Contacts of the strand formed by residues 467 - 472 (chain A) in PDB entry 1SIW
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 467 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU* 5.2 5.2 - - - +
459A ARG* 3.1 36.9 - - - +
460A LEU 2.7 21.5 + - - -
461A GLN* 3.8 13.7 + - - +
462A LEU* 4.3 4.8 - - - +
466A SER* 1.3 81.3 - - - +
468A ALA* 1.3 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A MET* 4.2 25.4 - - + -
342A LEU 5.1 6.3 - - - +
344A GLU* 6.0 1.3 - - - -
458A LYS 3.9 0.3 - - - +
459A ARG* 3.4 9.7 - - - +
460A LEU* 2.9 33.1 + - + +
462A LEU* 4.3 11.2 - - + +
467A THR* 1.3 81.5 + - - +
469A LEU* 1.3 67.6 + - - +
470A VAL* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A MET* 3.5 1.7 - - - +
342A LEU* 2.8 48.5 + - + +
349A TYR* 3.5 44.9 - - + +
425A GLU* 4.0 10.1 - - - +
427A ALA* 4.1 15.0 - - + -
457A VAL* 3.8 20.2 - - + -
458A LYS 3.8 0.7 - - - -
459A ARG* 3.4 51.1 - - + +
468A ALA* 1.3 74.8 - - - +
470A VAL* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.3 20.9 - - + -
340A VAL 3.2 11.9 - - - +
341A MET* 4.3 17.0 - - + -
342A LEU* 4.7 0.9 - - - +
355A LEU* 4.5 10.1 - - + -
377A PHE* 4.7 2.7 - - + -
419A LEU* 3.7 2.4 - - - +
457A VAL* 3.6 4.3 - - - -
458A LYS* 3.1 41.5 + - + +
460A LEU* 3.5 34.8 - - + -
462A LEU* 6.4 0.9 - - + -
468A ALA* 4.6 5.6 - - + +
469A LEU* 1.3 81.8 - - - +
471A THR* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.3 6.1 - - - -
340A VAL 2.5 43.0 + - - +
342A LEU* 4.1 14.6 - - + -
419A LEU* 3.8 9.0 - - - -
455A LEU* 4.4 5.6 - - + +
456A PRO 3.8 11.3 + - - -
457A VAL* 4.8 7.6 - - - -
470A VAL* 1.3 75.5 - - - +
472A THR* 1.3 67.3 + - - +
475A ASP* 3.5 23.2 + - - +
476A LEU* 3.3 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET 3.4 9.0 - - - -
337A PRO* 3.8 9.6 - - + +
338A MET 3.3 4.9 - - - -
339A LEU* 3.7 19.7 - - + -
340A VAL* 4.8 1.3 - - - -
377A PHE* 5.5 1.1 - - + +
416A GLN 4.8 2.5 - - - +
417A LEU 2.9 26.5 + - - +
419A LEU* 4.1 14.1 - - + +
471A THR* 1.3 82.5 + - - +
473A VAL* 1.3 65.6 + - - +
474A TYR* 3.4 0.2 - - - +
475A ASP* 2.7 33.9 + - - +
476A LEU* 3.0 22.6 + - - +
----------------------------------------------------------
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