Contacts of the strand formed by residues 182 - 188 (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 GLN 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D GLY 5.1 3.0 + - - -
181D THR* 1.3 77.4 + - - +
183D VAL* 1.3 71.3 + - - +
199D THR* 3.3 22.3 - - - +
200D ARG* 5.6 3.8 - - - +
201D LYS* 2.9 61.2 + - + +
202D LEU* 3.9 16.9 + - + -
187E VAL* 3.8 0.3 - - - -
188E ALA* 3.4 32.5 + - + +
219E LEU* 4.4 13.2 - - + -
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Residues in contact with VAL 183 (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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172D ALA* 3.6 31.2 - - + +
175D LEU* 4.4 13.2 - - + -
176D SER* 3.7 25.8 - - - +
181D THR* 3.9 9.9 - - - +
182D GLN* 1.3 83.1 - - - +
184D LEU* 1.3 70.6 + - - +
197D PHE* 3.5 7.6 - - + +
198D ALA* 3.3 4.9 - - - -
199D THR* 2.6 38.5 + - - +
202D LEU* 3.8 5.0 - - - +
168E ILE* 5.1 0.7 - - + -
185E LEU* 4.3 9.4 - - + -
186E LEU 3.4 9.4 - - - +
187E VAL* 4.5 5.8 - - + -
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Residues in contact with LEU 184 (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* 1.3 79.7 - - - +
185D LEU* 1.3 79.6 + - - +
186D LEU* 5.0 3.6 - - + -
197D PHE 3.4 9.6 - - - +
198D ALA* 3.8 15.9 - - + -
202D LEU* 3.9 17.0 - - + +
205D MET* 3.3 36.1 - - + -
206D ILE* 4.1 18.8 - - + -
184E LEU* 3.4 22.6 - - + +
185E LEU* 3.2 6.2 - - - +
186E LEU* 2.8 49.6 + - + -
205E MET* 5.0 1.1 - - + -
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Residues in contact with LEU 185 (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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168D ILE* 3.6 61.2 - - + +
169D MET* 3.8 23.3 - - + -
172D ALA* 4.4 14.1 - - + -
184D LEU* 1.3 78.5 - - - +
186D LEU* 1.3 77.7 + - - +
187D VAL* 4.1 7.4 - - + -
196D THR* 3.2 5.0 - - - -
197D PHE* 2.9 37.9 + - + +
168E ILE* 4.8 2.0 - - + -
183E VAL* 4.2 7.2 - - + -
184E LEU 3.3 7.9 - - - +
185E LEU* 4.3 14.6 - - + -
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Residues in contact with LEU 186 (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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184D LEU* 5.0 3.6 - - + -
185D LEU* 1.3 77.9 - - - +
187D VAL* 1.3 80.7 + - - +
188D ALA 4.6 1.6 - - - +
194D VAL* 4.9 5.6 - - + -
195D TYR 3.3 3.4 - - - +
196D THR* 3.8 22.2 - - + -
206D ILE* 4.4 13.5 - - + -
215D ILE* 3.9 30.3 - - + -
219D LEU* 4.7 16.2 - - + -
183E VAL* 3.4 3.8 - - - +
184E LEU* 2.8 44.1 + - + +
202E LEU* 4.0 20.4 - - + -
205E MET* 4.8 8.5 - - + -
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Residues in contact with VAL 187 (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* 3.6 33.7 - - + -
165D LYS* 4.4 9.4 - - + -
168D ILE* 5.1 3.4 - - + -
169D MET* 3.8 18.6 - - + -
185D LEU* 4.1 13.0 - - + -
186D LEU* 1.3 85.8 - - - +
188D ALA* 1.3 62.6 + - - +
193D HIS 3.8 0.7 - - - +
194D VAL* 3.1 2.8 - - - -
195D TYR* 2.6 50.1 + - + +
175E LEU* 4.3 17.5 - - + -
181E THR* 4.9 0.2 - - - +
182E GLN 3.5 7.2 - - - +
183E VAL* 4.5 8.3 - - + -
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Residues in contact with ALA 188 (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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186D LEU* 4.6 1.1 - - + +
187D VAL* 1.3 77.0 - - - +
189D SER* 1.3 64.0 + - - +
190D GLU 3.9 0.2 + - - -
192D GLY 5.1 1.3 - - - +
193D HIS 3.6 3.6 - - - -
194D VAL* 4.1 14.8 - - + +
219D LEU* 4.0 17.5 - - + -
181E THR* 3.2 24.9 - - - -
182E GLN* 2.9 32.8 + - + -
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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