Contacts of the strand formed by residues 181 - 184 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D MET* 3.6 17.5 - - - -
29D PHE* 3.5 7.5 - - + -
128D PHE* 4.4 1.1 - - + -
163D THR* 3.7 25.4 - - + -
164D LYS 3.3 12.3 - - - +
165D ARG* 3.1 38.9 + - + -
166D LEU* 3.8 2.4 - - - +
174D VAL* 2.6 30.7 + - + +
176D GLY 3.9 7.4 - - - -
177D GLY 2.9 13.3 + - - +
178D ALA* 3.3 18.9 - - - +
179D ASP 3.7 0.6 - - - -
180D LYS* 1.3 95.3 - - + +
182D HIS* 1.3 72.1 + - - +
4195D TTP 3.0 47.0 - + + -
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Residues in contact with HIS 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PHE* 4.0 2.7 - - - -
154D MET* 3.7 24.5 + - + +
155D GLU* 3.1 38.6 - - + +
163D THR* 3.5 3.1 - - - -
164D LYS* 2.8 41.2 + - + +
166D LEU* 3.7 31.8 - - + +
178D ALA* 4.0 9.6 - - + -
181D TYR* 1.3 83.4 + - - +
183D SER* 1.3 67.6 + - - +
184D VAL* 3.6 4.9 + - + -
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Residues in contact with SER 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 5.6 0.3 - - - +
27D PRO* 5.0 0.2 - - - -
28D MET 3.5 24.0 - - - -
29D PHE* 3.6 14.8 - - - +
151D ALA* 3.7 16.9 - - - +
152D VAL 2.7 23.4 + - - -
154D MET* 2.9 40.7 + - - +
160D ALA* 3.8 4.3 - - - -
162D TYR 3.4 9.0 - - - -
163D THR* 4.6 2.0 - - - +
182D HIS* 1.3 72.8 - - - +
184D VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D CYS* 3.9 3.6 - - - -
155D GLU* 3.8 26.7 - - + +
160D ALA* 3.3 9.4 - - - +
161D ALA 3.3 4.0 + - - -
162D TYR* 2.8 37.4 + - + +
164D LYS* 4.3 9.9 - - + +
182D HIS* 3.9 12.3 - - + +
183D SER* 1.3 79.7 - - - +
185D CYS* 1.3 73.3 + - - +
188D CYS* 3.8 19.1 - - + -
189D TYR* 3.3 35.2 - - + +
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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