Contacts of the strand formed by residues 396 - 404 (chain A) in PDB entry 1IVV
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 ILE 396 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TRP* 3.5 26.5 - - + -
257A LEU* 5.9 0.7 - - + -
260A ILE* 4.3 15.0 - - + -
271A ILE* 3.7 23.1 - - + -
272A ILE* 3.7 32.1 - - + -
388A TRP* 4.7 20.0 - - + -
389A TYR 3.5 9.0 - - - +
390A LEU* 4.2 9.4 - - + -
394A GLY 4.2 2.2 - - - +
395A THR* 1.3 72.3 - - - +
397A GLU* 1.3 63.5 + - - +
512A TYR* 4.4 8.7 - - + -
609A PHE* 6.0 0.4 - - + -
610A LYS* 3.1 3.3 - - - +
611A LEU* 2.7 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TRP* 5.7 0.2 - - - -
370A ARG* 4.0 2.8 + - - -
388A TRP* 3.5 7.8 - - - -
389A TYR* 2.8 56.1 + - + +
391A TYR* 2.4 44.9 + - + -
395A THR* 4.2 0.4 - - + -
396A ILE* 1.3 76.7 - - - +
398A PHE* 1.3 68.9 + - - +
399A GLU* 5.0 6.2 - - - +
517A HIS* 5.4 7.3 + - - -
609A PHE* 3.3 15.3 - - - +
610A LYS* 3.8 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 3.6 24.0 - - + -
386A PHE* 4.0 18.4 - + + -
387A TYR 3.1 31.6 - - - -
388A TRP* 3.5 37.2 - + + -
397A GLU* 1.3 77.7 - - - +
399A GLU* 1.3 68.6 + - - +
400A ALA* 3.7 25.8 - - + -
435A PHE* 4.9 1.6 - + - -
588A PHE* 3.4 35.9 - + - -
608A GLY* 3.2 21.5 - - - -
609A PHE* 3.0 38.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ARG* 4.6 3.5 + - - -
387A TYR* 2.8 43.7 + - - +
389A TYR* 2.6 44.9 + - + +
397A GLU* 5.0 7.4 - - - +
398A PHE* 1.3 79.1 - - - +
400A ALA* 1.3 62.4 + - - +
401A LYS* 3.6 17.8 - - + -
606A THR* 3.3 30.2 + - + +
607A VAL 3.6 10.3 - - - +
608A GLY* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A TYR* 6.3 0.4 - - + -
385A GLY 3.3 7.9 - - - +
386A PHE* 5.5 0.7 - - + -
398A PHE* 3.7 18.0 - - + -
399A GLU* 1.3 72.4 - - - +
401A LYS* 1.3 61.5 + - - +
402A ALA* 4.1 0.6 + - - +
435A PHE* 3.5 43.1 - - + -
588A PHE* 4.7 0.7 - - + -
590A LEU* 5.4 0.2 - - - +
605A ASP 3.8 0.2 - - - +
606A THR* 3.2 7.3 - - - -
607A VAL* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 4.3 5.7 - - + -
383A ASP 3.8 0.7 - - - +
384A TYR* 3.3 8.1 - - - -
385A GLY* 2.8 37.2 + - - +
387A TYR* 3.4 47.1 + - + +
389A TYR* 4.0 4.5 + - - -
399A GLU* 3.6 26.2 + - + -
400A ALA* 1.3 76.4 - - - +
402A ALA* 1.3 60.6 + - - +
403A THR* 4.0 0.6 + - - -
604A VAL* 3.8 25.6 - - + -
605A ASP 3.5 3.4 - - - -
606A THR* 3.7 12.1 - - + -
349B TRP 5.0 3.2 + - - -
350B GLY* 4.5 8.1 - - - -
351B ILE* 4.5 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A DAH 6.0 0.7 - - + -
383A ASP 3.8 3.8 - - - -
384A TYR* 3.9 23.1 - - + -
400A ALA 4.1 0.8 + - - +
401A LYS* 1.3 72.5 - - - +
403A THR* 1.3 59.4 + - - +
433A HIS* 5.1 9.9 - - + +
435A PHE* 5.7 3.4 - - + -
590A LEU* 4.4 14.8 - - + -
602A MET* 3.2 21.5 - - + +
604A VAL* 3.4 3.6 - - - -
605A ASP 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 3.7 20.8 - - - -
382A DAH 3.1 19.7 - - - -
383A ASP 3.0 23.8 + - - +
402A ALA* 1.3 71.8 - - - +
404A GLY* 1.3 61.5 + - - +
601A ILE* 5.3 0.4 - - + -
602A MET* 2.7 32.3 - - - +
604A VAL* 3.5 23.4 - - + +
353B ALA* 3.3 11.2 - - + -
354B LYS 3.3 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASN 3.4 2.7 - - - -
382A DAH 4.2 1.8 - - - -
383A ASP* 3.2 22.4 - - - -
403A THR* 1.3 83.7 - - - +
405A VAL* 1.3 64.8 + - - -
601A ILE* 3.2 8.7 - - - +
602A MET* 3.0 26.0 + - - +
354B LYS 3.3 7.8 + - - -
355B HIS* 3.9 3.6 - - - -
----------------------------------------------------------
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