Contacts of the strand formed by residues 348 - 351 (chain A) in PDB entry 2J0U
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 LEU 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 4.7 12.3 - - + -
272A TYR* 3.8 32.1 - - + +
279A GLN 4.2 3.8 + - - +
280A ALA* 2.9 41.6 - - + +
281A VAL 3.2 0.2 + - - -
346A VAL* 3.2 5.6 + - - +
347A SER* 1.3 82.5 + - - +
349A ILE* 1.3 78.7 + - - +
350A ILE* 4.1 13.5 - - + -
376A VAL* 3.4 25.8 - - + +
378A VAL* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 6.0 1.3 - - + -
281A VAL* 3.4 16.8 - - + +
283A PHE* 4.0 16.6 - - + -
343A VAL 5.8 3.6 - - - +
344A PRO 5.8 0.4 - - - +
346A VAL* 4.2 24.0 - - + +
347A SER 6.0 0.2 - - - -
348A LEU* 1.3 83.2 - - - +
350A ILE* 1.3 67.9 + - - +
351A ASN* 5.0 0.4 - - - +
364A ARG 3.7 21.3 - - - +
365A ILE* 3.6 38.8 - - + -
366A GLY 5.1 1.3 - - - +
376A VAL 2.8 10.5 + - - +
377A ALA* 3.1 5.5 - - - -
378A VAL 2.9 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 3.6 25.4 - - + -
271A LEU* 4.2 22.0 - - + -
272A TYR* 5.8 3.1 - - + -
280A ALA* 5.6 3.6 - - + -
281A VAL 2.8 11.3 + - - +
282A ILE* 3.4 21.9 - - + -
283A PHE* 2.9 28.1 + - - +
348A LEU* 4.1 14.1 - - + -
349A ILE* 1.3 81.9 - - - +
351A ASN* 1.3 67.4 + - - +
352A TYR 3.7 11.7 - - - +
378A VAL* 3.3 20.9 - - + +
380A PHE* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 4.0 4.3 - - - -
349A ILE* 5.2 0.2 - - - -
350A ILE* 1.3 73.9 - - - +
352A TYR* 1.3 63.4 + - - +
353A ASP 3.2 16.7 + - - +
354A LEU* 4.4 4.5 - - + -
355A PRO* 4.7 1.1 - - - +
361A TYR* 3.9 5.1 - - - -
364A ARG* 3.1 37.6 + - - +
365A ILE* 3.2 28.5 - - - +
377A ALA* 4.7 0.6 - - - +
378A VAL 2.7 10.7 + - - +
379A ASN* 2.7 33.8 + - - +
380A PHE* 2.9 27.9 + - - +
----------------------------------------------------------
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