Contacts of the helix formed by residues 193 - 201 (chain A) in PDB entry 5AM8
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 ASP 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ASN* 3.5 11.4 - - - +
186A TYR* 4.7 3.6 - - - -
187A LYS* 4.6 3.4 - - - +
191A PHE* 3.2 11.7 - - - +
192A THR* 1.3 87.9 + - - +
194A THR* 1.3 63.3 + - - +
195A GLY* 2.9 27.9 + - - -
196A ALA* 3.1 22.1 + - - +
197A TYR 3.3 7.4 + - - -
199A ARG* 4.5 7.0 + - - -
447A TRP 4.9 0.9 - - - +
450A PHE* 3.3 30.3 - - - +
451A SER* 3.5 20.6 - - - -
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Residues in contact with THR 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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182A SER* 2.7 42.3 + - - +
183A ASN* 2.9 21.3 + - - +
186A TYR* 3.8 15.8 - - + -
193A ASP* 1.3 69.8 - - - +
195A GLY* 1.3 59.4 + - - +
197A TYR* 3.1 8.6 + - - +
198A TRP* 2.9 50.4 + - + +
450A PHE* 3.5 21.3 - - + -
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Residues in contact with GLY 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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193A ASP* 2.9 9.7 + - - -
194A THR* 1.3 79.4 - - - +
196A ALA* 1.3 55.4 + - - +
198A TRP* 3.3 6.4 + - - +
199A ARG* 3.0 47.4 + - - +
447A TRP* 4.0 11.1 + - - -
450A PHE* 3.6 19.7 - - - -
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Residues in contact with ALA 196 (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 PHE* 4.0 9.6 - - + -
192A THR* 3.6 26.7 - - - +
193A ASP* 3.1 17.9 + - - +
195A GLY* 1.3 71.2 - - - +
197A TYR* 1.3 65.6 + - - +
199A ARG* 3.4 24.0 + - - +
200A SER* 3.1 22.9 + - - -
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Residues in contact with TYR 197 (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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97A THR* 3.9 23.5 - - + +
186A TYR* 3.3 49.9 + + + -
191A PHE* 3.6 39.6 - + + -
193A ASP 3.3 3.7 + - - +
194A THR 3.1 11.7 + - - +
196A ALA* 1.3 78.5 - - - +
198A TRP* 1.3 75.1 + + - +
200A SER* 2.6 27.4 + - - -
201A TRP* 3.5 40.1 + + - -
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Residues in contact with TRP 198 (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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178A PHE* 5.2 0.4 - + - -
186A TYR* 5.3 2.0 + - - -
194A THR* 2.9 31.6 + - + +
195A GLY* 3.3 8.0 + - - +
197A TYR* 1.3 91.4 - + - +
199A ARG* 1.3 61.7 + - - +
201A TRP* 3.1 55.9 + + + +
202A TYR* 4.2 5.7 - - - -
443A ASP* 4.3 9.4 - - - -
446A ARG* 3.6 42.0 - - + -
447A TRP* 4.9 9.9 - - - +
450A PHE* 3.7 31.2 - + - -
495A VAL* 3.9 28.5 - - + -
497A PRO* 3.7 31.4 - - + -
499A ILE* 5.9 1.9 - - + +
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Residues in contact with ARG 199 (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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192A THR* 5.2 1.6 + - - -
193A ASP* 4.5 7.5 + - - -
195A GLY* 3.0 32.3 + - - +
196A ALA* 3.5 27.2 - - - +
198A TRP* 1.3 74.9 - - - +
200A SER* 1.3 64.8 + - - +
202A TYR* 3.1 23.3 + - - +
203A ASN 4.3 1.2 + - - -
204A SER 5.4 1.4 + - - +
207A PHE* 4.2 20.6 - - + +
208A GLU* 3.3 38.4 + - - -
447A TRP* 3.3 61.3 + - + +
499A ILE* 6.3 0.7 - - - -
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Residues in contact with SER 200 (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 PHE* 3.9 18.9 - - - -
196A ALA 3.1 12.6 + - - -
197A TYR* 2.6 30.7 + - - -
199A ARG* 1.3 76.8 - - - +
201A TRP* 1.3 61.2 + - - +
202A TYR 3.1 0.4 - - - -
203A ASN* 3.0 24.4 + - - +
204A SER 6.1 0.2 - - - +
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Residues in contact with TRP 201 (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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197A TYR* 3.5 48.9 + + - -
198A TRP* 3.1 47.3 - + + +
199A ARG 3.1 0.2 - - - -
200A SER* 1.3 81.7 + - - +
202A TYR* 1.3 63.7 + + + +
203A ASN* 3.4 2.0 - - - +
381A ARG* 4.8 18.8 + - - +
383A ALA 4.9 1.7 - - - +
384A ASN* 4.0 15.1 - - - +
385A PRO* 4.1 29.5 - - + +
497A PRO* 3.6 30.3 - - + -
500A ARG* 3.7 11.7 - - - -
552A TRP* 4.7 2.3 - - - -
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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