Contacts of the strand formed by residues 226 - 230 (chain A) in PDB entry 1H1B
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 ASP 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A VAL* 5.8 2.1 - - - +
182A CYS* 3.1 6.9 - - - +
183A THR* 2.7 47.9 + - - +
184A LEU* 5.4 0.6 - - - +
188A ALA 5.4 1.0 - - - +
189A GLY* 3.3 11.6 - - - -
190A VAL* 2.9 46.5 + - + +
215A PHE 3.9 4.3 - - - -
216A VAL* 3.7 15.6 - - - +
221A ALA* 5.1 6.1 + - - -
224A TYR 4.4 5.0 - - - +
225A PRO* 1.3 73.3 - - - +
227A ALA* 1.3 60.0 + - - +
228A PHE* 3.8 11.4 - - + -
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Residues in contact with ALA 227 (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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180A ASN* 3.9 7.9 - - - +
181A VAL 3.7 3.8 - - - -
182A CYS* 3.9 13.9 - - - -
190A VAL* 5.9 1.0 - - - +
213A ALA* 4.3 0.2 - - - -
214A SER* 2.9 24.0 + - - -
215A PHE* 2.9 65.1 + - + +
217A ARG* 4.6 2.0 - - - +
225A PRO 3.9 1.0 + - - -
226A ASP* 1.3 71.3 - - - +
228A PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 228 (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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138A ALA* 4.3 14.4 - - + -
180A ASN* 3.0 10.9 + - - -
181A VAL* 2.8 42.6 + - + +
183A THR* 3.3 29.2 - - + -
190A VAL* 4.4 13.0 - - + -
197A SER 4.9 0.2 - - - -
198A PRO 5.0 0.9 - - - -
199A LEU* 3.4 48.5 - - + -
211A GLY* 3.8 7.2 - - - -
212A ILE 3.2 14.6 - - - +
213A ALA* 3.4 34.3 - - + -
214A SER* 4.5 0.2 - - - -
226A ASP* 3.8 17.5 - - + -
227A ALA* 1.3 79.2 - - - +
229A ALA* 1.3 60.4 + - - +
230A PRO 3.5 0.2 - - - -
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Residues in contact with ALA 229 (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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102A ASP* 3.6 38.6 - - + +
103A ILE* 4.7 4.7 - - + -
180A ASN* 4.4 3.4 - - - +
211A GLY* 3.2 5.5 - - - -
212A ILE* 3.0 41.4 + - + +
214A SER* 4.2 3.9 - - - -
228A PHE* 1.3 70.2 - - - +
230A PRO* 1.3 70.5 - - + +
231A VAL* 3.1 9.1 + - - +
234A PHE* 5.4 2.2 - - + -
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Residues in contact with PRO 230 (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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101A ASN* 6.0 3.8 - - - +
179A SER 3.0 32.3 - - - +
180A ASN* 4.1 2.5 - - - +
181A VAL* 3.8 20.2 - - + +
210A HIS 3.8 7.0 - - - +
228A PHE 3.8 2.2 - - - +
229A ALA* 1.3 84.2 - - + +
231A VAL* 1.3 65.3 + - - +
232A ALA* 2.9 5.3 + - + +
233A GLN* 3.0 41.0 + - + +
234A PHE* 3.3 22.6 - - + -
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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