Contacts of the helix formed by residues 192 - 199 (chain A) in PDB entry 1SHZ
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ARG* 4.0 4.7 - - - +
176A TYR* 4.3 0.7 + - - -
183A LYS* 3.8 12.1 + - - +
190A ILE 3.3 4.8 + - - -
191A PRO* 1.3 71.9 - - - +
193A GLN* 1.3 63.8 + - - +
194A GLN* 3.6 6.3 + - - +
195A ASP* 2.6 41.5 + - - +
196A ILE* 2.9 22.0 - - - +
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Residues in contact with GLN 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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70A ILE* 3.9 31.3 - - + +
75A ASP* 4.8 6.5 + - - +
76A PHE* 6.3 1.6 - - + -
81A ARG* 4.2 12.0 - - - +
192A SER* 1.3 76.2 - - - +
194A GLN* 1.3 72.5 + - - +
196A ILE* 3.7 6.5 + - - +
197A LEU* 3.6 24.1 + - - +
351A THR* 3.9 25.0 + - - +
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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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176A TYR* 4.3 11.2 - - + +
192A SER* 3.3 7.4 + - - +
193A GLN* 1.3 87.2 - - - +
195A ASP* 1.3 65.7 + - - +
197A LEU* 3.2 10.3 + - - +
198A LEU* 3.0 37.2 + - + +
349A THR* 2.9 38.5 + - - +
350A ASP* 5.0 4.0 - - - +
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Residues in contact with ASP 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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88A ILE* 4.3 2.9 - - + +
176A TYR* 2.6 41.3 + - - -
177A PHE* 3.7 14.2 - - + -
183A LYS* 2.9 22.7 + - - -
184A LEU* 4.6 1.0 - - - +
189A TYR* 2.8 27.6 + - - +
191A PRO* 4.0 4.3 - - + -
192A SER* 2.6 35.9 + - - +
194A GLN* 1.3 76.1 - - - +
196A ILE* 1.3 62.0 + - - +
198A LEU 3.2 2.1 + - - -
199A ALA* 3.0 22.9 + - - +
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Residues in contact with ILE 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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66A LYS* 3.1 38.6 + - + -
70A ILE* 5.5 0.2 - - + -
76A PHE* 4.1 20.4 - - + -
81A ARG* 3.5 28.5 - - + -
84A PHE* 3.7 37.9 - - + -
191A PRO* 3.3 23.3 - - + -
192A SER 2.9 25.1 + - - +
193A GLN* 3.8 9.4 - - - +
195A ASP* 1.3 78.4 - - - +
197A LEU* 1.3 65.1 + - + +
199A ALA* 3.1 16.0 + - - +
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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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63A THR* 4.0 20.3 + - + +
66A LYS* 3.7 34.6 + - + +
67A GLN* 3.2 39.5 - - + +
70A ILE* 4.0 13.2 - - + -
193A GLN* 3.6 17.9 + - - +
194A GLN* 3.2 19.6 + - - +
196A ILE* 1.3 81.1 - - + +
198A LEU* 1.3 53.2 + - - +
199A ALA 3.5 3.3 + - - +
349A THR* 3.4 22.2 - - + +
351A THR* 4.2 7.6 - - - +
475A GDP 2.7 26.0 + - - -
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Residues in contact with LEU 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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91A ASN* 4.6 0.3 + - - -
173A SER* 2.8 42.4 + - - +
176A TYR* 3.4 53.2 - - + -
177A PHE* 4.0 5.7 - - + -
194A GLN* 3.0 34.2 + - + +
195A ASP 3.2 4.0 + - - +
197A LEU* 1.3 76.1 - - - +
199A ALA* 1.3 66.4 + - - +
200A ARG 3.6 0.9 + - - -
349A THR* 4.3 20.4 - - + -
475A GDP 3.2 26.4 + - - +
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Residues in contact with ALA 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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66A LYS* 3.7 12.3 + - - +
84A PHE* 4.2 16.4 - - + -
87A THR* 4.6 6.7 - - - +
88A ILE* 4.0 19.3 - - + -
91A ASN* 3.8 7.4 - - - +
177A PHE* 4.3 4.0 - - - -
195A ASP 3.0 11.8 + - - +
196A ILE 3.1 15.8 + - - +
197A LEU 3.7 7.6 - - - +
198A LEU* 1.3 81.4 - - - +
200A ARG* 1.3 59.2 + - - +
201A ARG 4.4 0.2 + - - -
475A GDP 3.8 6.8 + - - -
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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