Contacts of the helix formed by residues 217 - 236 (chain A) 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 ARG 217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 6.0 4.0 - - - +
90A SER* 5.1 1.8 - - - -
100A LEU* 5.4 1.4 - - - +
101A ARG* 3.1 48.9 - - - +
201A THR* 3.4 24.0 + - - -
202A VAL 3.5 12.5 + - - -
203A SER* 3.6 31.2 + - - +
218A GLN* 1.3 64.2 + - + +
219A THR* 3.1 7.3 - - - +
220A THR* 3.4 16.0 + - - +
221A PHE* 2.8 31.0 + - - +
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Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 5.5 5.0 + - - -
27A TYR* 3.7 42.2 + - - -
217A ARG* 1.3 77.7 - - + +
219A THR* 1.3 51.0 + - - +
221A PHE* 3.5 11.9 - - - +
222A ASN* 2.6 49.4 + - - +
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Residues in contact with THR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 4.3 17.7 - - - +
217A ARG 3.1 4.2 - - - +
218A GLN* 1.3 76.6 - - - +
220A THR* 1.3 55.3 + - - +
222A ASN* 3.0 9.2 + - - +
223A ASP* 2.7 55.1 + - - +
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Residues in contact with THR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.2 48.6 + - - +
103A VAL* 5.2 3.4 - - + -
201A THR* 3.3 34.4 - - + +
217A ARG* 3.4 24.4 + - - +
219A THR* 1.3 79.0 - - - +
221A PHE* 1.3 57.7 + - - +
223A ASP* 3.1 14.3 + - + +
224A MET* 2.9 26.9 + - - +
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Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 5.2 2.7 - - + -
24A ARG* 3.7 51.1 - - + +
27A TYR* 3.8 27.4 - + - -
28A ILE* 4.1 11.0 - - + -
88A VAL 5.1 5.2 - - - -
89A GLY* 5.9 1.1 - - - -
201A THR* 5.2 3.1 - - - +
217A ARG 2.8 22.5 + - - +
218A GLN* 3.5 21.1 - - - +
219A THR 3.1 0.2 - - - -
220A THR* 1.3 72.0 - - - +
222A ASN* 1.3 67.8 + - - +
224A MET* 3.2 33.6 + - + +
225A ILE* 3.2 49.1 + - + +
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Residues in contact with ASN 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 2.6 38.6 + - - -
31A THR* 4.7 1.7 - - - +
32A PHE* 3.7 27.6 - - + -
218A GLN* 2.6 41.2 + - - +
219A THR* 3.5 7.2 - - - +
221A PHE* 1.3 74.1 - - - +
223A ASP* 1.3 64.1 + - - +
225A ILE 3.4 0.3 + - - -
226A LYS* 3.0 32.2 + - - +
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 5.8 0.2 + - - -
103A VAL* 5.6 4.3 - - + -
144A LEU* 4.5 0.7 - - - +
146A ILE* 3.9 26.7 - - + +
219A THR* 2.7 36.6 + - - +
220A THR* 3.2 16.5 + - + +
221A PHE 3.1 0.2 - - - -
222A ASN* 1.3 79.2 - - - +
224A MET* 1.3 56.8 + - - +
226A LYS* 3.3 14.6 + - - +
227A ILE* 2.9 36.8 + - + +
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Residues in contact with MET 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.7 23.1 - - + -
89A GLY* 3.4 38.6 - - - +
103A VAL* 5.6 2.0 - - + +
199A ILE* 3.5 32.7 - - + +
200A CYS 4.2 0.2 - - - -
201A THR* 3.7 23.8 - - + +
220A THR 2.9 11.8 + - - +
221A PHE* 3.2 37.4 + - + +
223A ASP* 1.3 77.0 - - - +
225A ILE* 1.3 57.2 + - + +
227A ILE* 3.3 12.6 + - - +
228A ALA* 2.8 28.2 + - - +
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.9 13.5 - - + -
28A ILE* 3.7 31.2 - - + -
32A PHE* 4.0 22.2 - - + -
88A VAL* 3.8 28.5 - - + -
221A PHE* 3.2 37.8 + - + +
222A ASN 3.9 5.2 - - - +
224A MET* 1.3 72.8 - - + +
226A LYS* 1.3 56.4 + - - +
228A ALA* 3.2 4.2 + - - +
229A LEU* 2.8 59.1 + - + +
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 4.2 21.4 - - + -
52A TYR* 4.6 9.6 - - - +
144A LEU* 3.6 29.4 - - + -
222A ASN* 3.0 23.0 + - - +
223A ASP* 3.5 16.0 + - - +
225A ILE* 1.3 78.1 - - - +
227A ILE* 1.3 52.6 + - - +
229A LEU* 3.8 4.2 - - - +
230A GLU* 2.8 48.8 + - + +
