ASN 2.9 5.8 - - - -
223C ASP* 3.2 26.0 + - - +
224C MET 3.2 9.7 + - - -
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Residues in contact with PHE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 4.7 6.7 - - - -
27C TYR* 5.7 1.8 - - + -
90C SER* 4.1 14.4 - - - -
101C ARG* 5.7 0.7 - - - -
201C THR* 3.5 36.6 - - + -
202C VAL 5.3 0.2 - - - -
203C SER* 3.9 11.9 - - - -
211C GLN* 3.1 30.1 - - - -
214C ALA 3.9 5.6 - - - +
215C ALA* 3.4 36.6 - - + +
217C ARG* 4.9 2.2 - - - -
218C GLN* 2.6 51.2 + - + +
220C THR* 1.3 72.5 - - - +
222C ASN* 1.3 58.4 + - - +
224C MET* 3.9 17.5 - - + +
225C ILE* 2.9 28.6 + - - +
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Residues in contact with ASN 222 (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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27C TYR* 2.7 36.0 + - - -
31C THR* 4.7 0.6 - - - +
32C PHE* 3.4 20.7 - - + -
218C GLN* 2.5 22.5 + - - +
219C THR* 2.8 28.0 + - + +
221C PHE* 1.3 80.0 - - - +
223C ASP* 1.3 57.3 + - - +
224C MET 3.3 0.4 - - - -
225C ILE* 3.3 6.8 + - - +
226C LYS* 2.9 42.8 + - - +
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Residues in contact with ASP 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ARG* 4.8 4.3 + - - -
103C VAL* 4.6 4.7 - - + -
146C ILE* 3.5 40.0 - - + +
219C THR* 2.6 26.0 + - - +
220C THR* 3.2 27.1 + - - +
222C ASN* 1.3 76.3 - - - +
224C MET* 1.3 64.3 + - - +
226C LYS* 3.2 16.3 + - - +
227C ILE* 2.9 32.4 + - - +
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Residues in contact with MET 224 (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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24C ARG* 4.1 15.0 - - - +
88C VAL* 3.3 45.5 - - + +
89C GLY* 3.1 26.0 - - - +
103C VAL* 4.7 6.1 - - + +
199C ILE* 3.8 24.9 - - + +
201C THR* 3.2 27.6 - - - +
220C THR 3.2 2.2 + - - +
221C PHE* 3.9 24.2 - - + +
223C ASP* 1.3 80.4 - - - +
225C ILE* 1.3 60.9 + - + +
227C ILE* 3.5 8.5 + - - +
228C ALA* 3.0 29.5 + - - +
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Residues in contact with ILE 225 (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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17C LEU* 4.6 3.4 - - + -
24C ARG* 5.6 2.0 - - + -
27C TYR* 5.6 2.2 - - + -
28C ILE* 3.5 39.5 - - + -
32C PHE* 3.8 28.5 - - + -
88C VAL* 4.2 9.9 - - + -
221C PHE 2.9 27.6 - - - +
222C ASN* 3.4 9.2 - - - +
223C ASP 3.1 0.4 - - - -
224C MET* 1.3 91.1 - - + +
226C LYS* 1.3 59.8 + - - +
228C ALA* 3.2 4.6 + - - +
229C LEU* 2.8 53.0 + - + +
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Residues in contact with LYS 226 (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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32C PHE* 4.1 16.4 - - + -
52C TYR* 5.3 5.6 - - - +
144C LEU* 3.5 29.2 - - + -
146C ILE* 5.0 2.2 - - + -
219C THR* 5.4 5.3 - - - +
222C ASN* 2.9 34.0 + - - +
223C ASP* 3.2 19.2 + - - +
225C ILE* 1.3 75.3 - - - +
227C ILE* 1.3 54.3 + - - +
229C LEU* 3.7 5.9 - - - +
230C GLU* 2.7 42.3 + - + +
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Residues in contact with ILE 227 (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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103C VAL* 4.1 25.8 - - + -
105C ILE* 5.4 3.1 - - + -
137C ALA* 3.5 35.7 - - + +
140C ALA* 3.6 6.3 - - + +
141C ALA* 4.0 22.4 - - + -
144C LEU* 4.0 17.7 - - + -
146C ILE* 4.0 20.4 - - + -
148C ALA* 5.0 2.0 - - + -
199C ILE* 4.2 10.8 - - + -
223C ASP 2.9 22.0 + - - +
224C MET* 3.6 4.0 - - - +
226C LYS* 1.3 76.0 - - - +
228C ALA* 1.3 58.0 + - - +
231C SER* 2.8 33.4 + - - -
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Residues in contact with ALA 228 (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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17C LEU* 3.9 12.1 - - + -
86C ILE* 3.9 9.7 - - + +
88C VAL* 3.8 24.2 - - + -
199C ILE* 3.9 13.5 - - + -
224C MET 3.0 19.1 + - - +
225C ILE 3.5 4.5 - - - +
227C ILE* 1.3 76.1 - - - +
229C LEU* 1.3 62.8 + - - +
