Contacts of the helix formed by residues 198 - 216 (chain B) in PDB entry 4Y2H
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 ILE* 4.0 8.1 - - + +
197B SER* 1.3 69.7 - - - +
199B GLN* 1.3 59.2 + - - +
200B MET* 2.9 23.7 + - - +
201B LEU* 3.0 21.0 + - + +
202B GLU* 3.0 24.3 + - - +
239B GLN* 3.2 14.6 - - - +
241B LEU* 4.2 15.7 - - + +
286B HIS* 2.9 21.7 + - - +
322B LEU* 3.4 7.3 - - - +
324B TYR* 2.7 34.3 + - + +
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Residues in contact with GLN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B SER* 3.7 4.0 + - - +
198B ASP* 1.3 71.7 + - - +
200B MET* 1.3 60.6 + - - +
202B GLU* 3.7 15.4 - - - +
203B TRP* 3.0 28.4 + - - +
241B LEU* 5.3 1.0 - - - +
242B SER* 4.7 1.0 + - - -
244B GLU* 3.5 24.8 + - - +
245B ASP* 2.6 32.0 + - - +
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Residues in contact with MET 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP* 2.9 9.5 + - - +
199B GLN* 1.3 76.5 - - - +
201B LEU* 1.3 64.8 + - - +
203B TRP* 3.3 18.4 + - - +
204B ARG* 3.0 44.9 + - - +
239B GLN* 4.0 21.1 - - - +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP* 3.0 24.0 + - + +
200B MET* 1.3 76.2 - - - +
202B GLU* 1.3 62.6 + - - +
204B ARG* 3.0 11.6 + - + +
205B LEU* 2.9 42.1 + - + +
230B LEU* 4.0 34.3 - - + +
231B MET* 3.8 19.5 - - + -
239B GLN* 5.2 0.2 + - - -
286B HIS* 3.7 25.1 - - + -
324B TYR* 3.6 31.2 - - + +
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B SER* 5.3 1.4 + - - -
198B ASP 3.0 18.0 + - - +
199B GLN* 3.7 16.1 - - - +
200B MET 3.4 0.2 - - - -
201B LEU* 1.3 76.1 - - - +
203B TRP* 1.3 61.6 + - - +
205B LEU* 3.5 6.3 + - - +
206B GLY* 3.0 21.0 + - - -
284B PRO* 3.5 27.8 - - + +
286B HIS* 4.0 17.1 - - + +
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Residues in contact with TRP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.9 19.3 - - + -
62A ALA* 4.7 10.1 - - + -
199B GLN 3.0 15.0 + - - +
200B MET* 3.3 20.2 + - - +
202B GLU* 1.3 74.8 - - - +
204B ARG* 1.3 71.1 + - + +
206B GLY* 3.4 1.7 + - - -
207B PHE* 3.0 55.6 + + - +
210B GLN* 3.8 26.5 + - - +
214B HIS* 6.4 0.2 - - - -
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.6 0.2 - - - +
55A SER* 2.7 35.4 + - - +
58A GLU* 2.8 46.2 + - - +
200B MET* 3.0 33.5 + - + +
201B LEU* 3.0 12.9 + - - +
203B TRP* 1.3 88.0 - - + +
205B LEU* 1.3 62.6 + - - +
207B PHE* 3.4 15.7 - - - +
208B TRP* 3.9 12.6 + - - -
226B ALA* 4.8 1.2 - - - +
230B LEU* 3.5 35.5 - - + +
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Residues in contact with LEU 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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201B LEU* 2.9 31.8 + - + +
202B GLU* 4.0 4.9 - - - +
204B ARG* 1.3 75.8 - - - +
206B GLY* 1.3 60.6 + - - +
207B PHE 3.5 0.3 + - - -
208B TRP* 4.2 11.4 + - - +
209B SER* 5.3 0.5 + - - -
223B GLU* 3.6 26.6 - - + +
226B ALA* 3.9 11.2 - - + +
227B THR* 3.7 40.6 - - - +
230B LEU* 4.1 13.7 - - + -
231B MET* 3.9 25.4 - - - -
286B HIS* 4.7 5.6 - - + +
328B PRO* 3.9 17.9 - - + -
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU 3.0 16.0 + - - -
203B TRP* 3.8 2.7 - - - -
205B LEU* 1.3 74.8 - - - +
207B PHE* 1.3 63.9 + - - +
208B TRP 3.2 2.9 - - - -
209B SER* 3.1 24.8 + - - -
210B GLN* 3.6 14.2 + - - +
223B GLU* 5.3 4.3 - - - -
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Residues in contact with PHE 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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58A GLU* 3.9 16.8 - - + -
61A ILE* 3.8 13.5 - - + -
62A ALA* 3.5 42.8 - - + -
203B TRP* 3.0 38.8 + + + +
204B ARG* 3.4 16.8 - - - +
205B LEU 3.2 1.4 - - - -
206B GLY* 1.3 77.8 - - - +
208B TRP* 1.3 92.0 + + - +
210B GLN* 3.0 33.3 + - + +
211B VAL* 3.5 23.7 + - + +
214B HIS* 5.0 13.9 - + - -
215B TYR* 5.6 0.4 - + - -
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Residues in contact with TRP 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.6 33.6 - - + +
