Contacts of the helix formed by residues 194 - 201 (chain A) in PDB entry 5UAK
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ASN 4.9 0.2 + - - -
190A LYS 4.0 15.3 + - - -
191A PHE 4.8 0.9 - - - -
192A ASP 3.5 0.8 - - - -
193A GLU* 1.3 74.8 - - - +
195A LEU* 1.3 63.0 + - - +
196A ALA 3.2 2.2 - - - -
197A LEU* 3.2 19.7 + - - +
198A ALA* 3.2 18.2 + - - +
360A THR* 3.3 22.6 + - - -
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Residues in contact with LEU 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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74A ARG* 5.2 11.7 - - - +
81A PHE* 4.0 32.3 - - + -
145A LEU* 3.5 24.5 - - - +
148A ILE* 3.7 27.8 - - + -
149A GLY* 3.7 9.0 - - - +
152A MET* 4.2 17.9 - - + -
191A PHE* 4.1 21.5 + - + +
192A ASP 3.9 13.8 + - - +
193A GLU 3.2 1.4 + - - -
194A GLY* 1.3 76.6 - - - +
196A ALA* 1.3 61.7 + - - +
198A ALA* 3.7 18.7 + - + +
199A HIS 4.0 3.5 + - - -
364A SER* 5.9 0.9 - - - +
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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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88A LEU* 4.6 0.2 - - - +
142A ILE* 3.7 32.1 - - + -
145A LEU* 3.8 25.2 + - + +
146A HIS* 4.2 9.2 - - + +
193A GLU 3.4 13.8 + - - +
194A GLY 3.2 0.4 - - - -
195A LEU* 1.3 79.5 - - - +
197A LEU* 1.3 64.0 + - + +
198A ALA 3.5 0.5 + - - -
199A HIS* 3.6 15.1 + - - +
200A PHE* 3.7 14.8 - - - -
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Residues in contact with LEU 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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142A ILE* 6.2 1.8 - - + -
193A GLU 5.3 1.3 - - - +
194A GLY* 3.2 19.5 + - - +
196A ALA* 1.3 78.1 - - + +
198A ALA* 1.3 61.2 + - - +
199A HIS 3.2 0.9 - - - -
200A PHE* 3.4 35.3 + - + -
353A GLN* 6.1 0.7 - - + -
356A TRP* 4.1 42.6 - - + -
357A ALA* 3.6 14.9 + - - +
360A THR* 3.9 11.4 - - + -
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Residues in contact with ALA 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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74A ARG* 5.8 3.6 - - - +
81A PHE* 5.4 4.7 - - + -
194A GLY 3.2 11.8 + - - +
195A LEU* 3.8 18.4 - - + +
196A ALA 3.3 0.6 - - - -
197A LEU* 1.3 76.4 - - - +
199A HIS* 1.3 60.9 + - - +
200A PHE 3.3 1.1 + - - -
201A VAL* 3.5 9.1 - - - +
357A ALA* 4.8 0.4 - - - +
360A THR* 3.4 18.6 - - + +
361A TRP* 2.9 42.1 + - + +
364A SER* 6.6 0.4 - - - -
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Residues in contact with HIS 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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81A PHE* 3.7 38.2 + + + -
82A MET* 4.8 9.4 - - + -
85A GLY* 3.2 43.7 - - - -
88A LEU* 4.0 17.8 - - + +
145A LEU* 4.8 4.3 - - + -
195A LEU 4.0 3.0 + - - +
196A ALA 3.6 12.9 + - - +
197A LEU 3.2 0.8 - - - -
198A ALA* 1.3 80.0 - - - +
200A PHE* 1.3 56.4 + - - +
201A VAL 3.2 6.3 + - - -
202A TRP* 3.4 51.4 + + - +
203A ILE* 3.5 12.6 - - + +
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Residues in contact with PHE 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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88A LEU* 4.3 26.0 - - + -
92A GLU* 3.3 26.0 - - + -
142A ILE* 5.1 8.7 - - + -
196A ALA 3.7 16.8 - - - -
197A LEU* 3.4 40.2 - - + +
198A ALA 3.3 2.6 - - - -
199A HIS* 1.3 73.6 - - - +
201A VAL* 1.3 62.5 + - - +
202A TRP 3.3 2.5 - - - -
203A ILE* 3.7 20.4 - - + -
204A ALA* 3.3 25.5 + - + +
353A GLN* 3.2 40.6 - - + +
354A PHE* 4.1 3.2 - - - -
356A TRP* 6.5 0.2 - - + -
357A ALA* 4.0 9.9 - - + -
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Residues in contact with VAL 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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198A ALA 3.5 16.6 - - - +
199A HIS 3.2 2.4 - - - +
200A PHE* 1.3 74.9 - - - +
202A TRP* 1.3 60.3 + - + +
205A PRO* 3.1 23.4 - - - +
354A PHE* 3.7 15.7 - - + -
357A ALA* 3.7 21.7 - - + +
358A VAL* 5.4 2.5 - - + -
361A TRP* 3.7 29.2 - - + +
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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