Contacts of the helix formed by residues 190 - 193 (chain D) in PDB entry 2AXT
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 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D PHE 2.8 6.1 + - - -
186D GLN* 3.2 34.5 + - - +
188D PHE 3.6 0.6 - - - -
189D HIS* 1.3 81.4 - - - +
191D TRP* 1.3 64.5 + - - +
192D THR* 3.5 4.5 + - - -
193D LEU* 3.1 36.1 + - - +
194D ASN* 4.1 0.5 + - - +
295D SER 3.8 4.5 - - - +
296D TYR* 2.7 49.5 + - + -
315D TYR* 5.1 1.0 - - - -
318D ASN* 5.4 4.3 - - - +
319D LEU* 4.4 7.7 - - - +
322D ASN* 3.3 12.7 + - - +
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Residues in contact with TRP 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D PHE* 3.7 18.7 + + + +
186D GLN* 4.3 1.0 - - - +
189D HIS* 3.1 3.7 - - - -
190D ASN* 1.3 70.4 - - - +
192D THR* 1.3 51.8 + - - +
193D LEU 2.6 4.8 + - - -
194D ASN* 2.5 80.9 + - + +
197D HIS* 3.0 42.7 - + + +
282D SER* 3.9 4.7 - - - -
285D GLY* 3.6 28.9 - - - -
286D VAL* 3.6 10.1 - - + -
289D LEU* 3.5 20.9 - - + -
354D CLA 3.3 77.9 + + + +
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Residues in contact with THR 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PHE* 2.9 61.6 - - + +
184A ILE* 5.0 1.9 - - + +
559A CLA 5.0 1.2 - - + +
186D GLN* 2.6 22.8 + - - +
190D ASN* 4.3 3.5 + - - -
191D TRP* 1.3 74.6 - - - +
193D LEU* 1.3 56.2 + - - +
194D ASN 3.3 2.2 - - - -
197D HIS* 4.4 12.8 - - + -
198D MET* 3.4 10.0 - - - +
354D CLA 3.3 48.9 - - + -
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 3.4 31.6 - - + -
177A SER* 4.2 15.0 - - - +
180A PHE* 4.5 7.2 - - + -
190D ASN* 3.1 25.0 + - - +
191D TRP 2.6 6.3 + - - -
192D THR* 1.3 76.2 + - - +
194D ASN* 1.3 54.8 + - - -
198D MET* 3.6 2.5 - - - -
295D SER* 2.9 20.6 + - - +
296D TYR 3.6 25.8 - - - +
297D ASP* 4.8 1.6 - - - +
298D PHE* 4.0 23.1 - - + -
315D TYR* 4.1 12.1 - - + -
34L TYR* 2.6 26.4 + - - +
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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