Contacts of the strand formed by residues 359 - 365 (chain B) in PDB entry 3I8E
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 359 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU* 3.8 15.3 - - + +
357B GLY 2.7 16.1 + - - +
358B PRO* 1.3 69.1 - - - +
360B VAL* 1.3 56.5 + - - +
361B ASP 3.6 19.7 - - - +
362B MET* 4.0 13.5 - - - -
377B THR* 3.7 24.5 - - + -
378B CYS 3.5 3.1 - - - -
379B SER* 4.6 2.2 - - - +
1005B ASN* 2.6 33.2 + - - +
1006B VAL* 4.4 2.0 - - + -
1031B GLY* 4.0 21.5 - - - -
1032B THR 3.3 15.9 + - - +
1035B GLY* 4.0 19.7 - - - +
1037B ILE* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B PRO* 3.8 10.8 - - + +
359B ILE* 1.3 74.5 - - - +
361B ASP* 1.3 61.7 + - - +
378B CYS* 2.9 14.9 + - + +
380B GLY 4.5 7.9 - - - +
721B PRO 3.7 16.6 - - - +
722B ARG* 3.2 37.0 - - - +
723B LYS* 5.0 1.9 - - - +
1005B ASN* 3.8 18.1 - - - +
1006B VAL* 4.3 3.5 - - - +
162D GLU* 3.3 37.6 - - + +
163D LEU* 4.3 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ILE* 3.4 4.1 - - - +
360B VAL* 1.3 78.7 - - - +
362B MET* 1.3 86.2 + - - +
378B CYS* 2.8 33.5 + - + +
722B ARG 3.6 15.7 - - - +
723B LYS* 3.2 34.1 - - + +
724B ILE* 3.1 28.8 + - - +
1006B VAL* 3.7 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ILE* 4.0 9.6 - - + -
361B ASP* 1.3 92.4 + - - +
363B CYS* 1.3 67.1 + - - +
375B LEU* 4.0 21.5 - - + -
376B VAL 3.4 9.0 - - - +
377B THR* 3.4 24.2 - - + -
724B ILE* 4.0 7.1 - - - +
1006B VAL* 3.9 18.1 - - + +
1008B CYS* 4.1 13.7 - - - +
1029B LEU* 3.8 42.8 - - + +
1030B PHE* 4.0 2.2 - - - +
1031B GLY* 3.9 29.4 - - - +
1037B ILE* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B MET* 1.3 81.1 - - - +
364B VAL* 1.3 64.3 + - - +
365B VAL* 3.8 23.2 + - - -
375B LEU* 3.6 5.8 - - - +
376B VAL* 3.0 43.3 + - - +
724B ILE* 4.4 19.3 - - + +
726B TYR* 4.7 11.2 - - - +
733B PHE* 4.5 7.2 - - - -
1008B CYS* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B CYS* 1.3 78.3 - - - +
365B VAL* 1.3 64.0 + - - +
366B ASP* 4.7 4.8 - - - +
373B GLY* 3.8 22.0 - - - +
374B GLN 3.4 15.0 - - - +
375B LEU* 3.8 15.7 - - + -
1008B CYS* 3.8 20.1 - - - -
1009B HIS 3.9 3.8 - - - +
1010B GLY* 3.8 20.4 - - - -
1011B SER 4.2 14.8 - - - +
1012B LEU* 5.6 0.7 - - + -
1029B LEU* 3.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B CYS* 3.8 12.9 + - - -
364B VAL* 1.3 78.8 - - - +
366B ASP* 1.3 65.8 + - - +
367B LEU* 3.3 28.6 + - + +
374B GLN* 2.8 36.1 + - - +
376B VAL* 4.4 7.0 - - + -
726B TYR* 3.5 58.3 - - + -
733B PHE* 3.7 16.2 - - + -
----------------------------------------------------------
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