Contacts of the strand formed by residues 364 - 371 (chain C) in PDB entry 3IW4
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 364 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LEU* 4.4 9.0 - - + -
355C LEU* 4.2 19.1 - - + -
356C ALA 3.4 7.2 - - - +
357C ASP* 3.9 22.2 - - + +
362C GLU 3.6 16.4 + - - +
363C GLU* 1.3 85.0 - - - +
365C TYR* 1.3 71.6 + - - +
418C GLU* 5.4 0.2 - - - -
419C TYR* 3.8 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C PHE* 3.9 15.0 - + + -
355C LEU* 3.3 10.6 - - - +
356C ALA 2.7 37.3 + - - +
358C ARG* 3.3 47.5 + - + -
363C GLU* 3.3 35.5 + - + -
364C LEU* 1.3 79.0 - - - +
366C ALA* 1.3 61.8 + - - +
367C ILE* 4.3 6.5 - - + -
404C HIS* 4.0 19.1 + + + -
416C VAL* 3.7 23.8 - - + -
417C MET 3.3 20.6 - - - +
418C GLU* 4.9 0.4 - - - -
419C TYR* 4.2 3.6 - - - -
663C PHE* 3.8 23.8 - + - -
665C HIS* 3.5 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LEU* 3.5 18.4 - - + -
353C VAL* 4.1 7.6 - - + -
354C MET 3.4 4.7 - - - -
365C TYR* 1.3 74.1 - - - +
367C ILE* 1.3 61.7 + - - +
368C LYS 4.0 0.9 - - - -
417C MET* 2.8 39.8 + - + +
418C GLU 3.7 3.9 + - - +
419C TYR* 4.2 1.2 - - - +
901C LW4 3.2 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C LEU* 6.3 0.9 - - + -
339C PHE* 3.8 32.5 - - + -
341C PHE* 4.7 8.3 - - + -
352C LYS 3.6 0.2 - - - +
353C VAL* 4.4 1.1 - - - -
354C MET* 2.8 42.3 + - + +
356C ALA* 3.5 31.4 - - + -
365C TYR* 4.2 8.3 - - + +
366C ALA* 1.3 79.4 - - - +
368C LYS* 1.3 67.6 + - - +
369C ILE* 3.5 7.9 + - + +
407C PHE* 5.9 0.9 - - + -
414C TYR* 4.1 23.1 - - + -
415C PHE 3.2 13.7 - - - +
416C VAL* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C SER 5.4 0.2 + - - -
350C PHE* 3.2 34.3 + - - +
352C LYS 3.2 9.6 - - - +
353C VAL* 4.3 5.0 - - + +
366C ALA 4.0 1.4 + - - -
367C ILE* 1.3 72.5 - - - +
369C ILE* 1.3 67.8 + - - +
370C LEU* 3.8 30.9 - - - +
387C GLU* 2.6 34.0 + - - +
413C LEU 3.8 0.3 - - - +
414C TYR* 3.3 5.0 - - - -
415C PHE* 2.9 54.0 + - + -
417C MET* 4.9 1.2 - - + +
481C ASP* 5.5 0.6 + - - -
483C GLY* 5.4 2.0 - - - -
901C LW4 3.6 29.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C PHE* 3.8 27.4 - - + -
352C LYS* 2.8 45.6 + - + +
354C MET* 4.3 15.5 - - + -
367C ILE* 3.8 11.9 - - + +
368C LYS* 1.3 77.5 - - - +
370C LEU* 1.3 76.8 + - - +
371C LYS* 6.1 0.2 - - + -
412C ARG* 4.0 23.8 - - - +
413C LEU 3.4 4.5 - - - +
414C TYR* 3.7 36.1 - - + -
637C LEU* 4.5 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C GLY* 4.0 15.7 - - - -
368C LYS* 3.8 31.6 - - + +
369C ILE* 1.3 87.8 - - - +
371C LYS* 1.3 60.4 + - - +
375C VAL* 3.5 30.5 - - + -
384C THR* 3.7 26.7 - - + +
412C ARG* 3.0 8.7 - - - +
413C LEU* 2.6 46.2 + - + +
415C PHE* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C LYS* 5.1 7.2 - - - +
370C LEU* 1.3 72.8 - - - +
372C LYS* 1.3 66.0 + - - +
373C ASP* 3.2 16.6 - - - +
374C VAL* 2.9 29.0 + - + +
375C VAL* 2.8 22.5 + - - +
411C ASP 3.8 5.4 - - - +
412C ARG* 3.0 34.7 - - + +
638C TPO 2.3 34.5 + - - -
----------------------------------------------------------
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