Contacts of the strand formed by residues 176 - 182 (chain B) in PDB entry 1H8O
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 LEU 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B GLN* 5.3 0.9 - - - +
47B PRO* 4.5 2.2 - - + -
90B PHE* 3.2 45.8 - - + -
101B PHE* 3.9 45.5 + - + +
102B GLY 4.8 1.4 + - - -
168B VAL* 3.7 16.4 - - + -
169B LYS 3.5 0.9 - - - -
170B GLN* 3.4 45.8 - - + +
175B GLY* 1.3 74.4 - - - -
177B GLU* 1.3 69.1 + - - +
226B PHE* 4.7 6.3 - - + -
233B TRP* 4.1 13.5 - - + -
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 4.9 0.9 - - - -
168B VAL* 3.2 6.1 - - - +
169B LYS* 2.7 61.1 + - + +
174B GLN* 5.4 5.5 - - + +
175B GLY 5.0 3.6 - - - +
176B LEU* 1.3 82.1 - - - +
178B TRP* 1.3 62.9 + - - +
179B ILE 3.5 0.7 + - - -
192B ASN* 5.4 3.6 + - - +
194B LYS* 2.6 45.2 + - - +
195B PHE* 3.8 18.0 - - + -
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Residues in contact with TRP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B GLN* 5.8 0.2 - - - -
97B TYR* 4.2 12.3 - + - -
98B PRO* 3.6 22.4 - - + -
99B LEU* 3.2 65.7 + - + +
101B PHE* 4.6 11.0 - + + -
166B ASN* 3.2 23.5 + - + -
167B TRP 4.1 4.5 - - - -
168B VAL* 4.6 10.3 - - + +
177B GLU* 1.3 71.3 - - - +
179B ILE* 1.3 59.2 + - - +
180B GLY* 3.1 32.8 + - - -
181B ASN* 3.4 18.4 - - - -
190B ASN* 3.6 27.8 - - + -
191B TYR 3.9 21.3 - - - -
192B ASN* 3.0 32.7 + - + +
195B PHE* 4.2 3.5 - - - -
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B TRP* 2.9 23.1 + - + +
168B VAL 4.5 1.3 - - - -
169B LYS* 4.1 8.7 - - + +
177B GLU 4.3 5.4 - - - +
178B TRP* 1.3 75.7 - - - +
180B GLY* 1.3 63.0 + - - +
191B TYR* 3.6 5.4 - - + +
192B ASN* 2.9 26.7 + - - +
195B PHE* 4.1 37.3 - - + +
199B ALA* 3.9 25.4 - - + -
201B LEU* 4.8 5.6 - - + -
212B MET* 3.6 35.4 - - + -
214B LEU* 5.1 2.0 - - + -
225B TYR* 3.9 20.2 - - + -
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ASN* 3.6 0.2 - - - -
167B TRP* 3.3 17.2 + - - +
178B TRP* 3.1 29.2 + - - -
179B ILE* 1.3 85.7 - - - +
181B ASN* 1.3 61.7 + - - +
190B ASN 2.9 15.5 - - - -
191B TYR* 4.2 1.6 - - - -
201B LEU* 4.1 9.0 - - - -
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Residues in contact with ASN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TYR* 2.9 37.4 + - - -
99B LEU* 5.6 0.2 - - - +
164B TRP* 3.7 18.5 - - + +
165B ILE 3.2 12.8 - - - +
166B ASN* 3.4 19.2 + - - +
178B TRP* 3.4 9.5 - - - -
180B GLY* 1.3 75.4 - - - +
182B ILE* 1.3 68.3 + - - +
189B THR* 3.4 2.4 - - - -
190B ASN* 2.9 47.0 + - - +
201B LEU* 3.6 9.6 - - - +
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B TRP* 3.5 6.6 - - - -
165B ILE* 3.0 41.5 + - + +
167B TRP* 4.8 5.8 - - - +
181B ASN* 1.3 83.3 - - - +
183B TYR* 1.3 74.4 + - - +
184B PRO* 3.6 4.8 - - + +
187B SER* 3.9 19.1 - - - +
188B TYR 3.2 13.0 - - - +
189B THR* 4.2 5.4 - - + -
201B LEU* 3.9 39.7 - - + +
202B THR* 4.0 9.6 - - - +
203B VAL* 3.9 26.7 - - + -
210B ALA* 5.4 1.1 - - + -
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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