Contacts of the strand formed by residues 328 - 334 (chain A) in PDB entry 6EJ9
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 ILE 328 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A VAL* 4.4 12.1 - - + -
327A ARG* 1.3 77.4 - - - +
329A ALA* 1.3 64.2 + - - +
330A PHE* 3.5 22.9 - - + -
354A HIS* 3.1 31.9 + - + +
355A PHE* 2.8 37.8 + - - +
418A PHE* 3.9 11.0 - - + +
420A ILE* 3.6 22.2 - - + -
435A LEU* 3.7 31.2 - - + -
436A VAL* 4.7 6.3 - - + -
439A LEU* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 1.3 72.7 - - - +
330A PHE* 1.3 62.4 + - - +
331A VAL* 3.8 1.1 + - - +
355A PHE* 3.5 10.8 - - + -
408A LEU* 4.1 25.6 - - + -
416A TRP* 3.7 32.5 - - + +
418A PHE 3.0 12.2 + - - +
419A PHE* 3.6 6.1 - - - -
420A ILE 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 3.5 34.8 - - + -
329A ALA* 1.3 71.4 - - - +
331A VAL* 1.3 60.6 + - - +
332A LEU* 3.9 10.7 + - + +
349A ILE* 4.1 16.4 - - + -
354A HIS* 4.1 10.5 - + - -
355A PHE 2.8 15.4 + - - +
356A TYR* 3.3 43.8 - + + -
357A TYR* 2.9 29.1 + - - +
420A ILE* 3.4 22.7 - - + -
422A LEU* 3.7 29.2 - - + -
432A ASN* 5.5 0.7 - - - -
435A LEU* 4.3 9.9 - - + -
596A PHE* 4.1 16.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ALA 3.8 1.1 + - - +
330A PHE* 1.3 74.8 - - - +
332A LEU* 1.3 63.3 + - - +
333A VAL* 3.8 20.4 + - + +
357A TYR* 3.3 14.8 - - + +
359A HIS* 5.6 3.8 - - + -
400A THR* 6.0 0.7 - - + -
401A TYR* 4.7 5.8 - - + -
404A SER* 4.2 21.5 - - - +
408A LEU* 3.7 19.5 - - + -
419A PHE* 3.3 40.8 - - + -
420A ILE 2.8 9.7 + - - +
421A ASN* 3.3 5.6 - - - +
422A LEU 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 4.3 16.4 - - + +
331A VAL* 1.3 74.3 - - - +
333A VAL* 1.3 57.7 + - - +
334A VAL* 3.9 9.2 - - + -
342A LEU* 4.4 18.4 - - + -
345A MET* 4.8 5.6 - - + -
346A PHE* 4.6 17.5 - - + -
349A ILE* 4.6 9.2 - - + -
356A TYR* 5.1 4.5 - - + -
357A TYR 3.0 7.8 + - - +
358A ILE* 3.4 37.5 - - + +
359A HIS* 2.8 33.3 + - - +
422A LEU* 3.4 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 3.8 12.8 + - + +
332A LEU* 1.3 73.0 - - - +
334A VAL* 1.3 62.5 + - - +
335A HIS* 5.5 1.3 + - - +
359A HIS* 3.5 18.8 - - + +
390A THR* 4.7 10.3 - - - +
397A LEU* 4.3 18.6 - - + -
400A THR* 4.2 17.3 - - + -
401A TYR* 3.9 31.2 - - + +
421A ASN* 5.9 0.4 - - + -
422A LEU 3.0 9.4 + - - +
423A SER* 3.4 24.9 - - - -
495A TRP* 5.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 4.2 9.6 - - + -
333A VAL* 1.3 87.8 - - - +
335A HIS* 1.3 66.1 + - - +
342A LEU* 4.1 28.7 - - + -
358A ILE* 4.2 9.2 - - + -
359A HIS 3.1 13.4 + - - +
360A VAL* 3.7 16.7 - - + -
361A ASP* 3.1 26.3 + - - +
367A LEU* 3.8 20.4 - - + -
390A THR* 5.7 0.2 + - - -
423A SER* 4.3 1.3 - - - -
424A ALA* 3.8 24.0 - - + +
----------------------------------------------------------
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