Contacts of the helix formed by residues 195 - 214 (chain K) in PDB entry 5MQF
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 ILE 195 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F ALA* 5.6 2.2 - - + +
191K LYS 3.3 13.2 + - - +
192K ASN* 4.0 5.2 - - - +
193K TYR 3.3 0.2 - - - -
194K GLU* 1.3 76.5 - - - +
196K GLU* 1.3 54.4 + - - +
198K THR* 4.7 3.8 - - - -
199K ILE* 2.7 39.8 + - - +
225K PHE* 4.8 2.1 - - - +
784L LEU* 4.0 25.6 - - + +
787L ARG* 4.9 11.0 - - + -
788L TYR* 5.6 6.1 - - + +
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Residues in contact with GLU 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I LYS 5.1 8.1 - - - +
136I PRO* 5.3 6.3 - - + -
192K ASN 3.1 15.4 + - - +
193K TYR* 3.3 14.1 - - + +
195K ILE* 1.3 75.5 - - - +
197K ARG* 1.3 59.6 + - - +
199K ILE* 3.0 7.2 + - - +
200K VAL* 2.9 27.1 + - - +
225K PHE* 5.7 3.1 - - - -
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Residues in contact with ARG 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K TYR 3.1 11.5 + - - +
194K GLU* 4.5 2.0 - - - +
196K GLU* 1.3 78.1 - - - +
198K THR* 1.3 58.3 + - - +
200K VAL* 3.1 8.9 + - - +
201K GLN* 2.9 29.2 + - - +
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Residues in contact with THR 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F ALA* 6.5 0.9 - - - -
194K GLU 3.2 18.8 + - - -
195K ILE* 4.5 2.7 - - - -
197K ARG* 1.3 77.8 - - - +
199K ILE* 1.3 56.1 - - - +
201K GLN* 3.8 8.0 - - - +
202K LEU* 2.9 27.5 + - - +
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Residues in contact with ILE 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195K ILE 2.7 23.5 + - - +
196K GLU* 3.0 4.9 + - - +
198K THR* 1.3 75.9 - - - +
200K VAL* 1.3 59.5 + - - +
202K LEU* 3.2 9.3 + - - +
203K GLU* 2.9 26.2 + - - +
223K GLN 5.1 1.0 - - - +
224K ASP* 5.3 3.9 - - - -
225K PHE* 3.7 33.0 - - + +
787L ARG* 6.3 0.9 - - + -
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Residues in contact with VAL 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K GLU 2.9 11.8 + - - +
197K ARG* 3.6 9.9 - - - +
199K ILE* 1.3 75.5 - - - +
201K GLN* 1.3 57.7 + - - +
203K GLU* 3.0 8.4 + - - +
204K ASN* 2.9 27.6 + - - +
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Residues in contact with GLN 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197K ARG 2.9 16.3 + - - +
198K THR* 3.8 7.6 - - - +
200K VAL* 1.3 75.6 - - - +
202K LEU* 1.3 57.0 + - - +
204K ASN* 3.9 7.3 - - - +
205K GLU* 2.9 31.7 + - - +
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Residues in contact with LEU 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198K THR 2.9 21.1 + - - +
199K ILE* 3.4 11.7 - - - +
200K VAL 3.1 0.6 - - - -
201K GLN* 1.3 78.3 - - - +
203K GLU* 1.3 50.4 + - - +
205K GLU* 4.6 2.5 - - - -
206K ILE* 2.6 36.7 + - - +
223K GLN* 5.2 1.0 - - - +
791L LEU* 4.8 18.2 - - + -
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Residues in contact with GLU 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K ILE 2.9 12.3 + - - +
200K VAL* 3.0 10.0 + - - +
202K LEU* 1.3 76.5 - - - +
204K ASN* 1.3 59.6 + - - +
206K ILE* 3.3 5.7 + - - +
207K TYR* 2.9 27.7 + - - +
220K ASN 4.3 3.6 - - - +
221K ILE* 5.3 6.0 - - - +
223K GLN 3.4 25.6 - - - +
224K ASP* 5.3 1.6 - - + -
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Residues in contact with ASN 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K VAL 2.9 15.4 + - - +
201K GLN* 4.1 6.7 - - - +
