Contacts of the strand formed by residues 334 - 338 (chain B) in PDB entry 1I43
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 VAL 334 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.2 39.0 - - + +
329B GLU* 4.4 6.5 - - - +
331B HIS* 3.4 22.3 + - + +
332B PRO 3.2 4.0 - - - +
333B LYS* 1.3 82.0 - - - +
335B ARG* 1.3 62.2 + - - +
336B HIS 3.4 13.5 - - - +
337B VAL* 3.4 33.0 - - + -
364B PHE* 4.1 12.8 - - + -
365B GLU 3.7 6.5 - - - +
366B VAL* 5.4 1.3 - - - -
442B LEU* 4.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LYS 3.8 3.0 + - - -
334B VAL* 1.3 74.4 - - - +
336B HIS* 1.3 61.6 + - + +
365B GLU* 2.9 28.9 + - + +
366B VAL 4.6 1.8 - - - +
367B ASP* 2.6 35.1 + - + +
368B GLY* 3.4 24.7 + - - +
420B ASN* 3.6 19.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLU* 5.7 1.3 - - - -
334B VAL* 3.4 2.0 - - - +
335B ARG* 1.3 83.2 - - + +
337B VAL* 1.3 94.5 + - - +
338B TYR* 3.9 29.9 - + - -
344B SER* 5.0 16.4 + - - -
345B HIS* 6.4 0.2 - - - -
346B PRO* 6.1 2.9 - - + -
364B PHE* 3.1 6.9 - - - +
365B GLU* 2.7 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA* 3.9 11.2 - - + +
328B LEU* 3.8 7.0 - - + -
329B GLU* 3.7 33.0 + - + +
334B VAL* 3.4 21.1 - - + -
336B HIS* 1.3 100.2 + - - +
338B TYR* 1.3 67.1 + - - +
339B TYR 4.0 1.4 + - - -
342B LEU* 3.5 32.5 - - + +
344B SER* 5.0 3.5 + - - -
345B HIS* 6.1 1.2 - - - +
362B VAL* 4.3 12.6 - - + -
363B SER 3.5 7.0 - - - +
364B PHE* 3.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE* 3.5 56.5 - + + +
214B LEU* 3.6 7.2 - - + +
215B ARG* 6.4 0.4 - - - -
336B HIS* 3.9 30.4 - + + -
337B VAL* 1.3 72.7 - - - +
339B TYR* 1.3 65.1 + - - +
345B HIS* 4.6 7.6 - + + -
346B PRO* 6.1 3.6 - - + -
362B VAL* 4.0 2.1 - - - +
363B SER* 2.5 55.9 + - - +
364B PHE* 4.2 0.7 - - - -
365B GLU* 3.1 43.5 + - + -
421B LEU* 4.2 2.7 - - + -
----------------------------------------------------------
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