Contacts of the strand formed by residues 194 - 198 (chain D) in PDB entry 1HBX
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 VAL 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D LEU* 4.9 8.7 - - + -
187D VAL 3.1 7.4 - - - +
188D ALA* 4.1 8.1 - - + -
192D GLY 3.4 10.3 + - - +
193D HIS* 1.3 75.0 - - - +
195D TYR* 1.3 62.6 + - - +
196D THR* 4.3 7.7 - - + +
215D ILE* 5.2 6.3 - - + -
216D GLN* 6.0 2.5 - - - +
219D LEU* 3.5 32.5 - - + -
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Residues in contact with TYR 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D PHE* 4.6 4.8 - + - -
165D LYS* 3.3 46.4 - - + -
169D MET* 4.0 14.1 - - + +
186D LEU* 4.0 0.2 - - - +
187D VAL* 2.6 44.8 + - + +
189D SER* 4.2 12.9 + - - -
193D HIS* 3.6 42.2 - + + +
194D VAL* 1.3 70.9 - - - +
196D THR* 1.3 68.4 + - - +
-9X A 3.9 9.7 + - - -
-8X A 2.8 36.1 + - - -
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Residues in contact with THR 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D MET* 3.4 15.5 - - - +
185D LEU 3.2 9.6 - - - +
186D LEU* 3.8 25.8 - - + -
194D VAL* 4.1 11.2 + - + +
195D TYR* 1.3 84.6 - - - +
197D PHE* 1.3 64.8 + - - +
206D ILE* 3.6 30.8 - - + +
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Residues in contact with PHE 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D MET* 4.1 17.3 - - + +
172D ALA* 3.3 33.7 - - + -
173D TYR* 3.5 39.0 - + + -
176D SER* 3.8 9.6 - - - -
183D VAL* 4.3 12.6 - - + -
184D LEU* 3.4 2.1 - - - +
185D LEU* 2.9 35.6 + - + -
196D THR* 1.3 79.4 - - - +
198D ALA* 1.3 73.5 + - - +
199D THR* 4.3 8.1 - - - -
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D VAL 3.3 5.4 - - - +
184D LEU* 3.8 17.7 - - + -
197D PHE* 1.3 87.4 - - - +
199D THR* 1.3 67.4 + - - +
202D LEU* 4.4 4.0 - - + -
203D GLN* 2.8 47.9 + - - +
206D ILE* 4.4 10.0 - - + +
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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