Contacts of the strand formed by residues 213 - 220 (chain A) in PDB entry 3B4M
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 LYS 213 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASN* 3.0 52.3 + - - +
179A VAL 3.5 13.2 - - - +
181A TYR 4.4 0.4 - - - +
205A CYS* 4.6 8.2 - - - -
206A ASP 5.1 2.6 + - - -
207A LYS* 5.2 4.2 + - - +
212A PRO* 1.3 79.6 - - - +
214A GLY* 1.3 59.2 + - - +
240A ARG* 3.7 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASN* 3.5 7.4 + - - -
179A VAL 2.7 30.6 + - - -
204A LEU 3.4 10.8 - - - -
205A CYS* 4.2 14.5 - - - -
206A ASP 5.1 0.9 - - - -
213A LYS* 1.3 75.5 - - - +
215A PHE* 1.3 69.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.4 37.5 - + + +
176A VAL 3.3 14.4 - - - +
177A GLY* 4.1 0.7 - - - -
179A VAL* 3.8 5.8 - - - +
203A ILE* 3.6 4.2 - - - +
204A LEU* 2.7 77.8 + - + +
205A CYS* 5.9 0.2 - - - -
206A ASP* 5.0 5.6 - - - -
214A GLY* 1.3 78.8 - - - +
216A ALA* 1.3 60.4 + - - +
217A TYR* 3.7 22.2 - + - -
200B ARG* 3.9 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.6 3.5 - - - -
176A VAL* 2.7 43.2 + - + +
179A VAL* 4.0 10.8 - - + -
188A LEU* 3.7 29.6 - - + -
201A VAL* 5.1 0.4 - - + -
202A THR 3.0 14.4 - - - +
203A ILE* 4.4 2.0 - - + -
204A LEU* 4.6 1.1 - - - -
215A PHE* 1.3 78.8 - - - +
217A TYR* 1.3 68.0 - - - +
218A ILE* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A SER* 5.0 5.6 - - - +
174A ILE 3.2 12.3 - - - +
175A TYR* 3.7 30.7 - + + -
200A ARG 3.8 1.6 - - - +
201A VAL* 3.7 2.4 - - - +
202A THR* 2.9 44.5 + - + +
204A LEU* 3.6 34.3 - - + -
215A PHE* 3.7 18.0 - + - -
216A ALA* 1.3 74.3 - - - +
218A ILE* 1.3 66.1 + - - +
219A GLU 3.9 0.2 - - - -
247A LYS* 3.9 41.3 - - + +
248A ARG* 5.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ARG 3.9 0.5 - - - +
173A SER* 3.2 3.0 - - - -
174A ILE* 2.8 44.9 + - + +
176A VAL* 3.6 22.0 - - + -
188A LEU* 4.4 18.2 - - + +
189A GLU* 6.4 0.7 - - - -
192A PHE* 3.6 34.5 - - + -
198A VAL* 4.2 19.7 - - + -
200A ARG 3.9 1.6 - - - -
201A VAL* 4.3 16.6 - - + -
216A ALA* 4.2 3.3 - - + -
217A TYR* 1.3 77.1 - - - +
219A GLU* 1.3 59.0 - - - +
220A PHE* 3.8 33.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA* 4.3 18.4 - - - +
172A ARG* 2.7 33.2 + - + +
173A SER* 3.5 19.9 + - - +
198A VAL* 3.5 5.0 - - - +
199A ASN* 2.7 48.9 + - - +
200A ARG* 3.0 41.6 + - + +
217A TYR* 3.9 1.2 - - + -
218A ILE* 1.3 70.1 - - - +
220A PHE* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ARG* 3.1 53.7 + - - +
174A ILE* 3.7 23.6 - - + -
192A PHE* 4.3 11.0 - + + -
195A CYS* 4.3 13.7 - - + -
196A GLY 4.2 4.7 - - - -
197A SER 3.4 7.9 - - - +
198A VAL* 3.8 28.7 - - + -
199A ASN* 3.4 4.8 - - - +
218A ILE* 3.8 12.8 - - + -
219A GLU* 1.3 74.5 - - - +
221A SER* 1.3 62.1 + - - +
222A ASP 3.8 14.8 - - - +
225A SER* 3.7 15.9 - - - -
226A VAL* 3.8 13.0 - - + -
229A SER* 3.4 36.3 - - - -
----------------------------------------------------------
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