Contacts of the strand formed by residues 420 - 426 (chain A) in PDB entry 2W8B
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 GLN 420 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL 3.9 0.2 - - - +
171A VAL* 3.3 4.5 - - - -
172A GLN* 2.9 70.7 + - + +
397A MET 4.3 4.1 + - - +
398A GLY* 3.2 18.6 - - - -
399A SER* 2.9 41.9 + - - +
419A GLY* 1.3 75.5 - - - -
421A VAL* 1.3 58.8 + - - +
422A LYS* 4.7 8.7 + - - +
156H LEU* 5.1 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 5.3 3.1 - - + -
169A TYR* 3.5 33.0 - - + -
170A VAL 3.4 5.2 - - - +
171A VAL* 4.5 9.6 - - + -
399A SER* 3.0 28.5 + - - +
400A VAL* 3.3 11.6 + - + -
401A LEU* 3.6 30.5 - - + +
414A LEU 5.6 2.2 - - - +
416A ALA* 3.6 31.0 - - + -
418A ASP* 5.5 0.2 - - - +
419A GLY 3.6 5.6 - - - +
420A GLN* 1.3 79.5 - - - +
422A LYS* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 3.5 4.7 - - - +
170A VAL* 3.0 35.4 + - + +
172A GLN* 2.9 38.1 + - - +
180A TYR* 5.8 0.9 - - - -
378A GLU* 4.7 9.6 - - - +
392A SER* 3.7 18.4 - - - +
399A SER* 3.9 18.7 + - - +
401A LEU* 4.1 2.0 - - - -
420A GLN* 4.7 10.3 + - - +
421A VAL* 1.3 77.1 - - - +
423A PHE* 1.3 94.5 + - + +
424A PRO* 3.3 5.0 - - - -
150H LYS 5.8 1.2 + - - -
151H GLU* 4.5 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 3.5 5.0 - - - -
170A VAL* 3.9 11.2 - - + -
202A LEU 3.4 23.8 - - - -
203A MET* 3.8 9.2 - - + -
204A SER* 3.3 30.7 - - - -
205A PRO* 3.2 30.1 - - + +
378A GLU* 5.4 1.4 + - - -
379A THR* 4.2 20.2 + - + -
392A SER* 4.5 0.2 - - - -
422A LYS* 1.3 101.6 - - + +
424A PRO* 1.4 71.7 - - - +
115H PRO* 3.5 28.9 - - + -
116H GLU* 5.6 0.2 - - + -
151H GLU* 3.4 39.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA 3.2 8.5 - - - +
169A TYR* 4.2 2.5 - - + -
205A PRO* 5.1 0.9 - - - +
379A THR* 3.5 23.3 + - - +
381A SER* 4.0 8.9 - - - -
390A LEU* 2.9 30.1 - - + +
391A TYR* 3.6 33.9 - - - +
392A SER* 4.0 3.6 - - - -
401A LEU* 3.8 17.5 - - + -
422A LYS 3.3 5.1 - - - -
423A PHE* 1.4 92.7 - - - +
425A ALA* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.4 2.3 - - - -
168A ALA* 2.9 22.4 + - + +
205A PRO* 3.4 33.9 - - + +
206A ALA* 4.8 1.1 - - - -
207A TRP* 2.8 35.4 + - + +
381A SER* 3.4 8.7 - - - +
390A LEU* 3.6 4.2 - - - +
424A PRO* 1.3 75.5 - - - +
426A TRP* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 4.7 0.2 + - - -
165A THR* 2.8 27.2 + - - +
166A ARG 3.7 7.7 + - - -
167A ILE* 4.2 11.2 - - + +
187A TYR* 4.2 16.0 - + + +
207A TRP* 3.4 8.7 - - - +
381A SER* 2.8 17.5 + - - +
382A LEU 3.5 19.1 - - - +
383A ALA* 3.5 26.0 - - + -
384A PRO* 3.8 6.7 - - + +
388A MET* 3.4 38.6 - - + -
389A VAL 4.0 0.2 - - - -
390A LEU* 3.5 32.9 - - + +
403A LEU* 3.7 15.9 - - + -
425A ALA* 1.3 70.8 - - - +
427A SER* 1.3 86.6 + - - +
428A PRO* 3.9 0.3 - - - +
1431A SO4 3.6 25.4 - - - -
----------------------------------------------------------
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