Contacts of the helix formed by residues 198 - 212 (chain B) in PDB entry 5H1C
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 ASP 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ASN* 3.1 6.8 - - + +
197B THR* 1.3 86.6 + - - +
199B HIS* 1.3 62.5 + - - +
200B GLN 3.2 0.2 - - - -
201B THR* 2.2 38.0 + - - +
202B GLN* 3.6 4.7 + - - +
232B TYR* 4.7 3.5 + - - -
244B HIS* 3.6 20.1 + - - -
56C PRO* 6.2 0.7 - - - -
57C LYS* 3.2 35.3 + - + +
58C LYS 5.1 0.5 + - - -
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Residues in contact with HIS 199 (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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193B ARG 3.4 13.9 - - - -
194B ALA* 3.3 6.7 - - + -
195B PHE* 3.3 19.9 + - - +
196B ASN* 3.1 29.9 + - + +
198B ASP* 1.3 79.2 - - - +
200B GLN* 1.3 61.9 + - - +
202B GLN* 3.1 25.1 + - + -
203B LEU* 3.0 33.1 + - + +
84C MET* 3.2 57.2 + - + +
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Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 5.4 6.1 - - + +
162B THR* 3.4 19.1 - - + +
194B ALA* 4.0 16.4 - - + -
196B ASN 4.1 0.2 - - - +
197B THR 3.7 9.3 - - - +
198B ASP 3.2 0.8 - - - -
199B HIS* 1.3 77.4 - - - +
201B THR* 1.3 57.5 + - - +
203B LEU* 3.3 11.8 + - + +
204B LEU* 2.9 32.4 + - - +
221B VAL* 5.2 1.2 - - - +
223B SER 3.9 3.8 + - - -
224B ALA* 3.7 18.9 + - - +
227B LEU* 3.3 28.8 - - + +
228B TYR* 3.6 27.5 + - - -
248B PHE* 3.9 24.7 - - + -
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Residues in contact with THR 201 (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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197B THR 4.3 0.7 - - - +
198B ASP* 2.2 32.0 + - - +
200B GLN* 1.3 75.6 - - + +
202B GLN* 1.3 67.1 + - - +
204B LEU* 2.8 26.6 + - + +
205B TYR* 2.9 32.3 + - - -
244B HIS* 3.8 33.7 - - + +
248B PHE* 5.2 6.7 - - + -
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP 4.3 5.2 - - - +
199B HIS* 3.1 25.7 + - + +
201B THR* 1.3 88.7 + - - +
203B LEU* 1.3 59.1 + - + +
205B TYR* 3.3 10.1 + - + +
206B GLN* 2.9 40.0 + - + +
84C MET* 6.0 0.9 - - - +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 4.2 23.8 - - + +
192B ALA* 4.5 11.2 - - + -
193B ARG 4.6 2.0 - - - +
194B ALA* 3.6 35.7 - - + +
199B HIS* 3.0 41.2 + - + +
200B GLN* 3.5 9.4 - - - +
201B THR 3.1 0.2 - - - -
202B GLN* 1.3 77.7 - - + +
204B LEU* 1.3 57.9 + - - +
206B GLN* 3.6 13.9 + - - +
207B ALA* 2.9 26.7 + - - +
84C MET 3.6 15.5 - - - +
86C PHE* 3.4 22.8 - - + -
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 4.6 17.3 - - + -
200B GLN 2.9 16.6 + - - +
201B THR* 2.8 15.2 + - + +
203B LEU* 1.3 75.8 - - - +
205B TYR* 1.3 67.1 + - + +
207B ALA* 3.0 6.9 + - + +
208B SER* 2.9 22.6 + - - -
219B LEU* 5.2 2.2 - - + -
221B VAL* 6.3 0.2 - - + -
248B PHE* 3.6 35.4 - - + +
251B MET* 3.7 36.1 - - + -
252B LEU* 3.8 23.6 - - + -
255B LEU* 4.4 16.3 - - + +
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Residues in contact with TYR 205 (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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44B ALA 3.4 26.9 - - - -
45B GLY* 3.8 14.5 - - - -
47B HIS* 4.7 2.3 + - - -
59B GLU* 4.7 9.8 + - - -
201B THR* 2.9 42.2 + - - -
202B GLN* 3.3 8.7 + - + +
204B LEU* 1.3 78.1 - - + +
206B GLN* 1.3 58.8 + - + +
