Contacts of the strand formed by residues 348 - 355 (chain B) in PDB entry 5J2P
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 ASN 348 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.9 18.6 - - + +
314B VAL* 4.4 19.1 - - + +
317B VAL* 3.8 12.4 - - - +
340B GLN* 3.9 8.0 - - - +
341B ILE 3.5 5.4 - - - +
342B TYR* 3.5 24.7 - - - +
346B PHE* 3.5 7.9 + - - +
347B LYS* 1.3 75.5 + - - +
349B LEU* 1.3 62.7 + - - +
350B LYS 4.3 0.9 - - - +
351B THR* 3.4 31.3 - - + +
427B TYR* 3.1 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B VAL* 3.6 27.4 - - + +
318B TYR 4.6 0.4 - - - -
319B TYR* 4.2 33.0 - - + +
325B LEU* 3.7 30.1 - - + -
341B ILE* 2.6 16.5 + - + +
342B TYR* 4.6 2.2 - - - -
343B GLN* 4.1 17.3 - - + +
347B LYS 3.3 3.3 + - - +
348B ASN* 1.3 74.0 - - - +
350B LYS* 1.3 59.7 + - - +
383B TRP* 3.5 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 4.8 12.1 - - - +
240B THR 3.1 28.4 + - - +
241B VAL* 4.2 18.3 - - + +
339B TYR* 3.2 25.7 + - + +
340B GLN* 3.4 1.0 - - - -
341B ILE* 2.9 39.8 + - + +
348B ASN* 3.3 1.2 - - - +
349B LEU* 1.3 81.0 - - - +
351B THR* 1.3 69.6 + - - +
352B GLY* 4.1 9.0 - - - +
378B GLU* 3.6 23.3 + - + +
382B ILE* 4.3 21.3 - - + -
383B TRP* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 3.4 12.1 - - - +
242B GLN* 2.6 48.8 + - - -
243B PRO* 4.7 2.6 - - - +
314B VAL* 6.4 0.4 - - + -
339B TYR 3.5 7.0 - - - -
340B GLN* 3.8 13.0 - - + -
348B ASN* 3.4 35.2 - - + +
350B LYS* 1.3 84.3 - - - +
352B GLY* 1.3 52.6 + - - +
427B TYR* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B THR 4.6 2.7 - - - -
242B GLN* 3.8 13.0 - - - +
338B THR* 3.5 5.4 - - - +
339B TYR* 2.9 55.5 + - - +
350B LYS* 4.1 6.1 - - - -
351B THR* 1.3 75.7 - - - +
353B LYS* 1.3 60.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLN* 3.5 37.1 + - + +
336B GLN* 4.7 16.2 + - - +
337B TRP 3.2 10.3 - - - +
338B THR* 4.3 10.8 - - + -
339B TYR* 3.8 9.6 + - - -
352B GLY* 1.3 75.2 - - - +
354B TYR* 1.3 64.5 + - - +
355B ALA* 4.9 10.6 - - + +
428B GLN* 4.6 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLY 3.4 4.7 - - - +
337B TRP* 2.5 47.2 + + + +
339B TYR* 4.5 11.9 - + + -
353B LYS* 1.3 77.0 - - - +
355B ALA* 1.3 57.1 + - - +
356B ARG* 3.3 41.7 + - + -
367B GLN 3.8 9.9 - - - -
370B GLU* 3.4 23.0 + - + +
371B ALA* 3.6 35.2 - - + -
374B LYS* 4.1 31.4 - - + +
375B ILE* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLY 3.3 5.2 - - - -
336B GLN* 3.3 37.0 - - - +
353B LYS* 4.1 13.7 - - + +
354B TYR* 1.3 74.6 - - - +
356B ARG* 1.3 68.0 + - - +
358B ARG* 6.2 0.2 - - - -
----------------------------------------------------------
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