Contacts of the helix formed by residues 177 - 195 (chain B) in PDB entry 4R0C
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 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 5.3 0.2 - - - -
131B LEU* 4.4 8.9 - - - +
175B LEU 4.0 0.6 + - - -
176B VAL* 1.3 74.6 - - - +
178B PRO* 1.3 78.3 - - - +
179B VAL* 2.9 5.4 + - - -
180B ASP* 3.0 17.9 + - - +
181B ALA* 3.1 11.8 + - - +
296B VAL* 3.8 16.5 - - - +
299B VAL* 5.8 1.1 - - - -
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Residues in contact with PRO 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.8 12.8 - - + +
89B ALA* 4.6 9.6 - - + -
90B MET* 3.6 36.3 - - + -
93B LEU* 3.7 28.0 - - + -
131B LEU* 5.4 4.5 - - + +
177B GLY* 1.3 82.2 - - - +
179B VAL* 1.3 64.5 + - + +
181B ALA* 3.9 7.6 - - + -
182B THR* 3.1 28.2 + - - -
296B VAL* 4.6 6.7 - - + +
300B ALA* 6.2 0.2 - - + -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 4.1 21.8 - - - +
170B PHE* 3.4 49.8 - - + +
171B SER* 4.9 4.9 - - - +
177B GLY 3.1 1.0 - - - -
178B PRO* 1.3 77.3 - - + +
180B ASP* 1.3 69.0 + - - +
182B THR* 3.4 4.5 + - - -
183B LEU* 3.1 39.1 + - + +
396B ALA* 5.3 2.2 - - + -
426B ARG* 4.4 11.0 - - - +
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN* 5.7 0.7 - - - +
175B LEU 4.0 4.5 - - - +
176B VAL* 3.2 22.6 - - + +
177B GLY 3.0 25.9 + - - +
179B VAL* 1.3 77.2 - - - +
181B ALA* 1.3 62.2 + - - +
183B LEU* 4.4 1.2 - - - +
184B ALA* 3.1 27.9 + - - +
202B ALA* 3.7 22.3 - - + +
205B ASN* 5.4 0.7 - - - +
209B ILE* 3.5 15.2 - - - +
296B VAL* 4.6 0.2 - - + -
422B GLN* 4.7 1.7 + - - -
426B ARG* 2.9 39.5 + - - +
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 4.2 4.2 - - - +
85B VAL* 3.6 30.0 - - + +
86B VAL* 3.9 13.0 - - + +
177B GLY 3.1 14.4 + - - +
178B PRO* 4.0 1.1 - - + +
180B ASP* 1.3 74.1 - - - +
182B THR* 1.3 63.7 + - - +
184B ALA* 3.9 1.4 - - - +
185B GLY* 3.0 22.7 + - - -
202B ALA* 4.5 8.9 - - + +
296B VAL* 4.2 17.5 - - + -
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Residues in contact with THR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 3.7 7.1 - - + +
86B VAL* 3.2 11.6 - - - +
178B PRO 3.1 14.7 + - - -
179B VAL* 3.4 5.1 + - - -
181B ALA* 1.3 77.7 - - - +
183B LEU* 1.3 70.1 + - + +
186B LEU* 3.2 32.9 + - + +
337B TYR* 2.6 34.1 + - + +
341B MET* 5.5 0.9 - - - -
396B ALA* 6.2 0.4 - - + -
397B SER* 3.3 28.9 + - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PHE* 5.8 0.4 - - + -
171B SER* 4.5 2.2 - - - +
179B VAL* 3.1 28.9 + - + +
180B ASP* 4.4 1.6 - - - +
182B THR* 1.3 87.3 - - + +
184B ALA* 1.3 58.9 + - - +
186B LEU 3.4 0.2 + - - -
187B SER* 3.0 14.9 + - - -
396B ALA* 4.2 17.9 - - + +
400B TRP* 2.9 55.5 + - + +
422B GLN* 3.5 15.5 - - + +
425B TYR* 3.9 16.8 - - + -
426B ARG* 3.7 35.9 - - + +
429B ASP* 5.5 2.0 - - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP 3.1 19.5 + - - +
181B ALA* 4.2 1.8 - - - +
183B LEU* 1.3 74.3 - - - +
185B GLY* 1.3 61.0 + - - +
187B SER* 3.5 1.8 - - - -
188B THR* 2.9 31.7 + - - -
200B VAL 3.2 21.6 - - - +
201B ALA 3.3 21.3 - - - +
202B ALA* 4.0 2.5 - - + +
422B GLN* 3.2 18.5 + - - +
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA* 3.4 23.6 - - - +
82B PRO* 3.6 14.1 - - - -
181B ALA 3.0 17.3 + - - -
183B LEU 3.3 0.2 - - - -
184B ALA* 1.3 75.1 - - - +
186B LEU* 1.3 63.6 + - - +
188B THR* 3.4 1.4 + - - -
189B GLU* 3.3 27.9 + - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 3.8 28.9 - - + -
82B PRO* 3.9 11.8 - - + +
182B THR* 3.2 28.3 + - + +
185B GLY* 1.3 76.5 - - - +
