Contacts of the strand formed by residues 180 - 183 (chain N) in PDB entry 2BDI
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 MET 180 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N LEU 4.7 2.0 - - - +
99N LEU* 4.5 1.3 - - + -
100N ALA* 4.0 25.4 - - + +
172N TYR* 6.3 0.4 - - - -
175N LEU 3.1 24.5 - - - +
176N TYR* 3.6 22.8 + - + -
177N HIS* 2.8 50.6 - - + +
178N PRO 3.0 6.2 + - - +
179N SER* 1.3 82.7 - - - +
181N PHE* 1.3 63.6 + - - +
214N SER* 6.1 0.4 - - - +
215N PHE* 3.6 33.9 - - + -
227N VAL* 3.4 16.6 - - + -
228N TYR 3.2 9.2 - - - +
229N THR* 5.0 0.4 - - - -
230N ASN* 3.8 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129N PRO* 3.6 31.2 - - + -
162N VAL* 4.5 9.2 - - + -
163N VAL 5.9 1.1 - - - +
168N CYS* 4.0 10.3 - - + -
176N TYR* 4.9 0.4 - - - -
180N MET* 1.3 75.5 - - - +
182N CYS* 1.3 73.2 + - - +
183N ALA* 4.5 3.6 - - + -
199N LEU* 3.3 34.8 - - + -
210N GLN* 3.8 13.5 - - + -
211N GLY* 4.0 5.2 - - - -
227N VAL* 3.4 2.7 - - - +
228N TYR* 2.8 50.7 + + + +
229N THR 3.5 20.9 - - - -
230N ASN* 3.2 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 182 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162N VAL* 4.0 0.3 - - - -
163N VAL* 3.2 25.3 + - + +
168N CYS* 2.1 57.9 - - + +
172N TYR* 3.6 28.5 - - - -
181N PHE* 1.3 83.1 - - - +
183N ALA* 1.3 62.7 + - - +
225N PRO* 3.7 16.8 - - + -
226N GLY 3.0 9.6 - - - +
227N VAL* 4.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136N CYS* 6.2 0.2 - - + -
160N VAL* 4.0 17.1 - - + +
161N SER 3.2 15.7 - - - +
162N VAL* 4.2 4.5 - - + -
163N VAL* 4.0 2.0 - - - -
181N PHE* 4.5 2.9 - - + -
182N CYS* 1.3 76.8 - - - +
184N GLY* 1.3 62.1 + - - +
189N ASP* 4.5 2.8 - - - +
199N LEU* 4.4 10.3 - - + -
225N PRO* 4.0 0.8 - - - +
226N GLY 3.0 24.8 + - - +
228N TYR* 3.6 27.0 + - + -
----------------------------------------------------------
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