Contacts of the helix formed by residues 169 - 179 (chain B) in PDB entry 6EKK
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 ASN 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE* 5.6 4.8 - - - -
107B GLU* 3.6 13.9 + - - -
164B PRO* 3.6 28.7 - - + +
165B SER 2.8 24.0 + - - +
167B PRO 4.1 0.4 - - - -
168B GLU* 1.3 72.5 - - - +
170B ARG* 1.3 62.2 + - - +
171B ASN* 3.6 12.0 + - - +
172B LEU* 3.0 31.9 + - + +
173B THR* 2.7 30.5 + - - -
213B GLY* 5.9 0.2 - - - -
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Residues in contact with ARG 170 (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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70B ASN* 2.8 37.2 + - - +
106B PHE* 5.2 0.2 - - + -
107B GLU* 2.8 34.9 + - + +
110B TYR* 3.6 28.7 - - + +
167B PRO 4.9 4.9 - - - -
168B GLU 3.3 2.4 + - - +
169B ASN* 1.3 72.1 - - - +
171B ASN* 1.3 62.1 + - - +
173B THR* 3.9 4.0 - - - -
174B GLU* 3.1 32.5 + - - +
205B SER* 6.0 0.6 - - - -
401B SO4 4.7 10.1 + - - -
406B EDO 3.6 25.3 - - - +
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Residues in contact with ASN 171 (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 PHE* 3.2 46.9 - - - -
107B GLU* 4.6 0.2 + - - -
110B TYR* 4.4 0.2 + - - -
169B ASN* 3.4 9.9 + - - +
170B ARG* 1.3 76.8 - - - +
172B LEU* 1.3 61.2 + - - +
175B TYR* 2.9 31.0 + - - +
209B ALA* 3.6 26.2 - - - +
212B HIS* 3.4 24.2 - - + +
213B GLY* 4.2 5.8 - - - +
406B EDO 2.7 29.2 + - - -
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Residues in contact with LEU 172 (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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164B PRO* 3.9 35.4 - - + +
166B ILE* 4.0 20.4 - - + -
169B ASN* 3.0 24.3 + - + +
171B ASN* 1.3 76.7 - - - +
173B THR* 1.3 57.8 + - - +
175B TYR* 3.3 20.7 + - + +
176B PHE* 2.8 31.0 + - + +
184B MET* 5.3 0.7 - - + -
213B GLY* 4.4 6.7 - - - +
216B ALA* 6.5 0.2 - - + -
217B MET* 3.7 26.2 - - + -
308B VAL* 4.0 26.7 - - + -
309B ALA 4.2 3.1 - - - +
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Residues in contact with THR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 3.6 28.3 - - + +
167B PRO* 3.1 35.5 + - + +
169B ASN 2.7 23.2 + - - -
170B ARG* 3.9 4.3 - - - -
172B LEU* 1.3 78.2 - - - +
174B GLU* 1.3 64.5 + - - +
176B PHE* 3.2 1.6 + - - +
177B VAL* 3.0 37.6 + - + +
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Residues in contact with GLU 174 (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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170B ARG* 3.1 22.6 + - - +
173B THR* 1.3 76.2 - - + +
175B TYR* 1.3 65.6 + - - +
177B VAL* 3.4 6.5 + - + +
178B ALA* 3.0 27.8 + - + +
203B LYS* 5.5 0.5 - - - +
205B SER* 2.8 26.4 + - - -
206B THR* 2.8 38.2 + - + +
209B ALA* 3.8 6.3 - - + -
406B EDO 3.8 21.5 - - - -
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Residues in contact with TYR 175 (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 ASN 2.9 19.0 + - - +
172B LEU* 3.6 15.9 - - + +
174B GLU* 1.3 78.2 - - - +
176B PHE* 1.3 59.6 + - - +
179B VAL* 3.1 42.9 + - + +
184B MET* 3.4 45.0 + - + +
187B LEU* 3.4 29.2 - - + +
209B ALA* 3.9 10.6 - - - +
210B CYS* 3.7 30.7 - - - +
213B GLY 3.7 7.2 - - - -
214B SER* 3.6 35.5 - - - -
217B MET* 4.8 5.4 - - + -
312B PHE* 5.6 1.1 - + - -
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Residues in contact with PHE 176 (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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166B ILE* 4.0 21.8 - - + -
172B LEU* 2.8 19.0 + - + +
173B THR 3.2 3.8 + - - +
175B TYR* 1.3 78.1 - - - +
177B VAL* 1.3 67.5 + - + +
178B ALA 3.6 0.2 + - - -
179B VAL 3.7 12.1 - - - +
181B VAL* 4.8 7.2 - - + -
184B MET* 3.6 34.3 - - + -
297B LEU* 3.7 30.7 - - + -
299B LYS 5.9 0.2 - - - -
302B THR* 4.1 11.7 - - - -
303B THR* 4.7 16.8 - - - -
308B VAL* 3.9 20.2 - - + -
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 6.3 0.9 - - + -
173B THR* 3.0 30.9 + - + +
174B GLU* 4.0 6.7 - - + +
175B TYR 3.3 0.2 - - - -
176B PHE* 1.3 84.6 - - + +
178B ALA* 1.3 60.3 + - + +
179B VAL 3.7 0.4 - - - -
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Residues in contact with ALA 178 (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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174B GLU* 3.0 19.0 + - + +
175B TYR 3.3 2.2 + - - +
177B VAL* 1.3 80.3 - - + +
179B VAL* 1.3 62.4 + - + +
206B THR* 3.5 28.0 - - + -
210B CYS* 4.6 0.4 - - - -
270B VAL* 4.0 14.4 - - + +
273B ASN* 2.9 21.0 + - - -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 3.1 25.4 + - + +
176B PHE 3.7 12.7 - - - +
177B VAL 3.7 0.4 - - - -
178B ALA* 1.3 81.6 - - - +
180B ASP* 1.3 77.1 - - - +
181B VAL* 3.6 0.3 + - - +
183B ASN* 3.5 21.3 - - + -
184B MET* 3.7 20.4 - - + +
210B CYS* 3.6 29.8 - - - -
268B LEU* 4.2 10.8 - - + -
270B VAL* 4.1 17.0 - - + -
273B ASN* 3.5 4.0 - - - +
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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