Contacts of the strand formed by residues 342 - 347 (chain A) in PDB entry 5IZL
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 GLU 342 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 5.9 2.9 - - + -
337A ILE 3.9 0.5 - - - +
338A THR* 4.7 1.0 - - - +
339A VAL* 3.0 30.9 + - - +
340A GLY 3.6 0.8 - - - -
341A HIS* 1.3 79.7 - - - +
343A THR* 1.3 70.6 + - - +
344A VAL* 4.2 2.3 + - + +
419A PRO 4.5 8.0 - - - +
420A VAL* 4.5 19.2 - - + +
421A THR* 4.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 2.6 71.4 + - + +
336A HIS* 5.5 7.5 - - - +
337A ILE 3.1 9.9 - - - -
338A THR* 2.9 31.9 - - + +
341A HIS 5.5 0.7 - - - -
342A GLU* 1.3 83.1 - - - +
344A VAL* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A HIS* 4.6 2.0 - - - -
337A ILE* 2.7 41.0 + - - +
339A VAL* 5.9 1.1 - - + -
342A GLU* 5.2 2.5 - - + +
343A THR* 1.3 76.0 - - - +
345A MET* 1.3 69.3 + - - +
416A PHE* 3.4 31.6 - - + -
417A GLU* 4.5 2.9 - - + +
418A LYS* 3.9 34.5 - - + +
419A PRO 5.3 0.2 - - - +
420A VAL* 3.5 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LYS* 4.3 21.8 - - + +
335A PHE 3.3 18.8 - - - +
336A HIS* 3.6 41.1 - - + -
337A ILE* 4.1 0.7 - - - -
344A VAL* 1.3 83.3 - - - +
346A GLY* 1.3 56.6 + - - +
416A PHE* 3.5 4.5 - - - -
417A GLU* 2.9 54.8 + - - +
434A ASP* 5.2 5.8 - - - +
440B ASN* 5.6 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA 3.8 0.3 - - - +
334A LYS* 3.4 4.6 - - - +
335A PHE 3.0 31.6 + - - +
337A ILE* 3.4 16.4 - - - +
345A MET* 1.3 76.8 - - - +
347A ARG* 1.3 65.5 + - - -
348A LEU* 4.3 1.3 - - - +
414A VAL* 4.4 3.6 - - - -
415A GLU 3.2 15.5 - - - -
416A PHE* 4.3 0.9 - - - -
417A GLU* 4.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LYS* 2.8 32.1 + - - +
333A ALA 3.4 7.4 - - - +
334A LYS* 3.6 24.3 - - - +
346A GLY* 1.3 74.1 - - - -
348A LEU* 1.3 62.3 + - - +
413A LEU 3.2 5.2 - - - +
414A VAL* 3.6 1.9 - - - -
415A GLU* 3.1 40.7 + - + +
417A GLU* 4.7 15.4 + - + +
----------------------------------------------------------
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