231C SER* 2.7 22.4 + - - -
232C VAL* 3.2 15.3 - - - +
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.7 14.4 - - + -
28C ILE* 5.2 1.1 - - + -
32C PHE* 3.8 28.5 - - + -
33C LEU* 4.5 7.4 - - + -
52C TYR* 3.9 39.5 - - + -
57C ILE* 3.2 32.3 - - + -
225C ILE* 2.8 42.8 + - + +
226C LYS* 3.8 3.8 - - - +
228C ALA* 1.3 72.4 - - - +
230C GLU* 1.3 61.9 + - - +
232C VAL* 3.4 19.5 + - - +
233C LEU* 3.5 13.7 + - - +
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Residues in contact with GLU 230 (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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52C TYR* 2.3 36.3 + - - +
53C LYS* 3.0 22.2 + - - -
140C ALA* 3.9 17.0 - - + -
144C LEU* 4.3 20.0 - - + -
226C LYS* 2.7 26.8 + - + +
227C ILE* 4.7 0.2 - - - -
229C LEU* 1.3 70.7 - - - +
231C SER* 1.3 65.3 + - - +
233C LEU* 3.1 26.4 + - - +
234C LEU* 3.2 15.9 + - + +
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Residues in contact with SER 231 (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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86C ILE* 4.2 8.8 - - - +
133C MET 4.9 1.2 + - - -
136C ASN* 3.4 21.6 + - - +
137C ALA* 3.6 34.7 - - - +
140C ALA* 3.7 6.9 - - - +
197C LEU* 5.5 1.6 - - - +
199C ILE* 5.3 0.7 - - - +
227C ILE 2.8 18.8 + - - -
228C ALA* 2.7 23.7 + - - -
230C GLU* 1.3 72.7 - - - +
232C VAL* 1.3 62.0 + - - +
234C LEU* 3.3 2.4 + - - +
235C GLY 3.0 17.2 + - - -
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Residues in contact with VAL 232 (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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15C VAL* 3.9 24.7 - - + -
17C LEU* 4.6 4.5 - - + -
55C ARG* 3.7 35.0 - - - +
57C ILE* 4.7 7.6 - - + -
84C LYS* 5.0 10.0 + - + +
86C ILE* 3.6 22.0 - - + -
228C ALA 3.2 17.3 - - - +
229C LEU* 3.4 11.4 - - - +
230C GLU 3.1 0.4 - - - -
231C SER* 1.3 78.1 + - - +
233C LEU* 1.3 58.7 + - + +
235C GLY* 2.9 17.8 + - - -
236C ASP* 2.9 17.5 + - - +
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Residues in contact with LEU 233 (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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52C TYR* 3.6 34.8 - - + +
53C LYS* 4.1 15.7 - - + +
55C ARG* 3.6 37.0 - - + -
229C LEU 3.5 7.8 + - - +
230C GLU* 3.1 27.3 + - - +
232C VAL* 1.3 81.3 - - + +
234C LEU* 1.3 61.7 + - + +
236C ASP* 3.2 17.3 + - - +
237C LYS* 3.5 11.1 + - - +
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Residues in contact with LEU 234 (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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136C ASN* 3.5 37.3 - - - +
139C ASP* 3.8 14.8 - - + +
140C ALA* 3.8 22.2 - - + +
143C ALA* 6.2 1.1 - - + -
230C GLU* 3.2 9.3 + - + +
231C SER 3.5 7.0 - - - +
232C VAL 3.2 0.2 - - - -
233C LEU* 1.3 78.9 - - + +
235C GLY* 1.3 63.3 + - - +
237C LYS* 3.3 22.7 + - - +
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Residues in contact with GLY 235 (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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84C LYS* 4.1 14.4 + - - -
136C ASN* 3.4 22.9 - - - -
231C SER 3.0 7.0 + - - -
232C VAL 2.9 9.3 + - - -
234C LEU* 1.3 79.2 - - - +
236C ASP* 1.3 60.9 + - - +
237C LYS 3.3 4.3 + - - -
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Residues in contact with ASP 236 (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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55C ARG* 2.9 53.8 + - - +
84C LYS* 5.6 1.7 + - - -
232C VAL* 2.9 20.4 + - - +
233C LEU* 3.2 14.2 + - - +
235C GLY* 1.3 79.7 - - - +
237C LYS* 1.3 58.0 + - - +
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Residues in contact with LYS 237 (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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233C LEU 3.5 7.5 + - - +
234C LEU* 3.3 19.6 + - - +
235C GLY 3.2 5.2 - - - -
236C ASP* 1.3 81.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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