Contacts of the helix formed by residues 192 - 197 (chain A) in PDB entry 4H3T
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 GLY 192 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A HIS 4.6 5.4 - - - -
166A ALA 3.2 22.2 - - - -
168A GLY 2.8 20.2 + - - -
190A ALA 3.7 0.8 + - - -
191A ILE* 1.3 76.6 - - - +
193A TYR* 1.3 67.0 + - - -
195A ALA* 3.1 4.8 + - - +
196A TRP* 3.1 18.9 + - - +
259A GLY* 6.3 0.9 - - - -
260A ARG* 3.9 8.2 - - - +
602A GOL 4.9 0.7 - - - -
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Residues in contact with TYR 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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55A ARG* 3.6 16.2 - - - -
165A HIS 4.9 1.4 + - - -
166A ALA* 3.3 5.2 + - - +
192A GLY* 1.3 71.6 - - - -
194A LEU* 1.3 63.0 + - + +
196A TRP* 3.1 18.2 + + - +
197A ILE* 3.0 55.7 + - + +
254A LEU* 4.1 12.6 - - + -
257A TRP* 5.5 6.1 - - + -
286A VAL* 3.9 28.7 - - + -
288A ARG* 5.9 0.7 - - + -
291A ALA* 3.5 33.3 - - + +
295A ASP* 2.6 35.7 + - - +
298A VAL* 4.1 3.5 - - - +
300A TRP* 4.8 0.5 - - - -
602A GOL 3.6 23.9 - - - -
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 4.1 3.4 - - + -
52A ALA* 4.0 21.3 - - - +
55A ARG* 3.6 37.7 - - + +
166A ALA* 2.9 32.6 + - + +
167A PHE* 3.6 40.1 - - + -
193A TYR* 1.3 77.4 - - + +
195A ALA* 1.3 60.5 + - - +
197A ILE* 3.3 42.1 - - + +
199A PHE* 4.5 9.9 - - + +
362A THR* 5.4 2.1 + - - -
363A SER* 5.8 1.2 - - - -
364A ALA* 5.7 0.5 + - - +
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Residues in contact with ALA 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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166A ALA 3.3 4.4 + - - -
167A PHE* 3.7 28.8 - - + +
191A ILE* 3.9 9.5 - - + +
192A GLY 3.1 16.9 + - - +
194A LEU* 1.3 78.8 - - - +
196A TRP* 1.3 58.5 + - - +
197A ILE 4.4 0.6 - - - +
316A ARG* 5.3 0.3 + - - -
364A ALA* 3.8 27.4 + - + +
366A PHE* 3.6 32.4 - - + -
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Residues in contact with TRP 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 ILE* 3.8 13.7 - - + +
192A GLY 3.1 11.6 + - - +
193A TYR* 3.1 24.4 + + - +
195A ALA* 1.3 77.0 - - - +
197A ILE* 1.3 80.6 + - + +
288A ARG* 3.2 71.6 - - + +
300A TRP* 3.7 35.2 - + - -
312A TYR 5.1 4.7 - - - -
313A VAL* 5.3 1.6 - - + -
314A PRO* 3.6 18.8 - - + +
316A ARG* 2.9 53.9 + - - +
602A GOL 3.9 10.5 - - - +
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Residues in contact with ILE 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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55A ARG* 4.5 4.9 - - - +
193A TYR* 3.0 43.0 + - + +
194A LEU* 3.3 42.8 - - + +
195A ALA 4.4 2.4 - - - +
196A TRP* 1.3 100.6 - - + +
198A GLY* 1.3 61.3 + - - +
199A PHE* 3.6 10.5 + - + +
295A ASP* 3.9 17.7 - - - +
297A HIS 4.3 9.6 - - - +
298A VAL* 3.8 28.9 - - + -
300A TRP* 4.9 0.4 - - + -
314A PRO* 4.1 4.3 - - + -
316A ARG* 4.7 2.0 - - - -
362A THR* 4.2 4.2 + - - +
363A SER* 4.5 6.4 - - - -
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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