Contacts of the strand formed by residues 225 - 229 (chain H) in PDB entry 1U8R
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 VAL 225 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H ARG* 3.6 2.7 - - - +
154H LEU* 3.0 51.3 + - + +
167H VAL* 4.8 7.4 - - + -
169H GLN 3.6 10.1 - - - +
170H LEU* 3.8 21.1 - - + -
174H VAL* 5.2 6.1 - - + -
184H LEU* 5.8 0.7 - - + -
189H VAL* 6.0 1.8 - - + -
207H ILE* 5.9 2.2 - - + -
217H LEU* 3.8 26.5 - - + -
221H MET 3.8 7.4 - - - +
222H ALA 2.9 5.2 + - - +
223H HIS 3.5 1.2 + - - -
224H ALA* 1.3 84.8 - - - +
226H LYS* 1.3 63.2 + - - +
227H VAL* 4.2 13.9 - - + -
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Residues in contact with LYS 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLU* 3.5 17.8 + - - +
151H LEU* 4.3 15.0 - - + -
152H VAL 3.2 12.3 - - - +
153H ARG* 2.9 42.0 - - + +
167H VAL* 4.2 0.2 - - - -
168H ARG* 3.0 7.9 + - - -
169H GLN* 3.0 77.4 + - + +
171H THR* 4.8 9.9 - - + -
223H HIS 5.9 0.4 - - - +
224H ALA 5.7 0.2 - - - -
225H VAL* 1.3 76.0 - - - +
227H VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H LEU* 2.9 10.5 - - - +
152H VAL* 2.8 52.4 + - + +
154H LEU* 4.1 22.2 - - + +
157H LEU* 5.1 2.0 - - + -
165H VAL* 4.0 31.9 - - + -
166H VAL 3.6 8.1 - - - +
167H VAL* 3.8 23.1 - - + +
168H ARG* 4.1 1.3 - - - +
195H VAL* 5.9 0.2 - - + -
197H VAL* 5.9 0.9 - - + -
225H VAL* 4.2 15.3 - - + -
226H LYS* 1.3 80.3 - - - +
228H GLU* 1.3 61.3 + - - +
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Residues in contact with GLU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H ASN* 3.3 28.9 + - - +
151H LEU* 4.5 1.6 - - + +
165H VAL* 3.3 4.5 - - - -
166H VAL* 3.1 35.6 + - + +
168H ARG* 2.9 39.6 + - + +
227H VAL* 1.3 76.9 - - - +
229H LYS* 1.3 63.1 + - - +
230H VAL* 2.8 31.8 + - + +
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Residues in contact with LYS 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H ASN* 4.9 6.8 + - - +
151H LEU 6.2 0.9 - - - +
152H VAL* 4.0 28.1 - - + +
157H LEU* 4.5 19.5 - - + -
158H PRO* 6.1 2.2 - - + -
163H VAL* 5.0 8.3 - - + -
164H ALA 4.3 0.7 - - - -
165H VAL* 3.9 16.6 - - + -
227H VAL 4.2 1.4 + - - -
228H GLU* 1.3 69.1 - - - +
230H VAL* 1.3 68.4 + - - +
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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