Contacts of the strand formed by residues 181 - 184 (chain A) in PDB entry 1XBT
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 TYR 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A MET* 3.5 23.1 - - - -
29A PHE* 3.5 7.7 - - + -
128A PHE* 4.4 1.3 - - + -
154A MET* 4.2 0.2 - - - +
163A THR* 3.7 15.9 - - + -
164A LYS 3.3 15.9 - - - +
165A ARG* 2.8 45.7 + - + -
166A LEU* 4.1 2.7 - - - +
174A VAL* 2.6 31.1 + - + +
176A GLY 3.9 7.0 - - - -
177A GLY 3.0 13.5 + - - +
178A ALA* 3.4 18.6 + - - +
179A ASP 3.7 0.6 - - - -
180A LYS* 1.3 94.8 - - + +
182A HIS* 1.3 72.1 + - - +
1195A TTP 3.2 38.8 - + + -
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Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.1 2.7 - - - -
154A MET* 3.6 26.5 + - + +
155A GLU* 2.9 37.9 - - + +
163A THR* 3.5 3.2 - - - -
164A LYS* 2.8 37.1 + - + +
166A LEU* 3.7 34.1 - - + +
178A ALA* 4.0 10.1 - - + -
181A TYR* 1.3 83.2 + - - +
183A SER* 1.3 67.9 + - - +
184A VAL* 3.7 2.9 + - + -
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PRO* 5.0 0.4 - - - -
28A MET 3.5 24.9 - - - -
29A PHE* 3.7 10.6 - - - +
151A ALA* 3.6 16.5 - - - +
152A VAL 2.6 25.1 + - - -
154A MET* 2.9 43.9 + - - +
160A ALA* 3.8 4.3 - - - -
162A TYR 3.4 8.5 - - - -
163A THR* 4.6 2.2 - - - +
182A HIS* 1.3 71.6 - - - +
184A VAL* 1.3 62.3 + - - +
45B ILE* 6.0 0.2 - - - +
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Residues in contact with VAL 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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153A CYS* 3.8 7.4 - - - -
155A GLU* 3.7 35.2 - - + +
160A ALA* 3.4 7.7 - - - +
161A ALA 3.4 3.1 + - - -
162A TYR* 2.8 34.3 + - + +
164A LYS* 4.3 9.2 - - + +
182A HIS* 4.1 9.2 - - + +
183A SER* 1.3 80.0 - - - +
185A CYS* 1.3 74.2 + - - +
188A CYS* 3.7 13.2 - - + -
189A TYR* 3.3 34.3 - - + +
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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