Contacts of the helix formed by residues 197 - 211 (chain B) in PDB entry 5IFM
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 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B GLN* 4.8 1.3 - - - -
147B SER* 4.9 0.4 - - - -
148B ALA* 3.5 14.7 - - - +
173B GLN 4.9 0.2 + - - -
195B PHE* 3.3 1.6 - - - +
196B SER* 1.3 83.7 + - - +
198B LYS* 1.4 64.2 + - - -
199B PRO* 3.4 9.2 - - - -
200B ALA* 3.4 17.9 + - - +
201B ALA 3.5 4.9 + - - -
305C HIS* 5.1 4.0 - - - -
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Residues in contact with LYS 198 (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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147B SER* 3.2 32.6 + - - +
148B ALA* 3.7 9.8 - - - +
197B GLY* 1.4 68.1 - - - -
199B PRO* 1.4 70.5 - - + +
201B ALA* 3.2 5.8 + - - +
202B ARG* 3.0 40.4 + - + +
205B LEU* 4.9 4.9 - - - +
301C GLU* 3.9 37.0 - - + +
305C HIS* 4.6 5.3 + - + +
246D GLN* 3.5 25.9 - - - +
249D LYS* 4.3 17.3 - - - +
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Residues in contact with PRO 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLY* 3.4 9.0 - - - -
198B LYS* 1.4 90.7 - - + +
200B ALA* 1.4 54.5 + - - +
202B ARG* 3.4 6.7 + - + +
203B LYS* 3.0 42.0 + - - +
294C GLU 5.8 0.7 - - - +
297C GLU* 3.6 32.9 - - + +
298C MET* 4.0 37.9 - - + +
301C GLU* 4.1 11.4 - - + +
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Residues in contact with ALA 200 (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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171B PHE* 3.6 27.6 - - - +
172B GLY* 3.8 10.1 - - - -
173B GLN 4.5 1.8 - - - +
195B PHE* 3.6 26.2 - - + -
196B SER* 5.9 0.4 - - - +
197B GLY* 3.4 11.5 + - - +
198B LYS 3.3 0.4 - - - -
199B PRO* 1.4 75.3 - - - +
201B ALA* 1.3 64.4 + - - +
203B LYS* 3.4 10.2 + - - +
204B ALA* 3.2 19.1 + - - +
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Residues in contact with ALA 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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147B SER 5.0 0.7 - - - +
148B ALA* 3.9 33.9 - - + +
150B LEU* 3.9 12.9 - - + +
195B PHE* 3.7 19.4 - - + -
197B GLY 3.5 1.8 + - - -
198B LYS* 3.2 13.3 + - + +
200B ALA* 1.3 76.6 - - - +
202B ARG* 1.4 58.1 + - - +
204B ALA* 3.4 3.3 + - - +
205B LEU* 3.0 34.4 + - + +
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Residues in contact with ARG 202 (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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198B LYS* 3.0 33.5 + - - +
199B PRO* 3.6 4.5 - - + +
200B ALA 3.4 0.2 - - - -
201B ALA* 1.4 71.9 - - - +
203B LYS* 1.3 60.6 + - - +
205B LEU* 3.4 6.6 + - - +
206B ASP* 3.0 49.2 + - - +
157C GLN* 4.6 10.7 + - - +
158C TYR* 5.8 0.4 - - - -
218C PHE* 3.9 14.6 - - - -
297C GLU* 3.8 17.3 + - - -
301C GLU* 3.3 26.2 + - - -
304C ARG* 3.9 9.5 - - - +
246D GLN* 3.3 21.1 + - - +
249D LYS* 3.5 21.4 - - - +
250D GLU* 2.8 31.1 + - - +
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Residues in contact with LYS 203 (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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171B PHE* 2.7 39.9 + - + +
172B GLY* 4.4 3.2 - - - -
199B PRO* 3.0 25.5 + - - +
200B ALA* 3.4 19.9 - - - +
202B ARG* 1.3 76.0 - - + +
204B ALA* 1.4 56.1 + - - +
206B ASP* 3.3 5.9 + - - +
207B ARG* 2.9 41.5 + - + +
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Residues in contact with ALA 204 (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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150B LEU* 3.8 18.2 - - + -
