Contacts of the helix formed by residues 189 - 195 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A MET 3.4 0.4 + - - -
188A GLY* 1.3 71.4 - - - -
190A SER* 1.3 62.2 + - - +
191A TYR 3.2 0.4 - - - -
194A GLN* 3.7 4.7 - - - +
195A TYR* 2.6 40.3 + - - -
203A PHE* 3.7 28.3 - - - -
312A THR* 5.7 0.7 - - - +
314A LEU* 4.0 0.3 - - - +
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Residues in contact with SER 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A MET* 3.1 15.9 + - - -
189A SER* 1.3 78.3 + - - +
191A TYR* 1.3 60.5 + - - +
203A PHE* 5.6 0.2 - - - -
296A TYR* 3.7 26.7 + - - -
312A THR* 5.5 1.4 - - - +
313A MET* 2.9 34.4 + - - +
314A LEU* 3.6 3.7 - - - +
315A VAL* 2.8 32.9 + - - +
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Residues in contact with TYR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL 4.7 0.7 + - - -
180A SER 6.0 0.2 - - - -
183A PRO* 3.4 24.6 - - + +
184A GLN* 3.7 29.6 - - + -
187A MET* 3.7 30.6 + - + +
188A GLY 3.2 13.8 + - - +
189A SER 4.4 0.4 - - - -
190A SER* 1.3 76.8 - - - +
192A GLY* 1.3 62.5 + - - +
193A PHE* 3.4 26.3 + + + -
194A GLN* 2.7 35.9 + - - +
195A TYR* 3.6 3.1 - - - -
288A SER* 5.0 0.9 + - - -
289A CYS* 5.6 2.9 - - - -
292A THR* 3.8 18.8 - - + -
315A VAL 4.1 0.7 - - - -
552A THR 3.5 21.5 - - - -
553A ALA* 3.3 7.6 - - + +
554A GLY* 3.1 26.7 + - - -
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A SER 3.3 1.4 + - - -
191A TYR* 1.3 70.0 - - - +
193A PHE* 1.3 57.8 + - - +
194A GLN 3.1 9.8 + - - -
195A TYR* 3.2 21.0 + - - +
200A ARG* 4.6 3.6 + - - +
314A LEU* 3.8 15.5 - - - -
315A VAL 2.9 17.4 + - - -
316A ASN* 3.4 26.7 + - - -
448A TYR* 3.9 6.8 + - - -
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Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A TYR* 3.4 32.9 - + + +
192A GLY* 1.3 75.3 - - - +
194A GLN* 1.3 55.2 + - - +
195A TYR 3.2 2.5 - - - -
288A SER* 3.5 21.3 - - - -
292A THR* 3.8 2.7 - - - -
316A ASN* 3.7 34.1 - - + -
317A GLY* 3.6 20.6 - - - -
448A TYR* 3.4 30.4 - + - -
551A PHE 3.1 21.0 - - - -
552A THR 3.2 8.0 + - - -
553A ALA 3.5 2.0 + - - +
554A GLY* 3.5 26.2 - - - +
556A SER* 5.6 1.6 - - - -
1001A 5EE 3.9 34.8 - - - -
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Residues in contact with GLN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A GLN* 3.0 38.8 - - + +
188A GLY 2.8 26.6 + - - +
189A SER* 3.7 9.7 - - - +
191A TYR* 2.7 28.2 + - + +
192A GLY 3.1 1.4 + - - -
193A PHE* 1.3 76.4 - - - +
195A TYR* 1.3 82.2 + - + +
199A GLN* 3.6 8.5 - - - +
551A PHE* 3.2 20.6 - - - +
552A THR* 3.9 8.3 + - - +
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Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A SER* 2.6 48.2 + - - -
191A TYR 3.6 11.0 - - - -
192A GLY* 3.2 21.0 + - - +
194A GLN* 1.3 100.6 + - + +
196A SER* 1.3 66.4 + - - +
199A GLN* 3.4 25.1 - - + -
200A ARG* 3.7 22.9 - - + +
203A PHE* 3.7 20.3 - + + -
314A LEU* 3.8 13.7 - - + -
448A TYR* 2.6 36.0 + - - -
551A PHE* 3.6 4.4 - - - +
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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