Contacts of the strand formed by residues 182 - 188 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A GLY 5.2 3.8 + - - -
181A THR* 1.3 76.6 - - - +
183A VAL* 1.3 63.7 + - - +
199A THR* 2.6 31.6 + - - +
200A ARG* 3.9 4.9 + - - +
201A LYS* 3.0 63.6 + - + +
202A LEU* 3.5 16.2 - - + +
187B VAL* 4.0 0.5 - - - -
188B ALA* 3.4 32.9 + - + +
219B LEU* 3.8 17.0 - - + -
223B ASP* 5.5 0.6 + - - -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA* 4.1 28.3 - - + +
175A LEU* 4.5 8.3 - - + -
176A SER* 3.5 32.1 - - - +
181A THR* 4.0 7.2 - - - +
182A GLN* 1.3 80.5 - - - +
184A LEU* 1.3 70.0 + - - +
197A PHE* 4.0 3.2 - - + -
198A ALA* 3.3 4.2 - - - -
199A THR* 2.9 39.2 + - + +
202A LEU* 3.6 4.1 - - - +
168B ILE* 5.0 1.3 - - + -
185B LEU* 4.2 11.2 - - + -
186B LEU 3.4 11.2 - - - +
187B VAL* 4.4 9.2 - - + -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL* 1.3 77.6 - - - +
185A LEU* 1.3 73.1 + - - +
186A LEU* 5.2 2.9 - - + -
197A PHE 3.4 16.8 - - - +
198A ALA* 4.0 9.9 - - + -
202A LEU* 3.9 15.7 - - + +
205A MET* 3.9 38.6 - - + -
206A ILE* 3.9 25.4 - - + -
184B LEU* 4.5 21.5 - - + +
185B LEU* 3.3 6.1 - - - +
186B LEU* 2.9 43.7 + - + +
205B MET* 5.1 3.1 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 3.7 43.1 - - + +
169A MET* 4.0 17.9 - - - -
172A ALA* 3.9 29.4 - - + -
184A LEU* 1.3 79.7 - - - +
186A LEU* 1.3 89.2 + - - +
187A VAL* 3.9 12.6 - - + -
196A THR* 3.3 3.8 - - - -
197A PHE* 2.9 32.5 + - + +
168B ILE* 5.2 2.7 - - + -
183B VAL* 4.2 11.7 - - + -
184B LEU 3.3 12.8 - - - +
185B LEU* 4.7 8.3 - - + -
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 5.2 4.3 - - + -
185A LEU* 1.3 83.7 - - - +
187A VAL* 1.3 68.6 + - - +
188A ALA 4.6 1.8 - - - +
194A VAL* 3.6 16.8 - - + -
195A TYR 3.5 6.1 - - - -
196A THR* 3.6 20.9 - - + +
206A ILE* 4.5 6.1 - - + -
215A ILE* 3.6 36.3 - - + -
219A LEU* 4.8 7.9 - - + -
182B GLN 5.3 0.2 - - - +
183B VAL* 3.2 4.9 - - - -
184B LEU* 2.9 38.4 + - + +
202B LEU* 3.4 29.6 - - + -
205B MET* 5.0 5.6 - - + -
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 3.3 37.9 - - + -
165A LYS* 4.7 4.7 - - + -
168A ILE* 4.8 1.8 - - + -
169A MET* 4.1 17.0 - - + -
185A LEU* 3.9 17.3 - - + -
186A LEU* 1.3 82.5 - - - +
188A ALA* 1.3 64.3 + - - +
189A SER 4.1 0.2 - - - -
194A VAL* 3.4 3.5 - - - +
195A TYR* 2.8 39.3 + - + +
175B LEU* 4.0 26.0 - - + -
181B THR* 4.4 0.2 - - - +
182B GLN 3.7 8.7 - - - +
183B VAL* 4.3 4.5 - - + +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 4.4 2.7 - - - -
186A LEU* 4.6 2.9 - - + +
187A VAL* 1.3 75.3 - - - +
189A SER* 1.3 65.4 + - - +
190A GLU* 3.7 0.3 + - - -
192A GLY 5.1 1.6 - - - +
193A HIS 3.4 10.8 - - - +
194A VAL* 3.9 14.4 - - + +
219A LEU* 4.0 24.5 - - + -
181B THR* 3.5 20.4 - - - -
182B GLN* 3.2 19.0 + - + +
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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