Contacts of the strand formed by residues 386 - 390 (chain B) in PDB entry 5H14
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 386 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ALA* 4.0 13.7 - - + -
379B LEU 3.8 6.5 - - - +
380B GLY* 4.7 0.4 - - - -
384B GLY 3.9 0.4 + - - +
385B LYS* 1.3 71.6 - - - +
387B TYR* 1.3 77.5 + - - +
388B VAL* 3.9 2.2 + - + -
403B THR* 3.7 2.2 - - - +
404B LEU* 2.8 53.6 + - + +
413B ILE* 4.3 10.8 - - + -
416B THR* 3.8 22.0 - - + -
425B LEU* 3.7 27.8 - - + -
427B ALA* 3.9 24.0 - - + -
437B TRP* 4.1 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B TYR* 3.9 26.7 - + + -
359B SER* 2.8 37.0 + - - -
360B GLN* 5.1 0.9 + - - -
378B ALA* 3.2 4.5 - - - -
379B LEU* 2.8 48.1 + - + +
380B GLY 4.8 0.4 - - - -
381B ASN* 2.8 40.0 + - + -
385B LYS* 4.4 10.9 - - + +
386B LEU* 1.3 73.9 - - - +
388B VAL* 1.3 61.9 + - - +
389B TRP* 3.6 14.7 - + + -
400B LYS* 3.1 28.7 - - + +
403B THR* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TYR* 5.3 0.2 - - + -
82B PHE* 4.4 10.1 - - + -
376B MET* 4.2 28.5 - - + -
377B LEU 3.2 10.3 - - - +
378B ALA* 4.3 2.7 - - + -
386B LEU* 3.9 6.2 + - + +
387B TYR* 1.3 79.7 - - - +
389B TRP* 1.3 65.1 + - - +
400B LYS* 3.4 8.7 - - - +
401B CYS* 2.9 47.8 + - + +
402B THR 5.1 4.2 + - - +
403B THR* 5.3 0.4 - - - +
404B LEU* 4.2 27.6 - - + -
418B PHE* 4.7 2.2 - - + -
425B LEU* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ILE* 4.2 13.5 - - + -
356B PHE* 3.5 43.5 - + + +
357B ASP 3.5 21.9 + - - +
358B TYR* 3.7 25.6 - + + -
376B MET* 3.4 8.0 - - - +
377B LEU* 2.9 58.9 + - + +
379B LEU* 4.1 17.0 - - + -
387B TYR* 3.6 27.4 - - + -
388B VAL* 1.3 77.0 - - - +
390B ASP* 1.3 61.9 + - - +
391B LEU* 3.5 1.1 + - + -
396B PRO 3.9 5.3 + - - -
399B ALA* 3.4 6.5 - - + +
400B LYS* 3.4 48.8 - - + +
401B CYS* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS 4.4 1.7 - - - +
78B CYS* 3.5 32.1 - - + -
79B LYS 4.3 2.8 + - - -
80B TYR* 3.7 25.2 + - + -
375B LYS 3.6 7.9 - - - +
389B TRP* 1.3 68.6 - - - +
391B LEU* 1.3 60.5 + - - +
392B GLU* 2.9 33.1 + - - +
393B VAL* 3.3 24.9 + - + +
399B ALA* 2.8 31.2 + - - +
401B CYS* 3.6 1.4 - - - -
----------------------------------------------------------
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