187B SER* 1.3 62.3 + - - +
189B GLU* 3.3 7.3 + - - +
190B ALA* 3.2 20.4 + - - +
341B MET* 4.6 4.5 - - + -
348B VAL* 5.6 2.2 - - + -
397B SER* 3.8 6.1 - - - +
400B TRP* 3.5 32.8 - - + +
401B SER* 3.1 47.8 - - - +
404B ALA* 4.2 4.1 - - + +
405B PRO* 5.5 1.5 - - + +
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU 3.0 5.9 + - - -
184B ALA 3.5 5.2 - - - -
186B LEU* 1.3 78.1 - - - +
188B THR* 1.3 56.6 + - - +
190B ALA* 3.3 3.1 + - - +
191B ALA* 2.8 30.7 + - - +
200B VAL* 3.7 14.7 - - - +
400B TRP* 3.0 29.4 + - - +
404B ALA* 4.6 1.8 - - - -
408B ILE* 3.7 16.0 - - - +
418B PRO* 4.9 0.7 - - - -
422B GLN* 2.8 30.2 + - - +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA* 4.4 13.2 - - + -
184B ALA 2.9 16.7 + - - -
185B GLY* 3.6 8.7 - - - -
186B LEU 3.3 0.4 - - - -
187B SER* 1.3 75.9 - - - +
189B GLU* 1.3 58.8 + - - +
191B ALA* 3.2 4.0 + - - +
192B HIS* 2.8 58.7 + - + +
198B ARG 3.8 5.6 - - - +
199B THR* 3.5 9.2 - - + -
200B VAL* 2.7 34.0 + - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY 4.0 3.8 - - - +
80B PHE* 3.4 39.1 - - + -
81B ALA* 3.0 28.5 + - + +
185B GLY 3.3 15.4 + - - +
186B LEU* 3.3 6.7 + - + +
188B THR* 1.3 76.8 - - - +
190B ALA* 1.3 63.4 + - - +
192B HIS* 3.4 29.7 + - - +
193B ILE* 3.7 5.9 + - - +
348B VAL* 3.9 22.8 - - + +
352B ASN* 5.1 1.0 + - - -
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU 3.2 11.9 + - - +
187B SER 3.6 6.7 - - - +
188B THR 3.2 0.4 - - - -
189B GLU* 1.3 72.5 - - - +
191B ALA* 1.3 58.6 + - - +
192B HIS 3.0 1.6 - - - -
193B ILE* 2.7 37.5 + - - +
194B ILE 4.1 0.7 + - - -
348B VAL* 4.6 0.8 - - - +
404B ALA* 3.3 40.2 - - + +
405B PRO* 3.6 13.5 - - + -
408B ILE* 3.9 10.1 - - + -
409B PRO* 4.0 6.0 - - + +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER 2.8 17.5 + - - +
188B THR* 3.5 7.9 - - - +
190B ALA* 1.3 76.8 - - - +
192B HIS* 1.3 58.3 + - - +
193B ILE 3.2 0.9 + - - -
194B ILE* 3.3 3.5 + - - -
195B ASP* 2.9 28.2 + - - +
198B ARG* 4.1 17.5 - - + -
200B VAL* 4.6 1.3 - - + -
408B ILE* 4.0 2.6 - - + +
412B MET* 3.8 27.1 - - - +
418B PRO* 4.0 16.6 - - + -
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B THR* 2.8 36.5 + - + +
189B GLU* 3.4 28.8 + - - +
190B ALA 3.0 0.4 - - - -
191B ALA* 1.3 77.0 - - - +
193B ILE* 1.3 60.9 + - - +
194B ILE 3.4 0.5 + - - -
195B ASP 3.3 18.8 + - - -
196B PRO* 3.5 34.5 + - + +
198B ARG 2.7 30.3 + - - -
199B THR* 4.6 5.1 - - + +
352B ASN* 3.6 15.8 + - - +
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B GLU 4.1 5.8 - - - +
190B ALA* 2.7 23.4 + - - +
192B HIS* 1.3 73.4 - - - +
194B ILE* 1.3 58.0 + - + +
348B VAL* 4.6 7.6 - - + -
351B PHE* 3.8 29.4 - - + -
352B ASN* 3.8 31.3 + - + +
357B GLY* 3.5 31.4 - - - +
358B LEU* 3.6 24.6 - - + +
405B PRO* 4.1 22.4 - - + +
409B PRO* 4.1 12.6 - - + -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 4.5 14.6 + - + +
50B LEU* 4.9 10.3 - - + -
190B ALA 4.1 1.0 + - - -
191B ALA 3.3 4.3 + - - +
192B HIS 4.0 1.1 - - - -
193B ILE* 1.3 78.4 - - + +
195B ASP* 1.3 70.2 + - + +
196B PRO* 3.8 7.1 - - - +
358B LEU* 3.8 17.4 - - + +
361B ALA* 3.6 16.6 - - + -
409B PRO* 3.5 41.7 - - + +
412B MET* 4.1 23.8 - - + -
413B LEU* 3.7 28.9 - - + -
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA 2.9 9.6 + - - +
192B HIS* 3.3 14.5 + - - -
194B ILE* 1.3 89.2 - - + +
196B PRO* 1.3 65.7 - - - +
197B ASP* 2.9 32.5 + - - +
198B ARG* 3.1 36.3 + - + +
412B MET* 4.6 5.4 - - + -
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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