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Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 4.2 22.0 - - + -
105A ILE* 5.7 1.8 - - + -
137A ALA* 3.7 25.1 - - + +
140A ALA* 3.6 5.8 - - - +
141A ALA* 4.0 19.7 - - + +
144A LEU* 3.7 20.4 - - + -
146A ILE* 3.7 21.3 - - + -
199A ILE* 4.2 21.1 - - + -
223A ASP 2.9 26.9 + - - +
224A MET* 3.4 11.7 - - - +
226A LYS* 1.3 76.8 - - - +
228A ALA* 1.3 63.6 + - - +
231A SER* 2.9 23.9 + - - -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.8 23.8 - - + -
86A ILE* 3.9 9.2 - - + +
88A VAL* 3.8 18.2 - - + -
199A ILE* 4.3 9.4 - - + -
224A MET 2.8 20.8 + - - +
225A ILE* 3.2 6.0 + - - +
227A ILE* 1.3 73.2 - - - +
229A LEU* 1.3 61.4 + - - +
231A SER* 2.5 25.7 + - - -
232A VAL* 3.3 10.4 + - - +
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.7 25.6 - - + -
28A ILE* 5.5 1.1 - - + -
32A PHE* 3.5 39.0 - - + -
33A LEU* 4.7 4.7 - - + -
52A TYR* 3.5 35.0 - - + -
57A ILE* 3.5 32.9 - - + +
225A ILE* 2.8 28.7 + - + +
226A LYS* 3.8 2.9 - - - +
228A ALA* 1.3 73.2 - - - +
230A GLU* 1.3 63.6 + - - +
232A VAL* 3.2 20.5 + - - +
233A LEU* 3.6 11.4 + - - +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 2.6 31.0 + - - +
53A LYS* 2.9 23.3 + - - -
140A ALA* 3.9 18.6 - - + +
144A LEU* 4.8 10.3 - - + -
226A LYS* 2.8 35.1 + - + +
227A ILE* 4.6 0.2 - - - -
229A LEU* 1.3 73.1 - - - +
231A SER* 1.3 62.7 + - - +
233A LEU* 3.4 18.8 + - - +
234A LEU* 3.3 26.6 + - + +
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE* 3.9 11.8 - - - +
133A MET 4.9 1.7 + - - -
136A ASN* 3.3 46.8 + - - +
137A ALA* 3.6 12.8 - - - +
140A ALA* 3.8 0.9 - - - +
197A LEU* 5.4 1.2 - - - +
199A ILE* 5.3 0.5 - - - +
227A ILE 2.9 15.5 + - - -
228A ALA* 2.5 22.5 + - - -
230A GLU* 1.3 75.3 - - - +
232A VAL* 1.3 58.5 + - - +
234A LEU* 3.3 2.0 + - - -
235A GLY 2.9 22.7 + - - -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.9 24.7 - - + -
17A LEU* 5.3 2.0 - - + -
55A ARG* 3.6 37.7 - - + +
57A ILE* 4.6 11.9 - - + -
84A LYS* 4.9 10.9 + - + +
86A ILE* 3.7 22.0 - - + -
228A ALA 3.5 15.3 - - - +
229A LEU* 3.2 11.8 + - - +
231A SER* 1.3 79.9 + - - +
233A LEU* 1.3 61.2 + - + +
235A GLY* 3.1 3.9 + - - -
236A ASP* 2.9 27.9 + - - +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.9 25.6 - - + +
53A LYS* 3.9 20.9 - - + +
55A ARG* 3.6 37.0 - - + -
57A ILE* 5.8 0.4 - - + -
229A LEU 3.7 10.8 - - - +
230A GLU* 3.7 25.4 - - - +
232A VAL* 1.3 74.6 - - + +
234A LEU* 1.3 69.8 + - + +
236A ASP* 3.1 20.1 + - + +
237A LYS* 3.6 6.6 + - - +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN* 3.6 35.5 - - - +
139A ASP* 3.8 15.9 - - + +
140A ALA* 3.7 18.2 - - - +
230A GLU* 3.3 17.3 + - + +
231A SER 3.5 7.9 - - - +
232A VAL 3.2 0.4 - - - -
233A LEU* 1.3 80.1 - - + +
235A GLY* 1.3 59.2 + - - +
237A LYS* 2.9 29.7 + - - +
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Residues in contact with GLY 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 4.2 14.7 + - - -
136A ASN* 3.1 25.3 - - - +
231A SER 2.9 11.0 + - - -
232A VAL 3.1 5.8 + - - -
234A LEU* 1.3 78.6 - - - +
236A ASP* 1.3 59.8 + - - +
237A LYS 3.1 5.2 + - - -
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Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 2.8 54.9 + - - +
84A LYS* 5.3 2.9 + - - -
232A VAL* 2.9 17.9 + - - +
233A LEU* 3.4 13.8 - - - +
234A LEU 3.0 1.0 - - - -
235A GLY* 1.3 77.8 - - - +
237A LYS* 1.3 58.6 + - - +
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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
------------------------------------------------------------
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