Contacts of the strand formed by residues 386 - 392 (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 SER 386 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B CYS* 3.9 0.7 - - - -
379B SER* 2.9 37.0 + - - +
380B GLY* 5.0 0.2 - - - -
384B GLU 4.0 4.2 + - - -
385B GLY* 1.3 75.8 - - - -
387B LEU* 1.3 66.9 + - - +
388B ARG* 3.3 29.8 + - - -
714B THR* 4.8 2.2 - - - -
715B VAL 3.4 19.3 - - - -
716B PRO* 4.2 3.4 - - - -
717B LEU* 3.5 14.5 - - - +
721B PRO* 3.4 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 4.8 5.6 - - + -
377B THR 3.3 9.6 - - - +
378B CYS* 4.5 9.0 - - - -
386B SER* 1.3 82.8 - - - +
388B ARG* 1.3 67.1 + - - +
389B ILE* 4.9 2.0 - - + -
714B THR* 3.6 0.2 - - - -
715B VAL* 3.1 42.4 + - + +
717B LEU* 3.6 19.0 - - + +
721B PRO* 5.2 0.2 - - + -
724B ILE* 3.7 30.7 - - + -
733B PHE* 5.5 0.9 - - + -
735B VAL* 4.0 12.3 - - + -
794B ILE* 4.3 21.1 - - + -
799B PHE* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLY* 5.6 1.8 - - - -
330B ASP* 3.1 37.0 + - - +
354B THR* 3.8 17.4 - - - +
355B ASN 3.5 17.4 + - - +
356B LEU* 4.3 11.6 - - + +
375B LEU 3.2 2.1 - - - +
376B VAL* 3.3 3.6 - - - +
377B THR* 2.8 44.0 + - - +
379B SER* 3.4 20.9 - - - +
380B GLY* 6.2 1.0 - - - -
384B GLU 5.0 5.5 + - - -
386B SER* 3.3 20.0 + - - -
387B LEU* 1.3 72.2 - - - +
389B ILE* 1.3 65.8 + - - +
390B ILE* 4.1 1.8 - - + -
712B ILE* 4.0 18.2 - - + +
714B THR* 3.2 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 3.6 14.6 - - + -
374B GLN* 3.5 33.7 - - + +
375B LEU 3.0 4.5 - - - +
376B VAL* 4.1 11.2 - - + -
387B LEU* 4.9 4.5 - - + -
388B ARG* 1.3 80.1 - - - +
390B ILE* 1.3 63.0 + - - +
391B ARG* 5.4 0.7 - - - +
711B HIS* 3.5 1.7 - - - +
712B ILE* 3.3 4.3 - - - -
713B ARG* 2.7 61.7 + - + +
715B VAL* 4.1 12.3 - - + -
799B PHE* 3.5 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU* 4.5 14.1 - - + -
374B GLN* 3.2 9.2 - - - +
375B LEU* 2.7 55.1 + - + +
377B THR* 4.3 15.9 - - + +
388B ARG* 4.9 0.7 - - + -
389B ILE* 1.3 78.5 - - - +
391B ARG* 1.3 64.1 + - - +
710B LEU* 3.9 36.3 - - + -
711B HIS 3.2 6.7 - - - +
712B ILE* 4.1 15.7 - - + -
1012B LEU* 4.3 13.0 - - + +
1037B ILE* 3.4 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 3.1 23.4 + - - -
372B GLN* 4.3 6.3 + - - +
373B GLY 5.4 0.2 - - - -
374B GLN* 3.1 33.3 - - - +
389B ILE* 5.4 0.7 - - + +
390B ILE* 1.3 74.2 - - - +
392B ASN* 1.3 71.0 + - - +
393B GLY 3.4 17.2 + - - +
395B GLY* 5.1 2.5 - - - +
672B ASN* 4.1 8.5 - - - +
705B ASP* 2.9 33.9 + - - -
710B LEU* 3.5 3.2 - - - -
711B HIS* 2.8 75.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLN* 5.2 3.3 - - - +
373B GLY 5.3 1.0 + - - -
390B ILE* 4.2 0.8 - - - +
391B ARG* 1.3 75.0 - - - +
393B GLY* 1.3 63.6 + - - +
670B ASN* 4.6 6.8 + - - +
672B ASN* 2.9 21.8 + - - +
709B LYS* 3.4 29.5 + - - +
710B LEU* 3.3 25.7 - - + +
1012B LEU* 3.3 38.2 + - + +
1013B VAL* 4.4 10.4 - - + +
1140B HIS* 3.5 28.1 + - - -
----------------------------------------------------------
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