Contacts of the strand formed by residues 246 - 256 (chain A) in PDB entry 4LL4
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 THR 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASN* 3.0 30.4 + - - +
242A ILE* 3.4 11.4 - - - +
243A ILE* 2.5 41.1 + - + +
245A GLY* 1.3 84.1 - - - +
247A CYS* 1.3 65.4 + - - +
34B PRO* 4.3 3.3 - - - +
73B CYS* 4.0 19.9 - - - -
74B MET 3.3 14.1 - - - +
75B PRO 4.2 0.7 - - - +
90B SER 4.2 0.2 - - - -
91B GLY* 3.4 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE 3.0 20.4 - - - +
202A GLU* 3.8 14.4 - - - -
242A ILE* 4.5 4.3 - - - -
246A THR* 1.3 73.8 - - - +
248A ALA* 1.3 59.3 + - - +
31B TRP* 3.6 17.3 - - + -
32B CYS* 2.7 45.8 - - + -
34B PRO* 3.7 13.9 - - - -
73B CYS* 3.0 6.6 - - - +
74B MET* 2.9 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE* 2.9 38.2 + - + +
240A ASN* 5.7 2.9 - - + +
242A ILE* 4.1 23.8 - - + +
247A CYS* 1.3 74.5 - - - +
249A SER* 1.3 63.5 + - - +
250A TRP* 6.3 0.4 - - + -
31B TRP* 3.8 2.4 - - - -
72B LYS 3.5 20.6 - - - +
73B CYS* 4.2 4.0 - - + -
74B MET* 3.9 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA 3.3 4.9 - - - -
200A ASP* 3.4 2.4 + - - -
201A PHE* 4.6 0.9 - - - -
248A ALA* 1.3 73.9 - - - +
250A TRP* 1.3 72.4 + - - +
251A ARG* 3.4 27.7 + - - +
31B TRP* 3.2 29.8 - - - -
59B VAL* 5.9 0.6 - - - +
60B ASP* 5.1 0.2 + - - -
72B LYS 4.7 2.5 + - - +
74B MET* 3.9 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 3.7 35.4 - - + +
198A HIS* 3.5 2.1 - - - -
199A ALA* 2.8 25.3 + - + +
201A PHE* 3.8 27.6 - + - -
211A PRO* 3.9 27.2 - - + +
212A LYS* 3.8 28.3 - - - -
213A ALA* 3.8 21.1 - - + -
237A VAL* 4.3 9.6 - - + -
238A ARG 4.7 0.7 - - - -
239A GLY* 4.0 18.2 - - - -
240A ASN 5.5 0.2 - - - +
248A ALA* 6.3 0.4 - - + -
249A SER* 1.3 86.5 - - - +
251A ARG* 1.3 79.4 + - - +
253A LYS* 3.5 39.5 - - + +
278A ILE* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE 4.0 0.2 - - - -
198A HIS* 3.1 38.2 + - - -
199A ALA 3.5 6.3 + - - -
200A ASP* 2.9 29.7 + - - -
249A SER* 3.4 20.6 + - - +
250A TRP* 1.3 99.2 + - - +
252A GLY* 1.3 60.4 + - - +
253A LYS* 3.3 5.2 + - - +
31B TRP* 4.0 2.0 - - - +
60B ASP* 3.0 35.1 + - - -
63B GLN* 3.8 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER* 3.3 22.1 + - - -
197A ILE 2.9 13.6 + - - -
198A HIS* 4.7 2.0 - - - +
251A ARG* 1.3 71.5 - - - +
253A LYS* 1.3 67.8 + - - +
254A SER* 3.3 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 2.6 39.9 + - + +
237A VAL* 4.5 23.7 - - + +
238A ARG 4.3 15.0 + - - -
239A GLY* 4.6 3.2 - - - -
250A TRP* 3.5 67.0 - - + +
251A ARG 3.3 4.7 + - - +
252A GLY* 1.3 74.2 - - - +
254A SER* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU* 2.9 30.0 + - - +
195A ILE 3.0 9.4 - - - -
196A SER* 4.3 6.1 - - - -
197A ILE* 5.5 0.7 - - - -
237A VAL* 4.4 11.7 - - - +
252A GLY 3.4 10.8 - - - -
253A LYS* 1.3 81.7 - - - +
255A LEU* 1.3 63.9 + - - +
256A ARG 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU* 3.3 3.8 - - - -
195A ILE* 2.5 48.9 + - + +
197A ILE* 4.5 6.2 - - + +
213A ALA* 4.3 11.7 - - + -
214A ALA* 4.3 1.6 - - - -
215A ILE* 4.0 27.1 - - + +
235A SER* 3.7 11.2 - - - -
236A SER* 3.6 38.1 - - - +
237A VAL* 4.1 15.9 - - + +
254A SER* 1.3 74.5 - - - +
256A ARG* 1.3 59.9 + - - +
276A LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLY* 3.5 27.3 + - - -
193A ASP 3.4 2.9 - - - -
194A GLU* 3.2 26.8 + - - +
215A ILE* 3.6 6.2 - - - +
235A SER* 2.4 35.4 + - - +
255A LEU* 1.3 74.5 - - - +
257A VAL* 1.3 76.8 + - - +
258A GLN* 3.6 12.1 + - + +
----------------------------------------------------------
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