Contacts of the helix formed by residues 222 - 236 (chain C) in PDB entry 4RPP
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 SER 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C LYS* 5.7 1.6 - - - +
116C GLY 4.3 13.7 + - - -
117C PRO* 4.8 9.7 - - - +
220C ALA 4.2 0.8 - - - -
221C VAL* 1.3 76.2 - - - +
223C GLU* 1.3 65.1 + - - +
224C LYS* 3.6 9.2 + - - +
225C ASP* 2.6 50.3 + - - +
226C ILE* 3.2 10.2 + - - +
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Residues in contact with GLU 223 (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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221C VAL 3.7 0.8 + - - -
222C SER* 1.3 73.3 - - - +
224C LYS* 1.3 60.6 + - - +
226C ILE* 3.5 32.3 - - - +
227C GLN* 3.8 19.5 + - + +
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Residues in contact with LYS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PHE* 2.7 31.5 + - - +
77C SER 4.9 2.8 - - - -
78C HIS* 5.6 0.2 - - - +
79C GLY 4.5 13.1 + - - -
81C HIS* 5.7 1.1 - - - -
115C LYS* 4.4 23.8 - - + +
222C SER* 3.1 9.1 + - - +
223C GLU* 1.3 78.1 - - - +
225C ASP* 1.3 63.9 - - - +
227C GLN* 3.4 8.6 + - - +
228C ASP* 3.3 54.5 + - - +
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Residues in contact with ASP 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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114C THR* 3.6 14.5 - - + -
115C LYS* 3.2 17.2 + - - +
116C GLY* 3.0 38.4 + - - -
117C PRO* 4.3 1.0 - - - +
221C VAL* 3.9 13.7 - - + +
222C SER* 2.6 38.0 + - - +
224C LYS* 1.3 72.7 - - - +
226C ILE* 1.3 67.4 + - - +
228C ASP* 2.9 11.3 + - - +
229C LEU* 2.9 30.7 + - + +
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Residues in contact with ILE 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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221C VAL* 3.7 25.8 - - + +
222C SER 3.3 15.5 - - - +
223C GLU* 3.5 31.6 - - - +
224C LYS 3.3 0.2 - - - -
225C ASP* 1.3 77.0 - - - +
227C GLN* 1.3 65.8 + - - +
229C LEU* 3.8 2.7 + - - +
230C LYS* 2.3 54.5 + - - +
257C VAL* 4.4 22.0 - - + -
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Residues in contact with GLN 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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81C HIS* 3.8 16.6 - - + +
223C GLU* 3.8 18.5 - - + +
224C LYS* 3.4 8.9 + - - +
225C ASP 3.1 0.4 - - - -
226C ILE* 1.3 86.3 - - - +
228C ASP* 1.3 60.7 + - - +
230C LYS* 3.4 25.5 - - - +
231C PHE* 2.9 28.9 + - - +
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Residues in contact with ASP 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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76C PHE* 3.3 32.7 - - + +
81C HIS* 2.9 22.5 + - - -
112C LEU* 3.3 19.7 - - + +
114C THR* 5.4 2.2 - - + -
115C LYS 5.0 0.9 + - - -
224C LYS* 3.3 45.8 + - - +
225C ASP* 2.9 14.6 + - - +
227C GLN* 1.3 74.7 - - - +
229C LEU* 1.3 56.6 + - + +
231C PHE* 3.3 6.7 - - - +
232C GLY 2.7 27.7 + - - -
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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
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112C LEU* 4.3 3.1 - - + -
114C THR* 3.7 17.3 - - + -
221C VAL* 4.7 11.2 - - + -
225C ASP* 2.9 23.4 + - + +
226C ILE* 3.9 5.4 - - - +
228C ASP* 1.3 73.0 - - - +
230C LYS* 1.3 60.1 + - - +
232C GLY* 3.0 5.1 + - - -
233C VAL* 2.9 29.4 + - - +
240C VAL* 3.6 39.6 - - + +
254C VAL* 4.3 22.4 - - + +
257C VAL* 3.7 30.3 - - + -
258C LEU* 4.0 15.0 - - + +
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Residues in contact with LYS 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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226C ILE* 2.3 50.6 + - - +
227C GLN* 3.4 29.4 - - - +
229C LEU* 1.3 75.3 - - - +
231C PHE* 1.3 65.9 - - - +
233C VAL* 3.1 21.7 + - + +
234C GLU* 3.3 17.8 + - - +
257C VAL* 3.9 20.9 + - + +
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Residues in contact with PHE 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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76C PHE* 3.6 37.0 - + - -
81C HIS* 3.4 58.3 - + + +
84C HIS* 4.3 5.6 - - + -
85C ALA* 3.9 13.0 - - + -
88C ILE* 4.8 5.4 - - + -
112C LEU* 4.4 2.5 - - + -
227C GLN 2.9 19.5 + - - +
228C ASP 3.3 4.0 - - - +
230C LYS* 1.3 75.6 - - - +
232C GLY* 1.3 64.5 + - - +
234C GLU* 3.5 6.1 + - + +
235C GLN* 3.0 56.7 + - + +
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Residues in contact with GLY 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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112C LEU* 3.7 17.7 - - - -
228C ASP 2.7 14.7 + - - -
229C LEU* 3.0 6.4 + - - -
231C PHE* 1.3 77.8 - - - +
233C VAL* 1.3 55.4 + - - +
235C GLN* 3.4 1.7 + - - -
236C ASP 2.9 22.9 + - - -
237C VAL* 3.0 31.1 + - - -
240C VAL* 6.1 0.4 - - - -
265C ILE* 4.8 0.2 - - - -
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Residues in contact with VAL 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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229C LEU 2.9 17.8 + - - +
230C LYS* 3.1 16.7 + - + +
232C GLY* 1.3 75.3 - - - +
234C GLU* 1.3 73.2 + - - +
236C ASP* 3.0 20.8 + - - +
257C VAL 5.7 0.2 - - - +
258C LEU* 3.9 34.5 - - + +
261C LYS* 4.0 25.4 - - + +
262C GLY* 4.5 5.6 - - - +
265C ILE* 4.3 15.1 - - + +
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Residues in contact with GLU 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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230C LYS 3.3 11.9 + - - +
231C PHE* 4.2 7.0 - - + +
233C VAL* 1.3 90.0 - - - +
235C GLN* 1.3 66.1 + - + +
236C ASP* 3.1 3.9 + - - +
261C LYS* 5.9 0.9 - - - +
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Residues in contact with GLN 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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85C ALA* 4.2 15.6 - - - +
88C ILE* 3.8 35.8 - - + +
92C ARG* 2.3 43.7 + - - +
231C PHE* 3.0 56.9 + - + +
232C GLY* 3.9 5.4 - - - +
234C GLU* 1.3 80.1 + - + +
236C ASP* 1.3 56.0 + - - +
237C VAL* 3.5 1.7 - - + -
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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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92C ARG* 3.1 18.7 + - - +
110C VAL* 5.2 0.3 - - - +
232C GLY 2.9 4.0 + - - -
233C VAL* 3.0 14.8 + - - +
234C GLU 3.1 3.8 - - - +
235C GLN* 1.3 81.3 - - - +
237C VAL* 1.3 66.4 + - - +
238C ASP* 3.8 7.6 + - - +
265C ILE* 5.8 2.1 - - - +
458C GLN* 3.9 18.3 + - - -
461C ARG* 4.0 17.1 + - - -
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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