Contacts of the helix formed by residues 232 - 248 (chain H) in PDB entry 7PRC
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 LEU 232 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H ARG* 3.9 43.2 + - + +
121H ALA* 3.5 10.3 - - + +
123H VAL* 2.8 32.3 + - + +
125H ASP* 3.6 36.9 - - + +
230H ILE 4.2 0.2 + - - -
231H THR* 1.3 70.9 - - - +
233H ARG* 1.3 64.3 + - - +
235H GLU* 3.4 18.0 + - - +
236H ASP* 3.2 18.7 + - - +
231M ARG* 4.3 3.8 - - - +
234M GLU* 5.3 7.4 - - + -
238M ASP* 3.6 22.2 - - + +
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Residues in contact with ARG 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H TYR* 4.1 11.7 + - + -
118H ALA 3.9 14.1 - - - +
119H GLU* 3.1 42.5 + - - +
120H ARG* 3.0 34.0 + - - +
121H ALA 3.0 12.6 + - - +
122H GLU* 3.5 33.4 + - - +
231H THR* 3.1 0.8 + - - -
232H LEU* 1.3 76.7 - - - +
234H GLU* 1.3 62.9 + - - +
236H ASP* 3.3 4.1 + - - +
237H LYS* 3.1 40.0 + - - +
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Residues in contact with GLU 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H GLU* 4.2 10.5 - - - +
223H ARG 4.0 7.1 - - - +
224H LEU* 3.5 19.6 - - + +
225H GLN* 3.1 34.5 + - - +
226H SER 5.4 0.3 + - - -
229H GLN 4.3 2.9 - - - +
230H ILE* 3.5 18.9 - - + +
231H THR* 2.7 48.9 + - - +
233H ARG* 1.3 70.0 - - - +
235H GLU* 1.3 65.7 + - - +
237H LYS* 2.8 25.0 + - + +
238H VAL* 2.8 19.1 + - + +
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Residues in contact with GLU 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H ARG* 6.0 2.0 - - - +
125H ASP* 4.4 3.3 - - - +
134H ILE* 3.8 11.7 - - - +
182H TYR* 2.7 32.4 + - - +
230H ILE* 3.8 31.4 - - + +
231H THR 2.8 18.5 + - - +
232H LEU* 3.5 24.4 + - - +
234H GLU* 1.3 69.7 - - - +
236H ASP* 1.3 58.6 + - - +
238H VAL* 3.8 2.5 - - - +
239H SER* 2.8 36.5 + - - -
231M ARG* 2.7 41.8 + - - +
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Residues in contact with ASP 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H TYR* 3.6 11.9 - - + +
118H ALA* 3.0 22.9 + - - +
120H ARG* 3.4 30.1 + - - -
232H LEU 3.2 6.1 + - - +
233H ARG* 3.5 9.9 - - - +
234H GLU 3.1 0.8 - - - -
235H GLU* 1.3 80.2 - - - +
237H LYS* 1.3 58.1 + - - +
239H SER* 3.9 3.9 - - - -
240H ALA* 2.9 33.3 + - - +
227M PHE* 4.7 8.8 - - - +
235M GLN* 5.0 0.5 + - - -
241M THR* 2.9 39.2 + - - +
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Residues in contact with LYS 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H TYR* 3.6 53.7 + - + -
122H GLU* 4.6 7.7 + - - -
222H PRO* 3.5 29.5 - - + +
233H ARG* 3.1 33.1 + - - +
234H GLU* 2.8 22.2 + - + +
236H ASP* 1.3 69.0 - - - +
238H VAL* 1.3 65.0 + - - +
240H ALA* 4.0 1.6 - - - +
241H TYR* 3.1 17.2 + - - +
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Residues in contact with VAL 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H TYR* 4.3 14.4 - - + -
195H LEU* 3.6 37.9 - - + +
197H PRO* 4.3 2.2 - - + -
221H VAL* 4.9 2.0 - - + -
222H PRO* 4.2 25.1 - - + +
224H LEU* 4.4 20.6 - - + -
230H ILE* 4.4 4.9 - - + -
234H GLU* 2.8 22.5 + - + +
235H GLU* 3.8 6.3 - - - +
237H LYS* 1.3 75.1 - - - +
239H SER* 1.3 61.9 + - - +
241H TYR* 3.2 8.9 + - - +
242H TYR* 3.0 29.1 - - + -
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Residues in contact with SER 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H TYR* 4.0 10.2 + - - -
197H PRO* 3.9 18.3 - - - +
200H PHE* 3.7 7.6 - - - -
235H GLU* 2.8 23.0 + - - +
236H ASP* 3.9 3.8 - - - -
238H VAL* 1.3 74.8 - - - +
240H ALA* 1.3 67.4 + - - +
241H TYR 3.2 0.7 + - - -
242H TYR 3.6 0.7 + - - -
243H ALA* 3.2 19.6 + - - +
226M ARG 3.6 22.7 + - - -
227M PHE* 3.8 21.3 - - - -
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Residues in contact with ALA 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H ALA* 3.5 21.2 - - - +
116H SER 3.1 30.1 - - - +
117H TYR* 4.2 2.5 - - + +
236H ASP 2.9 19.4 + - - +
237H LYS* 4.0 3.4 - - - +
239H SER* 1.3 77.7 - - - +
241H TYR* 1.3 58.2 + - - +
243H ALA* 3.1 3.3 + - - +
244H GLY 2.8 26.3 + - - -
227M PHE* 4.1 1.5 - - - -
