Contacts of the strand formed by residues 346 - 351 (chain A) in PDB entry 1UA4
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 TYR 346 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PRO* 3.9 13.7 - - + -
318A VAL* 2.8 30.1 + - - +
320A PRO* 3.4 14.7 - - + +
323A VAL* 3.6 13.3 - - - +
341A PHE* 4.0 7.6 - + - -
342A HIS* 4.2 0.2 - - - -
343A THR* 3.2 47.0 + - + +
345A GLY* 1.3 82.7 - - - +
347A TYR* 1.3 76.1 + - - +
348A LEU* 3.6 27.1 - - + -
396A ALA* 5.0 1.1 - - + -
399A VAL* 3.8 29.6 - - + -
423A PHE* 3.6 19.7 - + + -
424A ILE 3.2 16.4 - - - +
426A THR* 3.4 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A HIS* 3.9 19.5 - + + +
341A PHE* 3.3 11.0 - - - +
342A HIS* 3.6 13.2 - - + -
343A THR 4.1 0.9 - - - -
346A TYR* 1.3 84.9 - - - +
348A LEU* 1.3 70.5 + - - +
362A LEU* 3.8 11.4 - - + -
365A ALA* 4.2 0.7 - - + -
366A ALA* 3.5 30.9 - - + +
369A ALA* 3.3 15.8 - - - +
423A PHE* 3.6 0.5 - - - -
424A ILE* 3.3 48.6 + - + +
426A THR* 3.5 17.9 - - + +
442A ILE* 3.0 38.3 - - + +
1456A AMP 3.5 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 4.0 9.0 - - + +
323A VAL* 3.7 23.8 - - + -
324A THR* 3.7 22.9 - - - +
327A MET* 4.2 9.9 - - - -
339A ILE 4.4 0.2 - - - -
340A HIS* 3.6 3.3 - - - -
341A PHE* 2.8 39.4 + - + +
346A TYR* 3.6 21.8 - - + -
347A TYR* 1.3 81.2 - - - +
349A ALA* 1.3 61.4 + - - +
362A LEU* 4.4 2.2 - - - -
403A LEU* 3.9 9.0 - - + -
421A ILE* 4.4 11.2 - - + -
422A ALA 3.2 6.5 - - - +
423A PHE* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A MET* 4.2 0.7 - - - -
338A ARG* 5.6 3.6 - - - +
339A ILE 3.2 8.7 - - - +
340A HIS* 4.7 4.5 - - + -
348A LEU* 1.3 76.4 - - - +
350A LEU* 1.3 58.7 + - - +
351A THR* 4.0 5.4 + - + +
358A VAL* 3.7 27.5 - - + +
362A LEU* 3.8 21.3 - - + -
420A GLN 3.5 4.2 - - - +
421A ILE* 3.6 3.0 - - - +
422A ALA* 2.8 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR* 4.9 2.9 - - + -
327A MET* 3.5 53.0 - - + +
328A LEU* 3.9 19.3 - - + +
331A ALA* 4.2 13.7 - - + -
337A LYS 3.9 0.7 - - - +
338A ARG* 3.5 1.4 - - - -
339A ILE* 2.9 36.4 + - + +
349A ALA* 1.3 72.6 - - - +
351A THR* 1.3 61.9 + - - +
416A VAL* 3.9 19.3 - - + -
419A TYR* 3.6 29.2 - - + -
420A GLN 3.4 6.3 - - - +
421A ILE* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LYS 3.3 4.5 - - - -
338A ARG* 3.8 15.5 - - + -
349A ALA* 4.7 1.2 + - + -
350A LEU* 1.3 83.2 - - - +
352A GLU* 1.3 61.2 + - - +
353A TYR* 2.7 59.3 + - + +
358A VAL* 4.2 18.3 - - + +
419A TYR* 3.3 8.7 - - - -
420A GLN* 2.9 46.2 + - - +
----------------------------------------------------------
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