Contacts of the strand formed by residues 214 - 218 (chain A) in PDB entry 3BUC
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 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 5.3 7.2 - - - +
60A ILE* 3.9 30.3 - - + -
61A ARG 5.8 1.3 - - - +
62A ALA* 5.2 6.1 - - + -
65A LEU* 4.0 17.7 - - + -
195A PHE 4.0 0.3 - - - +
196A VAL* 3.6 1.0 - - - -
197A PHE* 2.7 54.8 + - + +
212A ALA* 4.8 1.3 - - + +
213A VAL* 1.3 78.3 - - - +
215A ARG* 1.3 66.3 + - - +
216A LEU* 5.3 2.7 - - + -
234A TRP* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 4.8 6.6 + - - -
194A ASP* 5.7 7.6 - - + +
195A PHE 3.3 9.9 - - - +
196A VAL* 3.9 21.0 - - + +
213A VAL* 3.5 31.5 + - + +
214A VAL* 1.3 79.1 - - - +
216A LEU* 1.3 64.4 + - - +
217A PRO* 4.8 0.7 - - - +
241A ARG* 5.3 7.0 - - - +
3C G 4.6 18.6 + - - -
4C C 5.2 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.6 27.1 - - - +
60A ILE* 4.4 13.5 - - + -
69A TYR* 4.0 40.2 - - + -
194A ASP* 4.2 4.3 - - - -
195A PHE* 2.9 49.8 + - + +
197A PHE* 4.5 22.7 - - + -
214A VAL* 5.3 2.9 - - + -
215A ARG* 1.3 78.0 - - - +
217A PRO* 1.3 77.5 - - + +
218A LEU* 3.5 6.9 + - + -
224A LEU* 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 5.3 1.8 - - - +
69A TYR* 4.0 10.9 + - - -
192A SER* 3.8 17.0 - - - +
193A ARG 3.6 7.9 - - - +
194A ASP* 3.9 15.0 - - - +
215A ARG 4.8 0.4 - - - +
216A LEU* 1.3 96.5 - - + +
218A LEU* 1.3 61.5 + - - +
219A ALA* 3.8 4.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.8 25.8 - - + -
186A SER* 4.4 5.8 - - - +
188A SER* 4.0 16.3 - - - +
191A ALA 4.4 1.9 - - - +
192A SER* 3.4 5.5 + - - -
193A ARG 2.8 33.3 + - - +
195A PHE* 3.8 35.9 - - + -
216A LEU* 4.2 10.3 - - + -
217A PRO* 1.3 73.3 - - - +
219A ALA* 1.3 62.9 + - - +
222A SER* 4.0 4.5 - - - +
224A LEU* 4.0 27.6 - - + -
238A LEU* 5.0 0.2 - - + -
248A ARG* 3.3 28.3 + - - +
259A AKG 3.9 2.7 - - - +
----------------------------------------------------------
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