Contacts of the helix formed by residues 230 - 246 (chain C) in PDB entry 4PHZ
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 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B TYR* 3.9 18.8 - - - -
182C ALA* 3.1 36.0 - - - +
185C ILE* 4.5 7.9 - - - -
186C VAL* 3.3 16.5 - - - +
228C ALA* 3.1 7.3 - - - +
229C LEU* 1.3 73.7 - - - +
231C VAL* 1.3 61.1 + - - +
232C PHE 3.2 2.0 - - - -
233C GLY 4.0 0.7 - - - -
234C VAL* 3.4 4.2 + - - +
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.0 18.4 - - + -
34B LEU* 3.6 25.1 - - + -
37B ALA* 4.9 12.3 - - + -
38B VAL* 6.3 0.7 - - + -
111C LEU* 5.1 10.3 - - + -
114C TYR* 3.8 32.8 - - + -
186C VAL* 3.5 13.3 - - + +
228C ALA 4.8 3.3 + - - +
229C LEU* 3.0 5.1 - - + -
230C GLY* 1.3 75.9 - - - +
232C PHE* 1.3 68.6 + - + +
233C GLY 3.2 0.7 - - - -
234C VAL* 3.7 8.4 - - + +
235C VAL* 2.9 25.8 + - + +
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Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.1 12.1 - - + -
38B VAL* 4.0 23.1 - - + -
79B ALA* 3.8 14.4 - - + -
80B SER* 4.1 14.8 - - - -
83B PHE* 3.5 58.5 - + + -
84B TRP* 5.3 2.2 - - - -
240B GLY 4.0 9.6 - - - -
243B TYR* 3.6 12.1 - - + +
244B SER* 3.8 12.6 - - - +
229C LEU* 3.2 46.8 + - + +
231C VAL* 1.3 81.1 - - + +
233C GLY* 1.3 56.0 + - - +
235C VAL 3.6 0.2 + - - -
236C LEU* 3.2 30.7 + - - +
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Residues in contact with GLY 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B TYR 3.2 9.6 + - - -
244B SER 3.8 8.7 - - - -
245B THR 3.3 22.2 - - - -
246B THR* 3.8 0.3 - - - +
182C ALA* 3.7 10.1 - - - -
230C GLY 3.6 1.8 + - - -
231C VAL 3.2 0.4 - - - -
232C PHE* 1.3 74.9 - - - +
234C VAL* 1.3 61.4 + - - +
236C LEU* 3.2 3.7 + - - +
237C GLN* 2.8 35.1 + - - +
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Residues in contact with VAL 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU* 4.1 23.3 - - + -
175C PHE* 4.9 2.2 - - + -
182C ALA* 3.7 0.8 - - + +
183C PHE* 3.4 65.7 - - + +
186C VAL* 4.5 4.5 - - + -
230C GLY 3.4 16.5 + - - +
231C VAL* 3.4 11.1 + - + +
233C GLY* 1.3 73.2 - - - +
235C VAL* 1.3 64.8 + - - +
237C GLN* 3.2 10.8 + - - +
238C ILE* 2.9 27.8 + - + +
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Residues in contact with VAL 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.5 22.2 - - + -
33B LEU* 4.2 18.6 - - + -
34B LEU* 3.9 22.7 - - + -
83B PHE* 3.7 30.1 - - + -
88B PHE* 4.9 0.7 - - + -
111C LEU* 4.9 7.9 - - + -
231C VAL* 2.9 24.5 + - + +
232C PHE 3.8 3.6 - - - +
234C VAL* 1.3 71.8 - - - +
236C LEU* 1.3 57.3 + - + +
238C ILE* 3.2 8.9 + - + +
239C LEU* 2.6 49.0 + - + +
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Residues in contact with LEU 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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212A TYR* 3.9 17.3 + - + +
83B PHE* 4.1 3.8 - - + -
87B ASN* 3.3 48.7 - - + +
88B PHE* 4.0 18.6 - - + -
244B SER* 3.5 32.3 - - - +
246B THR* 3.7 13.0 - - + -
232C PHE 3.2 11.4 + - - +
233C GLY 3.2 7.1 + - - +
234C VAL 3.2 0.8 - - - -
235C VAL* 1.3 78.6 - - - +
237C GLN* 1.3 56.8 + - - +
239C LEU* 3.2 5.2 + - + +
240C MET* 2.9 33.0 + - + +
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Residues in contact with GLN 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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245B THR 4.8 1.1 + - - -
246B THR* 3.0 41.7 + - + -
247B LYS 3.8 4.6 + - - -
248B VAL* 3.9 1.2 - - - +
174C TYR* 3.2 32.6 + - + +
175C PHE* 3.7 17.2 - - + -
180C SER* 2.6 33.3 + - - -
182C ALA* 4.5 0.8 - - - +
233C GLY 2.8 23.4 + - - +
234C VAL* 3.2 12.7 + - - +
236C LEU* 1.3 72.2 - - - +
238C ILE* 1.3 66.0 + - - +
240C MET* 3.3 17.0 + - - +
241C ARG* 3.3 16.6 + - - +
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Residues in contact with ILE 238 (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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30B LEU* 5.4 4.9 - - + -
104C LEU* 4.4 18.8 - - + -
107C LEU* 3.6 35.2 - - + -
108C VAL* 4.1 24.5 - - + -
