Contacts of the strand formed by residues 205 - 211 (chain A) in PDB entry 3L6B
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 205 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP 2.9 15.7 + - - +
179A ALA* 3.2 8.5 - - + -
180A LEU* 2.8 26.3 + - - +
198A LYS* 5.2 1.1 - - - +
202A PRO 5.4 1.0 + - - -
203A SER* 3.3 21.3 + - - +
204A VAL* 1.3 75.4 - - - +
206A VAL* 1.3 62.8 + - - +
207A TYR* 3.4 37.7 - - + +
257A ASP* 3.3 23.9 + - + +
305A VAL* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.7 6.3 - - + +
182A VAL* 4.7 2.2 - - + -
190A LEU* 3.9 24.2 - - + -
193A ILE* 4.3 14.1 - - + -
194A ALA* 4.3 15.7 - - + -
197A VAL* 3.7 36.8 - - + -
198A LYS* 4.1 9.9 - - - -
205A LYS* 1.3 76.3 - - - +
207A TYR* 1.3 62.1 + - - +
255A LEU 4.5 8.1 - - - +
256A VAL* 3.4 13.8 - - + +
257A ASP* 2.9 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 3.8 22.0 - - + -
180A LEU 2.8 9.3 + - - +
181A VAL* 3.3 13.4 - - + -
182A VAL* 2.9 28.4 + - - +
190A LEU* 4.5 3.4 - - - -
205A LYS* 3.4 37.4 - - + +
206A VAL* 1.3 75.8 - - - +
208A ALA* 1.3 61.3 + - - +
257A ASP* 4.0 8.7 - - + -
258A ASP* 3.4 27.4 - - + -
260A PHE* 3.7 27.1 - + + -
298A PHE* 3.9 27.4 - + - -
301A VAL* 3.4 28.1 - - + +
305A VAL* 4.1 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 5.1 0.8 - - - +
182A VAL 3.3 5.6 - - - +
184A VAL* 3.9 15.3 - - + -
190A LEU* 3.6 31.2 - - + -
207A TYR* 1.3 75.0 - - - +
209A ALA* 1.3 60.9 + - - +
256A VAL* 4.2 3.6 - - + +
258A ASP 3.0 7.4 + - - +
259A ILE* 3.5 21.7 - - + -
260A PHE* 2.9 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 4.1 4.9 - - + -
182A VAL 2.9 11.1 + - - +
183A PRO* 3.3 4.6 - - + +
184A VAL* 2.9 25.2 + - - +
208A ALA* 1.3 72.8 - - - +
210A GLU* 1.3 62.8 + - - +
211A PRO* 4.7 0.2 - - - +
260A PHE 3.3 4.9 - - - -
288A VAL* 3.5 19.9 - - + +
289A GLY* 3.7 13.2 - - - -
292A ALA* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 3.8 10.0 - - + +
209A ALA* 1.3 77.2 - - - +
211A PRO* 1.3 73.3 - - + +
214A ALA 3.2 17.3 - - - +
215A ASP* 3.4 5.2 - - - +
217A CYS* 2.8 27.6 + - - +
218A TYR* 2.8 35.7 + - - +
259A ILE* 4.1 6.8 - - + +
260A PHE 2.9 9.7 + - - +
261A THR* 3.1 7.8 - - + -
262A VAL* 2.9 24.5 + - - +
288A VAL* 3.6 5.7 - - - +
347A MN 2.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL 4.5 1.8 - - - +
209A ALA 4.7 0.2 - - - +
210A GLU* 1.3 93.9 - - + +
212A SER* 1.3 59.3 + - - +
213A ASN 4.0 3.6 - - - +
214A ALA* 2.9 44.9 + - + +
215A ASP* 3.4 4.9 + - - +
235A THR* 4.0 15.3 - - + +
237A ALA* 3.8 15.7 - - + -
240A VAL* 3.7 32.3 - - + +
261A THR* 4.7 0.4 - - - -
262A VAL* 3.4 7.2 - - + +
264A GLU* 4.4 1.1 - - - +
267A ILE* 4.0 9.0 - - + -
288A VAL* 4.1 10.3 - - + -
----------------------------------------------------------
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