Contacts of the strand formed by residues 320 - 326 (chain B) in PDB entry 3UAJ
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 THR 320 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B MET* 3.8 23.3 - - - +
313B ALA 3.4 3.8 - - - +
314B GLU* 4.0 9.9 - - + -
318B GLY 4.2 0.2 - - - +
319B THR* 1.3 77.0 - - - +
321B VAL* 1.3 61.8 + - - +
367B ILE 3.7 1.0 - - - +
368B GLU* 3.4 1.8 - - - -
369B LEU* 2.7 60.5 + - - +
371B PRO* 3.6 16.0 - - + +
378B ILE* 5.6 0.7 - - - +
391B TRP* 3.5 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TRP* 3.9 30.0 - - + -
108A PHE* 4.3 10.8 - - + -
1B MET* 3.8 23.6 - - + -
4B VAL* 3.7 26.9 - - + -
312B MET* 3.4 3.6 - - - -
313B ALA 3.0 28.5 + - - -
315B THR* 3.9 15.7 - - + -
320B THR* 1.3 75.8 - - - +
322B VAL* 1.4 62.7 + - - +
366B ASN* 4.4 2.7 - - - +
367B ILE 3.4 8.1 - - - +
368B GLU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TRP* 4.4 3.6 - - - -
308B ILE* 3.9 22.0 - - + -
310B LYS 3.7 14.8 - - - +
312B MET* 3.8 27.4 - - + +
321B VAL* 1.4 75.5 - - - +
323B LYS* 1.3 66.2 + - - +
324B VAL* 4.2 7.2 - - + -
337B ILE* 5.7 1.6 - - + -
365B THR 3.5 2.9 - - - +
366B ASN* 3.8 1.6 - - - -
367B ILE* 3.0 43.0 + - + +
369B LEU* 3.9 26.5 - - + -
380B ILE* 4.9 11.4 - - + -
389B LEU* 5.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TRP* 3.7 23.0 - - + -
308B ILE* 3.5 6.9 - - - +
309B ASP* 2.8 34.9 + - + +
310B LYS* 3.5 35.0 + - + +
322B VAL* 1.3 74.5 - - - +
324B VAL* 1.3 58.3 + - - +
364B VAL* 3.8 24.3 - - + +
365B THR 3.4 2.0 - - - -
366B ASN* 2.8 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PHE* 4.0 25.2 - - + -
307B SER 3.4 9.9 - - - +
308B ILE* 3.8 21.1 - - + -
309B ASP* 4.7 0.4 - - - -
322B VAL* 4.6 7.4 - - + -
323B LYS* 1.3 78.6 - - - +
325B LYS* 1.3 59.4 + - - +
326B TYR 4.2 0.2 + - - -
335B VAL* 4.4 3.8 - - + -
337B ILE* 5.2 0.7 - - + -
363B SER 3.5 1.9 - - - +
364B VAL* 3.4 4.9 - - - -
365B THR* 3.0 31.5 + - - +
367B ILE* 3.8 26.0 - - + -
380B ILE* 4.3 30.7 - - + -
387B LEU* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LYS 4.0 0.2 - - - +
306B PHE* 3.4 8.1 - - - -
307B SER* 2.8 42.9 + - - +
309B ASP* 4.6 15.7 - - + +
324B VAL* 1.3 71.7 - - - +
326B TYR* 1.3 62.8 + - - +
327B GLU* 3.8 20.6 + - - +
362B ASN* 3.7 50.5 + - + +
363B SER 3.4 5.6 - - - +
364B VAL* 4.5 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B CYS* 3.7 14.1 - - + -
303B SER* 3.8 6.8 + - - -
304B GLY* 3.5 27.2 + - - -
305B LYS 3.9 2.9 - - - -
306B PHE* 3.4 32.4 - + + -
325B LYS* 1.3 70.9 - - - +
327B GLU* 1.3 62.4 + - - +
328B GLY* 3.5 27.4 - - - -
329B ALA 3.6 2.3 + - - -
330B GLY* 3.1 23.0 + - - -
331B ALA* 3.6 36.1 - - + -
333B CYS* 3.7 8.8 - - - -
358B ALA* 3.9 16.4 - - + -
360B ASN 4.1 9.4 - - - +
361B THR* 4.4 1.1 - - - -
362B ASN* 2.9 32.6 + - - +
363B SER 3.3 12.0 + - - +
----------------------------------------------------------
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