Contacts of the strand formed by residues 181 - 184 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G MET* 3.6 23.6 - - - -
29G PHE* 3.4 7.5 - - + -
128G PHE* 4.4 1.6 - - + -
154G MET* 4.3 0.2 - - - +
163G THR* 3.7 16.2 - - + -
164G LYS 3.2 16.6 - - - +
165G ARG* 2.9 47.1 + - + -
166G LEU* 3.8 2.2 - - - +
174G VAL* 2.7 31.4 + - + +
176G GLY 4.0 6.5 - - - -
177G GLY 3.0 13.4 + - - +
178G ALA* 3.4 19.2 - - - +
179G ASP 3.7 0.6 - - - -
180G LYS* 1.3 95.3 - - + +
182G HIS* 1.3 72.7 + - - +
7195G TTP 3.3 38.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 182 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G PHE* 4.1 2.2 - - - -
154G MET* 3.8 26.5 + - + +
155G GLU* 2.8 35.8 - - + +
163G THR* 3.5 3.4 - - - -
164G LYS* 2.8 40.6 + - + +
166G LEU* 3.7 34.2 - - + +
178G ALA* 4.0 9.4 - - + -
181G TYR* 1.3 83.6 + - - +
183G SER* 1.3 67.2 + - - +
184G VAL* 3.7 5.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PRO* 5.0 0.2 - - - -
28G MET 3.5 23.8 - - - -
29G PHE* 3.6 15.1 - - - +
151G ALA* 3.6 18.3 - - - +
152G VAL 2.8 21.7 + - - -
154G MET* 2.9 41.1 + - - +
160G ALA* 3.8 4.0 - - - -
162G TYR 3.4 8.7 - - - -
163G THR* 4.6 2.2 - - - +
182G HIS* 1.3 72.2 - - - +
184G VAL* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G CYS* 3.8 7.6 - - - -
155G GLU* 4.1 21.5 - - + +
160G ALA* 3.4 9.7 - - - +
161G ALA 3.3 4.0 + - - -
162G TYR* 2.8 34.2 + - + +
164G LYS* 4.4 8.1 - - + -
182G HIS* 4.0 13.0 - - + +
183G SER* 1.3 78.9 - - - +
185G CYS* 1.3 74.3 + - - +
188G CYS* 3.7 21.3 - - + +
189G TYR* 3.3 34.8 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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