111C LEU* 3.7 26.9 - - + -
175C PHE* 4.5 8.3 - - + -
234C VAL* 2.9 20.9 + - + +
235C VAL* 3.6 10.8 - - + +
237C GLN* 1.3 75.1 - - - +
239C LEU* 1.3 65.6 + - + +
241C ARG* 3.0 15.2 + - - +
242C ILE* 3.1 31.1 + - + +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 4.5 0.9 - - + -
209A ILE* 3.9 28.5 - - + -
212A TYR* 2.9 42.4 - - + -
30B LEU* 4.0 22.0 - - + -
88B PHE* 3.4 39.9 - - + -
235C VAL* 2.6 27.5 + - + +
236C LEU* 3.2 6.9 + - + +
238C ILE* 1.3 74.1 - - + +
240C MET* 1.3 61.1 + - - +
242C ILE* 3.8 17.1 - - + +
243C HIS* 3.1 15.6 + - - +
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Residues in contact with MET 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.0 24.2 - - - +
246B THR* 4.3 27.1 - - + -
174C TYR* 4.3 23.8 - - + +
236C LEU* 2.9 15.2 + - + +
237C GLN* 3.4 11.9 - - - +
238C ILE 3.2 0.2 - - - -
239C LEU* 1.3 73.2 - - - +
241C ARG* 1.3 69.3 + - + +
243C HIS* 3.3 6.5 + - - +
244C ALA* 3.2 22.5 + - - +
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Residues in contact with ARG 241 (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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100C GLU* 2.8 45.6 + - - -
104C LEU* 3.8 26.7 - - + -
172C ILE* 4.9 2.0 - - + -
173C PRO* 5.5 1.0 - - - +
174C TYR* 4.0 34.0 - - + +
175C PHE* 5.7 1.8 - - + -
237C GLN 3.3 11.2 + - - +
238C ILE 3.0 9.0 + - - +
240C MET* 1.3 78.4 + - + +
242C ILE* 1.3 65.4 + - - +
244C ALA* 3.1 33.1 + - - +
245C LEU* 2.9 36.5 + - + +
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Residues in contact with ILE 242 (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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209A ILE* 4.4 27.8 - - + -
212A TYR* 6.3 0.2 - - + -
213A ILE* 4.9 3.1 - - + -
23B VAL* 6.1 1.8 - - + -
26B VAL* 4.5 21.1 - - + -
101C MET* 4.2 20.6 - - + -
104C LEU* 3.8 18.8 - - + +
105C VAL* 6.3 2.0 - - + -
108C VAL* 5.6 0.9 - - + -
238C ILE* 3.1 32.3 + - + +
239C LEU* 3.8 22.0 - - + +
241C ARG* 1.3 76.0 - - - +
243C HIS* 1.3 63.5 + - - +
245C LEU* 3.2 1.4 + - - +
246C VAL* 3.0 36.1 + - + +
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Residues in contact with HIS 243 (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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212A TYR* 4.1 9.3 + + + -
213A ILE* 3.6 29.2 - - + +
216A ALA* 4.0 27.1 - - + +
217A GLU* 3.0 42.7 + - + +
239C LEU 3.1 15.4 + - - +
240C MET* 3.4 9.8 - - - +
241C ARG 3.2 0.2 - - - -
242C ILE* 1.3 78.1 - - - +
244C ALA* 1.3 57.6 + - - +
246C VAL* 3.1 18.8 - - - +
251C VAL* 3.5 16.3 - - + +
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Residues in contact with ALA 244 (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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240C MET 3.2 8.1 + - - +
241C ARG* 3.1 30.8 + - - +
243C HIS* 1.3 79.4 - - - +
245C LEU* 1.3 64.0 + - - +
246C VAL 3.1 9.0 - - - +
247C GLY* 4.9 1.2 - - - -
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Residues in contact with LEU 245 (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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11B GLY 4.2 1.2 - - - +
12B PRO* 3.4 21.6 - - + +
97C PRO* 4.1 33.2 - - + +
100C GLU* 3.1 43.7 - - + +
101C MET* 3.7 28.3 - - + +
104C LEU* 4.1 18.2 - - + -
241C ARG* 2.9 26.7 + - - +
244C ALA* 1.3 73.8 - - - +
246C VAL* 1.3 63.9 + - - +
247C GLY* 3.5 2.1 + - - -
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE* 6.5 0.2 - - + -
213A ILE* 5.3 6.7 - - + -
10B VAL* 5.7 2.0 - - + -
12B PRO* 5.0 2.9 - - - -
13B PHE* 4.5 17.7 - - + -
23B VAL* 6.0 5.6 - - + -
101C MET* 4.4 13.2 - - + -
242C ILE* 3.0 26.4 + - + +
243C HIS* 3.1 16.5 - - - +
244C ALA 3.1 7.2 - - - +
245C LEU* 1.3 77.8 - - - +
247C GLY* 1.3 66.6 + - - +
250C GLY* 3.3 17.0 - - - +
251C VAL* 3.2 37.0 - - + +
255C THR* 5.8 1.6 - - + +
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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
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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