203K GLU* 1.3 77.4 - - - +
205K GLU* 1.3 56.4 + - - +
207K TYR* 3.0 9.1 + - - +
208K GLN* 2.9 25.9 + - - +
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Residues in contact with GLU 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K GLN 2.9 21.6 + - - +
202K LEU* 4.6 3.8 - - - +
204K ASN* 1.3 72.7 - - - +
206K ILE* 1.3 59.7 - - - +
208K GLN* 3.6 9.5 - - + +
209K ILE* 2.9 32.4 + - - +
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Residues in contact with ILE 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K LEU 2.6 25.7 + - - +
203K GLU* 3.4 7.9 - - - +
204K ASN 3.2 0.4 - - - -
205K GLU* 1.3 76.4 - - - +
207K TYR* 1.3 50.0 + - - +
209K ILE* 4.7 1.5 - - - +
210K LYS* 2.5 38.1 + - - +
220K ASN* 3.3 26.7 - - + +
223K GLN* 4.4 8.5 - - + -
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Residues in contact with TYR 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K GLU 2.9 13.9 + - - +
204K ASN* 3.0 10.1 + - - +
206K ILE* 1.3 75.7 - - - +
208K GLN* 1.3 59.6 + - - +
210K LYS* 3.3 6.4 - - - +
211K GLN* 2.9 31.4 + - - +
220K ASN 4.5 2.7 + - - -
221K ILE* 5.0 14.1 - - + +
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Residues in contact with GLN 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K ASN 2.9 12.8 + - - +
205K GLU* 3.2 13.0 + - + +
207K TYR* 1.3 76.4 - - - +
209K ILE* 1.3 57.9 + - - +
211K GLN* 3.9 1.8 - - - +
212K GLN* 2.9 30.0 + - - +
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Residues in contact with ILE 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205K GLU 2.9 18.0 + - - +
206K ILE* 4.7 2.0 - - - +
208K GLN* 1.3 70.1 - - - +
210K LYS* 1.3 60.5 + - - +
212K GLN* 1.9 42.1 - - - +
213K HIS* 5.5 1.8 - - + -
214K GLY* 2.9 9.3 + - - +
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Residues in contact with LYS 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206K ILE 2.5 24.5 + - - +
207K TYR* 3.3 11.4 - - - +
209K ILE* 1.3 72.8 - - - +
211K GLN* 1.3 56.6 + - - +
213K HIS 1.9 36.7 - - - +
214K GLY* 3.1 19.7 - - - +
215K GLU 4.1 1.6 - - - +
216K ALA 4.3 7.9 - - - +
217K ASN* 4.7 6.7 - - + -
220K ASN* 3.5 20.2 - - + -
221K ILE* 5.2 0.4 - - + +
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Residues in contact with GLN 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K TYR 2.9 13.2 + - - +
208K GLN* 4.4 1.3 - - - +
210K LYS* 1.3 78.3 - - - +
212K GLN* 1.3 58.3 + - - +
213K HIS 3.7 3.9 + - - +
215K GLU 5.7 0.2 - - - -
216K ALA* 5.8 0.7 - - - +
217K ASN* 5.3 13.2 - - + +
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Residues in contact with GLN 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K GLN 2.9 18.4 + - - +
209K ILE* 1.9 35.2 - - - +
211K GLN* 1.3 73.2 - - - +
213K HIS* 1.3 57.1 + - - +
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Residues in contact with HIS 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209K ILE* 2.9 2.5 - - + +
210K LYS 1.9 22.4 - - - +
211K GLN 3.7 5.0 + - - +
212K GLN* 1.3 71.8 - - - +
214K GLY* 1.3 64.7 + - - +
215K GLU 3.0 14.1 + - - +
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Residues in contact with GLY 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209K ILE* 2.9 5.2 + - - +
210K LYS* 3.1 21.6 - - - +
213K HIS* 1.3 79.3 - - - +
215K GLU* 1.3 56.2 + - - +
216K ALA 2.8 28.1 + - - +
220K ASN* 4.9 5.0 - - - +
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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