57A HIS* 3.9 15.9 - - + -
58A GLU* 3.7 34.6 + - + +
61A ILE* 3.7 23.6 - - + -
93A THR* 4.5 4.9 - - + -
204B ARG 3.9 15.0 + - - -
205B LEU 4.2 6.3 - - - +
206B GLY 3.2 0.8 - - - -
207B PHE* 1.3 88.8 - + - +
209B SER* 1.3 59.5 + - - +
210B GLN 3.3 0.4 + - - -
211B VAL* 3.7 18.4 + - + +
212B LYS 4.8 0.2 + - - -
219B MET* 3.2 61.7 + - + +
220B SER* 3.3 3.6 + - - +
222B LEU* 4.2 22.4 - - + -
223B GLU* 4.5 8.1 - - + +
226B ALA* 3.7 22.0 - - + +
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU 5.3 0.4 + - - -
206B GLY* 3.1 13.5 + - - -
208B TRP* 1.3 77.0 - - - +
210B GLN* 1.3 62.7 + - - +
211B VAL 3.3 0.4 - - - -
212B LYS* 4.3 10.5 + - - +
213B GLN* 5.0 1.6 + - - +
220B SER* 3.6 23.7 - - - -
223B GLU* 4.0 16.8 + - - +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TRP* 3.8 32.7 + - - +
206B GLY* 3.8 16.2 + - - +
207B PHE* 3.0 17.6 + - + +
209B SER* 1.3 80.2 - - - +
211B VAL* 1.3 63.3 + - - +
212B LYS 3.3 1.3 - - - -
213B GLN* 3.2 29.0 + - + +
214B HIS* 3.3 35.0 + - + +
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Residues in contact with VAL 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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61A ILE* 4.3 7.0 - - + -
95A ILE* 4.4 7.6 - - + -
207B PHE* 3.5 37.2 - - + +
208B TRP* 3.7 25.6 - - + +
209B SER 3.3 1.6 - - - -
210B GLN* 1.3 74.9 - - - +
212B LYS* 1.3 65.0 + - - +
214B HIS* 3.2 8.0 + - + -
215B TYR* 2.9 38.8 + - + -
216B GLY 3.6 2.1 + - - -
217B VAL* 3.4 16.8 - - + +
219B MET* 3.7 22.0 - - + -
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Residues in contact with LYS 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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208B TRP 4.8 0.6 + - - -
209B SER 4.3 9.0 + - - +
210B GLN 3.3 0.8 - - - -
211B VAL* 1.3 76.6 - - - +
213B GLN* 1.3 58.1 + - - +
216B GLY* 2.8 31.8 + - - -
217B VAL 3.2 19.7 + - - +
218B ASP* 3.8 38.1 - - - +
219B MET 4.9 0.4 - - - +
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Residues in contact with GLN 213 (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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209B SER 5.0 1.5 + - - +
210B GLN* 3.2 25.9 + - + +
212B LYS* 1.3 82.4 - - - +
214B HIS* 1.3 85.2 + - + +
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Residues in contact with HIS 214 (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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68A ASP* 4.6 1.6 - - - +
71A ARG* 4.2 11.3 + - - -
203B TRP* 6.4 0.4 - - - -
207B PHE* 5.0 13.8 - + - -
210B GLN* 3.3 42.5 + - + +
211B VAL* 3.2 5.9 + - - +
213B GLN* 1.3 111.5 + - + +
215B TYR* 1.3 93.2 + + + +
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Residues in contact with TYR 215 (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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61A ILE* 2.7 40.7 + - + -
62A ALA* 4.3 1.9 - - - -
64A ARG* 3.5 23.8 + - + +
67A THR* 3.6 28.0 - - + -
68A ASP* 3.6 36.1 - - - -
71A ARG* 3.9 16.3 - - - +
95A ILE* 4.4 4.9 - - + -
99A PHE* 3.7 29.7 - + + -
102A GLN* 4.7 2.6 - - - +
207B PHE* 5.6 0.7 - + - -
211B VAL* 2.9 25.1 + - + +
214B HIS* 1.3 104.7 - + + +
216B GLY* 1.3 64.6 + - - +
217B VAL* 3.4 2.1 + - - +
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Residues in contact with GLY 216 (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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102A GLN* 3.1 23.1 + - - -
127A ASN* 5.2 0.7 - - - +
212B LYS* 2.8 24.7 + - - -
214B HIS 3.9 0.4 - - - -
215B TYR* 1.3 79.9 - - - +
217B VAL* 1.3 60.3 + - - +
218B ASP 4.2 0.4 + - - -
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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
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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