Contacts of the helix formed by residues 206 - 218 (chain B) in PDB entry 4FZ5
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 PHE 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ALA 4.5 7.4 - - - -
102B ASP* 3.2 28.7 - - + -
103B LEU* 3.2 37.2 - - + -
106B TYR* 2.9 43.7 - + + -
107B LEU* 5.2 0.7 - - - +
146B LEU* 5.9 3.4 - - + -
178B LEU* 4.0 12.1 - - + -
202B PRO 3.6 1.4 + - - -
203B ASP* 3.2 20.6 - - + +
204B GLY* 3.8 7.0 - - - -
205B GLY* 1.3 84.3 - - - +
207B ARG* 1.3 60.1 + - - +
208B GLN* 2.8 5.5 + - - -
209B VAL* 2.9 22.0 - - - +
210B LYS* 3.4 8.3 + - - +
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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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106B TYR* 3.4 23.5 + - + +
202B PRO* 3.5 36.7 + - + +
203B ASP* 4.3 10.0 + - - +
206B PHE* 1.3 75.6 - - - +
208B GLN* 1.3 61.9 + - - +
210B LYS* 3.2 8.3 + - + +
211B GLU* 2.6 67.3 + - + +
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Residues in contact with GLN 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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195B TYR* 4.6 1.0 + - - -
197B VAL* 3.6 27.1 - - + +
198B ASP 4.2 2.4 + - - -
201B GLY* 2.7 43.6 - - - +
202B PRO* 3.3 14.1 - - + +
205B GLY* 3.2 14.1 - - - -
206B PHE 2.8 8.1 + - - -
207B ARG* 1.3 86.2 + - + +
209B VAL* 1.3 60.5 + - - +
211B GLU* 3.1 17.6 + - - +
212B ALA* 2.8 29.1 + - - +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.1 19.3 - - + -
107B LEU* 5.2 5.8 - - + -
144B VAL* 5.0 17.5 - - + -
176B ILE* 3.9 28.1 - - + +
178B LEU* 4.3 19.5 - - + -
197B VAL* 4.5 7.9 - - + -
205B GLY 3.6 15.0 - - - +
206B PHE* 2.9 26.9 - - - +
208B GLN* 1.3 76.9 - - - +
210B LYS* 1.3 62.4 + - + +
212B ALA* 3.3 2.2 + - - +
213B VAL* 3.1 28.8 + - + +
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TYR* 3.3 42.4 + - + -
107B LEU* 3.7 34.8 - - + +
108B GLU 3.8 14.6 + - - +
109B GLY* 4.8 3.4 + - - -
206B PHE 3.8 6.7 - - - +
207B ARG* 3.2 11.8 + - + +
208B GLN 3.1 0.6 - - - -
209B VAL* 1.3 80.2 - - - +
211B GLU* 1.3 64.3 + - - +
213B VAL* 3.2 6.9 + - + +
214B MET* 3.0 48.9 + - + +
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Residues in contact with GLU 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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207B ARG* 2.6 59.0 + - + +
208B GLN* 3.1 21.5 + - - +
210B LYS* 1.3 74.8 - - - +
212B ALA* 1.3 56.5 + - - +
214B MET* 3.9 18.2 + - + +
215B ARG* 3.0 34.2 + - + +
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Residues in contact with ALA 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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176B ILE* 3.8 21.3 - - + -
195B TYR* 3.3 34.1 - - + +
208B GLN 2.8 15.3 + - - +
209B VAL* 3.9 2.0 - - - +
210B LYS 3.2 0.4 - - - -
211B GLU* 1.3 72.1 - - - +
213B VAL* 1.3 67.9 + - - +
215B ARG* 3.1 16.6 - - - +
216B TYR* 3.0 30.5 + - + -
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Residues in contact with VAL 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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87B ASP* 5.2 2.2 - - + +
88B VAL* 4.4 24.7 - - + -
142B CYS* 3.5 25.4 - - + -
144B VAL* 5.2 4.7 - - + -
176B ILE* 3.5 20.0 - - + -
209B VAL 3.1 15.7 + - - +
210B LYS* 3.2 8.9 + - + +
212B ALA* 1.3 72.9 - - - +
214B MET* 1.3 58.0 + - + +
215B ARG 2.9 3.8 - - - -
216B TYR* 2.4 30.2 + - - +
217B LEU* 2.7 32.3 + - + -
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Residues in contact with MET 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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210B LYS* 3.0 41.8 + - + +
211B GLU* 4.2 17.0 - - + +
213B VAL* 1.3 80.8 - - + +
215B ARG* 1.3 60.1 + - - +
216B TYR 3.4 0.2 + - - -
217B LEU* 3.5 22.2 + - + -
218B GLN* 3.1 32.3 + - - +
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Residues in contact with ARG 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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195B TYR* 3.9 32.1 + - - -
211B GLU* 3.0 26.2 + - - +
212B ALA* 3.1 24.0 + - - +
213B VAL 2.8 0.6 + - - -
214B MET* 1.3 77.4 - - - +
216B TYR* 1.3 71.8 + - + +
218B GLN* 4.0 11.7 + - - +
219B THR* 3.9 7.3 + - - -
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Residues in contact with TYR 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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142B CYS* 4.2 9.0 - - - -
174B CYS* 4.0 24.0 - - + -
175B THR 5.2 3.3 + - - -
176B ILE* 3.3 38.2 - - + +
195B TYR* 3.7 27.5 - + - -
212B ALA* 3.0 17.9 + - + -
213B VAL* 2.4 20.8 + - - +
215B ARG* 1.3 82.5 + - + +
217B LEU* 1.3 60.6 + - - +
218B GLN 3.2 2.7 - - - -
219B THR* 2.8 28.2 + - - +
220B LEU* 3.9 6.7 + - - +
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Residues in contact with LEU 217 (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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81B ARG* 3.7 37.9 + - - +
87B ASP* 3.4 31.2 - - + +
141B HIS* 5.4 3.8 - - + -
142B CYS* 5.8 2.7 - - - -
213B VAL* 2.7 38.5 + - + +
214B MET* 3.5 21.9 + - + +
216B TYR* 1.3 72.9 - - + +
218B GLN* 1.3 68.8 + - - +
219B THR 3.3 0.2 + - - -
220B LEU* 3.4 40.3 + - + +
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Residues in contact with GLN 218 (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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81B ARG* 6.0 2.2 - - - +
214B MET* 3.1 29.7 + - - +
215B ARG* 4.3 8.7 - - - +
216B TYR 3.2 1.0 + - - -
217B LEU* 1.3 85.8 - - - +
219B THR* 1.3 62.4 + - - +
220B LEU 3.5 5.9 + - - +
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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