168B PHE* 4.2 7.0 - - + -
171B PHE* 3.7 34.7 - - + -
195B PHE* 3.9 6.5 - - + -
200B ALA 3.2 10.1 + - - +
201B ALA 3.6 8.5 - - - +
203B LYS* 1.4 75.8 - - - +
205B LEU* 1.3 58.6 + - - +
208B CYS* 3.0 37.1 + - - +
224B VAL* 4.6 1.8 - - - -
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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
----------------------------------------------------------
150B LEU* 3.7 21.5 - - + -
198B LYS* 4.9 4.0 - - - +
201B ALA* 3.0 22.1 + - + +
202B ARG* 3.7 6.1 - - - +
204B ALA* 1.3 76.1 - - - +
206B ASP* 1.3 62.0 + - - +
208B CYS* 4.1 0.9 - - - +
209B SER* 3.1 24.4 + - - -
224B VAL* 3.4 33.7 - - + +
225B GLU* 3.7 19.3 - - - -
226B PRO* 3.9 17.9 - - + -
244D ASN* 4.4 5.2 + - - +
246D GLN* 3.9 34.3 - - + +
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Residues in contact with ASP 206 (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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202B ARG* 3.0 32.6 + - - +
203B LYS* 3.8 4.4 - - - +
205B LEU* 1.3 75.2 - - - +
207B ARG* 1.4 58.2 + - + +
209B SER* 2.7 23.0 + - - -
210B GLU* 3.0 32.5 + - - +
157C GLN* 2.6 34.9 - - - +
158C TYR* 3.1 21.1 + - - -
246D GLN* 3.9 14.2 - - - +
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Residues in contact with ARG 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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257A PHE* 3.3 43.3 - - + +
170B VAL* 4.0 25.9 + - - +
171B PHE* 3.7 26.7 - - + -
203B LYS* 2.9 30.5 + - + +
206B ASP* 1.4 74.3 - - + +
208B CYS* 1.4 53.4 + - - +
210B GLU* 4.0 11.4 - - - +
211B GLY* 2.8 30.0 + - - -
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Residues in contact with CYS 208 (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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257A PHE* 4.1 3.4 - - - -
272A LYS* 3.3 9.4 + - - -
168B PHE* 4.3 0.9 - - - -
171B PHE* 3.6 28.5 - - - -
204B ALA 3.0 22.8 + - - +
205B LEU 4.1 1.1 - - - +
207B ARG* 1.4 73.4 - - - +
209B SER* 1.4 56.8 + - - +
211B GLY 3.0 15.5 - - - +
213B PHE* 3.7 30.7 + - + -
222B VAL 4.4 10.1 - - - +
223B THR* 5.8 0.3 - - - -
224B VAL* 3.7 33.5 + - + +
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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
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272A LYS* 2.9 19.0 + - - +
205B LEU 3.1 12.3 + - - -
206B ASP* 2.7 21.3 + - - -
208B CYS* 1.4 75.3 - - - +
210B GLU* 1.4 63.2 + - - +
211B GLY 3.5 0.2 - - - -
224B VAL 6.0 1.6 - - - -
158C TYR* 4.6 0.9 + - - -
242D ILE* 4.1 16.7 - - - +
244D ASN* 3.1 35.4 + - - -
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Residues in contact with GLU 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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269A MET* 5.9 4.7 - - - +
272A LYS* 4.5 1.4 + - - -
206B ASP* 3.0 23.8 + - - +
207B ARG* 4.0 10.9 - - - +
209B SER* 1.4 86.2 + - - +
211B GLY* 1.3 57.1 + - - +
157C GLN* 3.5 24.6 + - - -
158C TYR* 5.5 1.4 + - - -
186C ARG* 3.2 45.1 + - - +
242D ILE* 4.5 10.9 - - + +
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Residues in contact with GLY 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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257A PHE* 4.1 9.4 - - - -
258A ALA 6.0 0.7 - - - -
265A TYR* 6.4 1.6 - - - -
272A LYS* 2.6 27.6 + - - -
207B ARG 2.8 19.1 + - - -
208B CYS 3.0 12.0 - - - +
210B GLU* 1.3 74.2 - - - +
212B SER* 1.3 57.7 + - - -
213B PHE 3.8 0.9 - - - -
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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