Contacts of the strand formed by residues 193 - 199 (chain B) in PDB entry 1HDZ
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 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B VAL* 3.2 21.5 - - - +
190B THR* 2.5 31.0 + - - -
191B PRO 3.2 1.8 + - - -
192B GLY* 1.3 77.5 - - - +
194B THR* 1.3 60.7 + - - +
195B CYS* 4.1 0.6 - - - -
216B ALA* 3.4 3.0 - - - -
217B ALA 2.7 30.3 + - - +
218B ARG 3.2 3.1 + - - -
263B ASP* 3.5 15.7 - - - -
264B PHE* 3.3 21.9 - - - -
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ARG* 5.8 0.9 - - - +
192B GLY 4.7 1.9 + - - -
193B SER* 1.3 75.3 + - - +
195B CYS* 1.3 62.2 + - - +
217B ALA* 5.0 1.7 - - - +
218B ARG* 3.3 31.9 + - + +
220B ILE* 4.7 1.1 - - + -
258B THR* 3.6 22.7 - - + +
261B GLY 4.9 1.1 - - - +
262B VAL* 3.5 27.4 - - + -
263B ASP* 2.8 42.1 + - - +
264B PHE 3.2 2.1 + - - -
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Residues in contact with CYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 3.6 25.4 - - - -
193B SER* 4.1 2.5 - - - -
194B THR* 1.3 78.0 - - - +
196B ALA* 1.3 60.8 + - - +
211B CYS* 3.9 24.9 - - + -
216B ALA* 3.4 29.6 - - - -
218B ARG 2.8 8.1 + - - +
219B ILE* 3.3 6.9 - - + -
220B ILE* 3.0 25.9 + - - +
262B VAL* 3.9 4.3 - - - +
264B PHE* 3.1 18.8 - - + +
266B PHE* 4.2 3.1 - - + -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B CYS* 1.3 73.9 - - - +
197B VAL* 1.4 61.4 + - - +
198B PHE* 4.3 20.0 - - + -
220B ILE* 3.3 10.5 - - + +
222B VAL* 5.1 1.3 - - + -
254B LEU* 4.5 12.8 - - + -
262B VAL* 3.9 24.4 - - + +
264B PHE 3.0 4.9 + - - -
265B SER* 3.5 2.9 - - - -
266B PHE* 3.1 27.8 + - - -
281B CYS* 4.4 5.4 - - - -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ALA* 1.4 76.1 - - - +
198B PHE* 1.3 63.6 + - - +
199B GLY 3.6 13.8 + - - +
200B LEU* 4.6 4.7 - - + +
204B GLY 3.8 19.5 - - - +
207B ALA* 4.0 3.6 - - + -
208B VAL* 4.1 30.1 - - + +
211B CYS* 4.3 6.1 - - - -
219B ILE* 4.3 14.1 - - + -
220B ILE 2.9 9.9 + - - +
221B ALA* 3.8 0.6 - - - -
222B VAL* 2.8 29.1 + - - +
266B PHE* 3.8 16.8 - - + -
268B VAL* 3.9 17.0 - - + -
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Residues in contact with PHE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ALA* 4.3 7.6 - - + -
197B VAL* 1.3 77.5 - - - +
199B GLY* 1.3 58.2 + - - +
222B VAL* 3.8 26.7 - - + -
243B PRO* 5.8 0.7 - - + -
250B ILE* 4.1 10.8 - - + -
254B LEU* 3.7 26.7 - - + -
265B SER* 5.0 0.7 - - - -
266B PHE 2.9 21.7 + - - +
267B GLU* 4.0 8.1 - - + -
268B VAL 2.8 22.6 + - - -
269B ILE* 3.1 17.9 - - + +
274B THR* 3.8 22.9 - - + -
277B ALA* 4.0 32.5 - - + -
278B SER* 4.1 14.8 - - - -
281B CYS* 4.0 18.8 - - - -
377B NAD 5.2 0.9 - + - -
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Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B VAL* 3.6 4.3 + - - +
198B PHE* 1.3 76.0 - - - +
200B LEU* 1.3 68.1 + - - +
201B GLY 3.7 2.7 - - - -
204B GLY* 3.2 20.5 - - - -
222B VAL 2.8 16.2 + - - -
223B ASP* 3.9 1.6 - - - -
268B VAL* 3.9 5.3 - - - +
269B ILE* 3.5 18.7 - - - +
377B NAD 3.8 10.1 - - - -
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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