Contacts of the strand formed by residues 405 - 411 (chain A) in PDB entry 4WPN
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 405 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 3.6 14.2 - - - +
296A PHE* 4.2 1.2 - - - -
307A SER* 5.2 0.9 - - - -
354A ILE* 4.2 3.8 - - + -
358A ILE* 3.8 31.2 - - + -
385A THR* 3.3 7.9 - - + +
387A PHE* 4.0 24.7 - - + -
396A ILE* 5.4 1.6 - - + -
401A ILE* 3.7 32.9 - - + +
403A GLY 2.7 10.6 + - - +
404A PRO* 1.3 86.4 - - + +
406A GLN* 1.3 59.6 + - - +
407A GLN* 3.3 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA* 4.0 13.3 + - - +
292A HIS* 4.1 12.7 + - - +
295A VAL* 3.7 22.4 - - + +
296A PHE* 3.9 11.9 - - + -
309A ILE* 3.3 28.1 - - + +
319A PHE* 5.2 0.4 - - - -
323A SER* 3.8 24.3 + - - +
385A THR 2.8 14.2 + - - +
386A VAL* 3.5 21.6 - - + +
387A PHE* 2.8 32.6 + - - +
404A PRO 4.3 0.2 - - - -
405A VAL* 1.3 73.0 - - - +
407A GLN* 1.3 61.4 - - - +
408A ILE* 3.9 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LYS* 3.7 3.0 - - - +
307A SER* 2.9 35.5 + - - +
308A ARG* 4.0 1.1 - - + -
309A ILE* 3.1 29.6 + - - +
387A PHE* 3.7 3.7 - - - -
390A VAL* 4.1 11.2 - - + -
396A ILE* 3.2 52.6 + - + +
397A ALA* 4.9 0.7 - - - -
401A ILE* 3.5 11.8 - - - +
405A VAL* 3.3 38.6 + - - +
406A GLN* 1.3 76.0 - - - +
408A ILE* 1.3 62.3 + - - +
409A MET* 4.5 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ILE* 3.5 12.3 - - + +
311A VAL* 4.2 16.6 - - + -
316A TYR* 3.6 17.2 + - + -
319A PHE* 4.2 7.4 - - + -
320A VAL* 4.0 24.5 - - + -
323A SER* 3.9 20.6 - - - +
386A VAL* 3.9 23.6 - - + -
387A PHE 2.9 14.2 + - - +
388A SER* 3.5 2.6 - - - -
389A ASN 3.3 23.7 + - - -
390A VAL* 3.4 8.2 + - - +
406A GLN* 3.9 23.3 - - + +
407A GLN* 1.3 77.5 - - - +
409A MET* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 4.1 28.0 - - - +
309A ILE 2.8 16.8 + - - +
310A PHE* 3.4 34.0 - - + -
311A VAL* 2.9 24.9 + - - +
316A TYR* 3.5 11.7 - - - -
389A ASN* 5.4 0.4 - - - +
390A VAL* 3.1 37.5 - - + +
392A ASP* 3.5 24.9 - - - +
397A ALA* 4.2 21.1 - - + -
407A GLN* 4.5 4.7 - - - -
408A ILE* 1.3 78.2 - - - +
410A LYS* 1.3 59.2 + - - +
420A ARG* 4.3 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE* 4.8 0.8 - - - -
311A VAL 3.4 7.2 - - - +
313A GLU* 4.2 27.0 + - + +
316A TYR* 3.6 43.5 + - + -
389A ASN* 3.9 13.1 + - - +
390A VAL 5.2 0.6 + - - -
409A MET* 1.3 76.3 - - - +
411A PHE* 1.3 62.9 + - - +
420A ARG* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 4.0 20.6 - - + -
278A VAL 3.6 12.3 - - - -
279A LEU* 4.7 5.2 - - + -
310A PHE* 3.6 12.6 - - + -
311A VAL 3.2 20.3 + - - -
312A GLU* 3.3 38.9 - - + -
313A GLU* 2.8 29.5 + - - +
410A LYS* 1.3 76.9 - - - +
412A LYS* 1.3 62.9 + - - +
413A SER 3.7 25.1 - - - +
414A LEU* 4.4 12.1 - - + -
416A ASP* 5.9 0.7 - - + +
417A VAL* 3.6 34.3 - - + -
420A ARG* 3.8 8.5 - - - +
----------------------------------------------------------
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