208B SER* 2.5 22.6 + - - -
209B ALA* 2.9 14.6 + - - +
251B MET* 4.5 30.8 - - + +
254B ARG* 5.0 4.7 - - - -
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Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLN* 2.9 25.6 + - + +
203B LEU* 3.9 18.4 - - - +
205B TYR* 1.3 74.9 - - + +
207B ALA* 1.3 60.9 + - - +
209B ALA* 3.2 10.0 + - + +
210B MET* 2.9 31.2 + - + +
84C MET 4.2 2.2 + - - +
85C GLY* 3.6 27.9 - - - +
86C PHE* 3.7 14.2 + - + -
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Residues in contact with ALA 207 (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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158B MET* 4.8 12.6 - - - -
160B ILE* 5.4 1.3 - - + -
203B LEU 2.9 16.0 + - - +
204B LEU* 3.0 14.6 + - + +
206B GLN* 1.3 76.5 - - - +
208B SER* 1.3 58.7 + - - +
210B MET* 2.8 19.5 + - - +
211B MET* 2.9 19.1 + - + +
219B LEU* 4.8 9.0 - - + -
255B LEU* 4.7 12.6 - - + -
86C PHE* 3.5 19.0 - - + -
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 3.3 21.9 + - - -
47B HIS* 3.8 9.1 - - - +
48B THR* 5.9 0.3 - - - +
204B LEU 2.9 9.7 + - - -
205B TYR* 2.5 29.3 + - - -
207B ALA* 1.3 76.3 - - - +
209B ALA* 1.3 61.1 + - - +
211B MET* 3.3 24.1 + - - +
212B VAL* 3.9 7.1 - - - +
251B MET* 6.4 1.8 - - - -
254B ARG* 6.6 0.2 - - - -
255B LEU* 3.9 19.4 - - - +
259B PHE* 5.1 3.5 - - - -
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B HIS* 3.5 26.6 - - + +
205B TYR 2.9 14.0 + - - +
206B GLN* 3.3 14.4 - - + +
207B ALA 3.1 0.2 - - - -
208B SER* 1.3 79.8 + - - +
210B MET* 1.3 62.8 + - + +
211B MET 3.5 0.2 + - - -
212B VAL* 3.8 15.1 + - - +
213B GLU* 4.7 6.9 - - - +
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Residues in contact with MET 210 (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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158B MET* 5.1 0.4 - - + -
206B GLN* 2.9 15.5 + - + +
207B ALA* 2.8 9.2 + - - +
209B ALA* 1.3 77.6 - - + +
211B MET* 1.3 64.8 + - - +
212B VAL 3.1 4.2 + - - -
213B GLU* 3.5 41.0 + - + +
214B SER* 4.2 7.1 + - - +
216B TYR* 4.6 28.9 - - + +
86C PHE* 3.6 27.8 - - + -
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Residues in contact with MET 211 (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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158B MET* 3.2 36.3 - - + +
207B ALA* 2.9 21.0 + - - +
208B SER* 3.5 16.8 - - - +
209B ALA 3.3 1.0 - - - -
210B MET* 1.3 79.1 - - - +
212B VAL* 1.3 62.4 + - + +
213B GLU 3.3 0.9 + - - -
214B SER 4.0 13.9 + - - +
215B ARG* 4.8 3.4 + - - +
216B TYR* 4.2 8.1 - - + +
219B LEU* 5.8 6.3 - - + -
255B LEU* 4.7 9.9 - - + -
259B PHE* 3.4 57.4 - - + -
261B VAL* 4.1 19.1 - - + -
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Residues in contact with VAL 212 (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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24B PRO* 4.8 15.3 - - + -
47B HIS* 3.5 42.4 - - + +
48B THR* 4.4 12.3 - - + -
208B SER 3.9 4.5 - - - +
209B ALA 3.9 13.9 - - - +
210B MET 3.1 0.6 - - - -
211B MET* 1.3 78.8 - - - +
213B GLU* 1.3 67.1 + - + +
259B PHE* 6.0 0.2 - - - -
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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
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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