Contacts of the strand formed by residues 194 - 198 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E LEU* 3.9 29.8 - - + -
187E VAL 3.5 2.7 - - - -
188E ALA* 4.4 2.7 - - + -
193E HIS* 1.3 75.8 - - - +
195E TYR* 1.3 65.3 + - - +
196E THR* 3.8 2.0 + - - -
215E ILE* 5.0 2.5 - - + -
216E GLN* 5.8 0.9 - - - +
219E LEU* 3.8 24.2 - - + -
149H SER* 3.5 3.1 - - - -
150H PHE* 2.7 62.5 + - + +
152H LEU* 3.7 28.3 - - + -
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Residues in contact with TYR 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E PHE* 4.0 19.1 - + - -
165E LYS* 3.1 35.7 - - + +
169E MET* 4.5 8.6 - - + +
186E LEU* 3.6 2.1 - - - +
187E VAL* 2.8 46.0 + - + +
189E SER* 4.1 4.2 + - - -
193E HIS* 3.2 41.2 + + + +
194E VAL* 1.3 72.1 - - - +
196E THR* 1.3 61.2 + - - +
8F T 4.1 17.3 + - - -
9F A 4.3 18.7 + - - -
147H TYR* 3.5 27.1 - - + +
148H SER 3.6 2.9 - - - -
149H SER* 3.4 21.8 - - - -
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Residues in contact with THR 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E MET* 4.8 0.9 - - - +
185E LEU 3.6 9.7 + - - -
186E LEU* 4.5 10.2 - - - +
194E VAL* 4.6 1.1 - - - -
195E TYR* 1.3 77.6 - - - +
197E PHE* 1.3 60.6 + - - +
198E ALA 4.3 0.2 + - - -
206E ILE* 2.9 37.9 - - + +
146H LEU 3.7 1.7 - - - +
147H TYR* 3.6 6.3 - - - -
148H SER* 2.9 62.7 + - - +
150H PHE* 3.8 20.4 - - + -
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Residues in contact with PHE 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E MET* 3.8 24.5 - - - +
172E ALA* 3.5 38.6 - - + -
173E TYR* 3.7 17.3 - + + -
176E SER* 3.7 17.7 - - - -
183E VAL* 4.3 16.2 - - + -
184E LEU* 3.3 1.2 - - - +
185E LEU* 2.6 46.8 + - + +
196E THR* 1.3 72.7 - - - +
198E ALA* 1.3 64.1 + - - +
199E THR* 4.4 7.6 - - + -
141H TYR* 4.8 9.0 - - + -
144H SER* 4.0 8.5 - - - -
146H LEU* 3.5 44.9 - - + -
147H TYR* 4.3 7.0 - - + +
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Residues in contact with ALA 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E VAL 3.5 5.8 - - - +
184E LEU* 3.2 24.0 - - + -
196E THR 4.2 0.2 - - - -
197E PHE* 1.3 77.9 - - - +
199E THR* 1.3 60.9 + - - +
202E LEU* 3.5 17.5 - - + +
203E GLN* 2.5 27.4 - - - +
206E ILE* 4.1 14.8 - - + -
146H LEU* 3.3 24.8 + - - +
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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