Contacts of the helix formed by residues 189 - 195 (chain B) in PDB entry 2AX1
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 SER 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B MET 3.4 0.8 + - - -
188B GLY* 1.3 71.8 - - - -
190B SER* 1.3 62.4 + - - +
191B TYR 3.2 0.7 - - - -
194B GLN* 3.6 4.9 - - - +
195B TYR* 2.6 39.2 + - - -
203B PHE* 3.5 29.3 - - - -
312B THR* 5.5 1.9 - - - +
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Residues in contact with SER 190 (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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187B MET* 3.4 14.8 + - - -
188B GLY 3.1 1.2 - - - -
189B SER* 1.3 79.8 + - - +
191B TYR* 1.3 59.3 + - - +
192B GLY 3.3 0.2 + - - -
296B TYR* 3.7 27.7 + - - -
312B THR* 5.7 0.7 - - - +
313B MET* 3.0 33.9 + - - +
314B LEU* 3.4 2.9 - - - +
315B VAL* 2.7 34.0 + - - +
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Residues in contact with TYR 191 (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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179B VAL 4.5 1.0 + - - -
180B SER 5.8 0.9 - - - -
183B PRO* 3.4 38.9 - - + +
184B GLN* 3.9 21.5 - - + -
187B MET* 3.6 23.9 + - + +
188B GLY 3.3 13.0 + - - +
189B SER 3.2 1.0 - - - -
190B SER* 1.3 74.5 - - - +
192B GLY* 1.3 64.6 + - - +
193B PHE* 3.3 26.1 + + + -
194B GLN* 2.8 33.7 + - - +
195B TYR* 3.7 2.2 - - - -
288B SER* 5.0 1.0 + - - -
289B CYS* 5.5 3.5 - - - +
292B THR* 3.7 19.5 - - + -
315B VAL 4.1 1.1 - - - -
552B THR 3.5 22.4 - - - -
553B ALA* 3.3 8.1 - - + +
554B GLY* 3.0 26.5 + - - -
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Residues in contact with GLY 192 (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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190B SER 3.3 1.0 + - - -
191B TYR* 1.3 73.6 - - - +
193B PHE* 1.3 56.3 + - - +
194B GLN 3.2 4.9 + - - -
195B TYR* 3.3 19.6 + - - +
200B ARG* 4.7 3.6 + - - +
314B LEU* 3.7 17.3 - - - -
315B VAL 2.9 22.2 + - - -
316B ASN* 3.5 22.5 + - - -
448B TYR* 4.0 5.9 + - - -
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Residues in contact with PHE 193 (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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191B TYR* 3.3 30.5 - + + +
192B GLY* 1.3 74.4 - - - +
194B GLN* 1.3 54.5 + - - +
195B TYR 3.2 5.6 - - - -
288B SER* 3.6 20.2 - - - -
292B THR* 3.9 2.5 - - - -
316B ASN* 3.6 35.2 - - + -
317B GLY* 3.6 20.9 - - - -
448B TYR* 3.4 33.8 - + + -
551B PHE 3.1 21.8 - - - -
552B THR 3.2 6.5 + - - -
553B ALA 3.6 2.5 - - - -
554B GLY* 3.4 25.8 - - - +
556B SER* 5.5 1.8 - - - -
1002B 5EE 3.8 33.9 - - - -
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Residues in contact with GLN 194 (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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184B GLN* 3.5 33.4 - - + +
188B GLY 2.7 28.5 + - - +
189B SER* 3.6 12.6 - - - +
191B TYR* 2.8 26.3 + - + +
193B PHE* 1.3 75.5 - - - +
195B TYR* 1.3 82.5 + - + +
199B GLN* 3.6 9.4 - - - +
551B PHE* 3.1 19.9 - - - +
552B THR* 3.8 10.0 + - - +
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Residues in contact with TYR 195 (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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189B SER* 2.6 47.2 + - - -
191B TYR 3.7 10.5 - - - -
192B GLY* 3.3 21.3 + - - +
193B PHE 3.2 0.8 - - - -
194B GLN* 1.3 99.1 + - + +
196B SER* 1.3 65.7 + - - +
199B GLN* 3.5 22.0 - - + -
200B ARG* 3.7 21.9 - - + +
203B PHE* 3.5 24.9 - + + -
314B LEU* 3.7 15.7 - - + -
448B TYR* 2.6 34.7 + - - -
551B PHE* 3.8 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