Contacts of the strand formed by residues 182 - 188 (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 GLN 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D LEU 4.0 0.2 - - - +
187D VAL* 3.5 1.7 - - - +
188D ALA* 2.9 36.9 + - + +
219D LEU* 3.7 28.3 - - + -
180E GLY 4.5 4.6 + - - -
181E THR* 1.3 83.3 + - - +
183E VAL* 1.3 65.0 + - - +
199E THR* 3.1 20.5 + - - +
200E ARG* 4.0 2.8 + - - +
201E LYS* 2.9 55.3 + - + +
202E LEU* 4.0 6.4 - - + +
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Residues in contact with VAL 183 (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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168D ILE* 5.0 2.2 - - + -
185D LEU* 4.2 16.2 - - + -
186D LEU 3.4 9.0 - - - +
187D VAL* 4.5 4.9 - - + -
172E ALA* 4.1 20.9 - - + +
175E LEU* 3.7 26.7 - - + -
176E SER* 3.8 17.7 - - - -
181E THR* 3.7 9.0 - - - +
182E GLN* 1.3 80.2 - - - +
184E LEU* 1.3 68.0 + - - +
197E PHE* 4.0 8.5 - - + +
198E ALA* 3.5 2.6 - - - -
199E THR* 3.0 41.4 + - + +
202E LEU* 3.9 2.6 - - - +
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Residues in contact with LEU 184 (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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184D LEU* 3.4 18.3 - - + +
185D LEU* 3.3 4.0 - - - -
186D LEU* 2.8 45.4 + - + +
183E VAL* 1.3 77.0 - - - +
185E LEU* 1.3 66.8 + - - +
186E LEU* 5.4 3.4 - - + -
197E PHE 3.3 7.4 - - - +
198E ALA* 3.2 28.3 - - + -
202E LEU* 3.5 19.5 - - + +
205E MET* 3.3 43.7 - - + -
206E ILE* 4.1 18.2 - - + -
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Residues in contact with LEU 185 (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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168D ILE* 5.1 0.4 - - + -
183D VAL* 4.3 3.1 - - + -
184D LEU 3.2 11.0 - - - +
185D LEU* 4.3 16.2 - - + -
168E ILE* 3.5 55.9 - - + +
169E MET* 3.2 28.0 - - + -
172E ALA* 3.7 16.8 - - + -
183E VAL* 4.2 0.8 - - + +
184E LEU* 1.3 76.9 - - - +
186E LEU* 1.3 68.2 + - - +
187E VAL* 4.2 10.8 - - + -
196E THR* 3.6 4.2 + - - -
197E PHE* 2.6 44.4 + - + +
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Residues in contact with LEU 186 (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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183D VAL* 3.4 4.2 - - - +
184D LEU* 2.8 49.8 + - + +
202D LEU* 4.4 24.0 - - + -
205D MET* 5.7 0.9 - - - -
184E LEU* 5.4 5.4 - - + -
185E LEU* 1.3 76.4 - - - +
187E VAL* 1.3 81.8 + - - +
188E ALA* 4.2 5.8 - - + +
194E VAL* 3.9 16.4 - - + -
195E TYR 3.6 7.2 - - - +
196E THR* 4.4 6.3 - - - +
206E ILE* 4.9 5.4 - - + -
215E ILE* 3.8 39.9 - - + -
219E LEU* 5.0 3.6 - - + -
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Residues in contact with VAL 187 (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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175D LEU* 3.7 24.5 - - + -
181D THR* 4.6 0.7 - - - +
182D GLN 3.8 7.6 - - - +
183D VAL* 4.5 5.4 - - + -
161E PHE* 3.2 37.7 - - + -
165E LYS* 4.8 4.0 - - + -
168E ILE* 4.9 2.5 - - + -
169E MET* 4.0 19.1 - - + -
185E LEU* 4.2 13.2 - - + -
186E LEU* 1.3 84.2 - - - +
188E ALA* 1.3 62.0 + - - +
193E HIS 3.9 0.2 - - - +
194E VAL* 3.5 2.1 - - - -
195E TYR* 2.8 50.0 + - + +
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Residues in contact with ALA 188 (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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181D THR* 3.2 25.3 - - - -
182D GLN* 3.4 21.9 + - + +
161E PHE* 4.2 3.8 - - - -
186E LEU* 4.2 2.7 - - + +
187E VAL* 1.3 77.7 - - - +
189E SER* 1.3 64.5 + - - +
192E GLY 6.1 0.4 - - - -
193E HIS 3.3 7.6 - - - +
194E VAL* 4.4 4.7 - - + +
219E LEU* 3.8 28.9 - - + -
152H LEU* 5.5 4.0 - - + -
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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