241M THR* 5.0 0.9 - - + -
245M ARG* 3.4 14.8 - - - +
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Residues in contact with TYR 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H ASN* 5.5 1.2 + - - -
108H LEU* 3.5 63.3 - - + +
109H VAL* 4.4 3.3 - - + +
115H ALA* 5.2 2.9 - - - -
213H ILE* 3.6 21.5 - - + +
217H GLN* 2.6 32.9 + - - +
220H ASN* 3.6 24.3 + - + +
221H VAL* 3.8 23.1 - - + -
222H PRO* 3.5 20.0 - - + -
237H LYS 3.1 13.5 + - - +
238H VAL 3.3 11.7 - - - +
239H SER 3.1 1.2 - - - -
240H ALA* 1.3 79.5 - - - +
242H TYR* 1.3 67.3 + + + +
244H GLY* 3.2 8.1 + - - -
245H GLY* 3.2 8.8 + - - -
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Residues in contact with TYR 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194H ALA* 4.0 5.4 - - - +
195H LEU 2.5 31.1 + - - -
196H ILE* 3.3 30.7 - - + +
197H PRO* 3.6 18.6 - - + -
200H PHE* 3.7 29.5 - + + -
210H VAL* 4.8 0.2 - - + -
212H SER* 3.2 24.1 - - - +
213H ILE* 3.6 37.9 - - + -
218H PHE* 4.2 8.3 - + - -
221H VAL* 3.5 26.6 - - + +
238H VAL* 3.0 29.8 - - + -
239H SER 3.6 0.2 + - - -
241H TYR* 1.3 74.3 - + + +
243H ALA* 1.3 61.7 + - - +
245H GLY* 2.8 17.2 + - - +
246H LEU* 3.6 0.9 + - - +
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Residues in contact with ALA 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H PRO* 3.7 15.2 - - - +
200H PHE* 3.4 14.5 - - + -
239H SER 3.2 5.0 + - - +
240H ALA 3.1 7.3 + - - +
242H TYR* 1.3 77.0 - - - +
244H GLY* 1.3 57.8 + - - +
246H LEU* 3.0 30.5 + - - +
112L GLY* 4.1 5.1 - - - +
227M PHE* 3.1 43.5 - - + -
245M ARG* 3.8 1.6 - - - +
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Residues in contact with GLY 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H LEU* 3.4 12.3 - - - -
114H PRO* 3.7 22.6 + - - -
115H ALA* 3.9 4.5 - - - -
240H ALA 2.8 14.9 + - - -
241H TYR 3.2 3.8 + - - -
242H TYR 3.1 0.2 - - - -
243H ALA* 1.3 73.1 - - - +
245H GLY* 1.3 66.6 + - - +
246H LEU 3.0 1.5 + - - -
247H LEU 3.4 1.6 + - - -
248H TYR* 3.0 30.1 + - - +
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Residues in contact with GLY 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H LEU* 3.6 4.7 - - - +
212H SER 3.2 21.3 - - - -
213H ILE* 3.5 13.9 - - - -
241H TYR 3.2 6.5 + - - -
242H TYR 2.8 10.8 + - - -
244H GLY* 1.3 76.3 - - - +
246H LEU* 1.3 59.9 + - - +
249H ALA* 2.5 36.5 + - - +
253H ARG* 3.2 1.2 + - - -
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Residues in contact with LEU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H PHE* 4.2 2.5 - - + -
211H THR* 5.2 2.5 - - - +
212H SER* 4.0 23.8 - - - +
242H TYR 4.0 4.7 - - - +
243H ALA* 3.0 22.7 + - - +
244H GLY 3.0 0.6 - - - -
245H GLY* 1.3 78.2 - - - +
247H LEU* 1.3 57.6 + - - +
253H ARG* 3.3 27.3 - - - +
109L ARG* 5.2 5.4 + - - +
112L GLY* 3.9 27.8 - - - +
113L ILE 6.0 0.7 - - - -
226M ARG* 3.8 13.0 - - - +
803M SO4 3.5 39.5 - - - +
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Residues in contact with LEU 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H PRO* 3.5 39.7 - - + +
243H ALA 4.1 1.0 + - - -
244H GLY 3.4 2.6 + - - -
245H GLY 3.3 0.2 - - - -
246H LEU* 1.3 79.5 - - - +
248H TYR* 1.3 76.8 + - + +
250H THR 4.3 0.5 - - - +
253H ARG* 3.2 10.1 - - - +
254H ALA* 3.2 33.6 + - + +
11L VAL* 4.3 4.5 - - + -
12L ARG 3.8 22.7 - - - +
13L GLY* 4.4 3.6 - - - -
14L GLY* 3.5 31.6 - - - +
109L ARG* 4.2 18.6 - - - +
110L LYS* 4.6 3.4 - - - +
112L GLY* 6.0 0.2 - - - -
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Residues in contact with TYR 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H PRO* 3.6 27.9 - - + +
107H PRO* 3.5 36.8 - - + -
108H LEU* 4.1 11.3 - - + +
112H VAL 3.9 7.8 - - - -
114H PRO* 3.4 25.1 - - + -
115H ALA* 5.1 0.4 - - + -
217H GLN* 4.6 2.4 + - - -
244H GLY* 3.0 19.7 + - - +
245H GLY* 3.0 1.4 + - - -
247H LEU* 1.3 100.8 - - + +
249H ALA* 1.3 68.5 + - - +
250H THR* 3.0 10.7 + - - -
254H ALA* 4.7 10.5 - - + -
11L VAL* 3.3 32.9 - - - +
12L ARG* 4.2 3.2 + - + -
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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