Contacts of the strand formed by residues 386 - 393 (chain A) in PDB entry 3HS0
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A PHE* 4.7 0.9 - - - -
384A ALA* 3.5 5.9 - - - +
385A GLN* 1.3 81.7 + - - +
387A LEU* 1.3 63.8 + - - +
388A PRO* 3.7 9.4 - - - +
409A THR* 5.1 6.8 - - - +
410A ALA 3.9 4.3 - - - -
411A ILE* 4.1 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A PHE* 4.1 21.5 - - + -
338A TYR* 5.0 4.0 - - + -
362A PHE* 4.0 23.6 - - + -
378A LEU* 5.3 0.4 - - + -
380A ILE* 3.9 40.2 - - + -
381A PRO* 4.9 7.6 - - + -
384A ALA* 5.2 4.7 - - + -
386A SER* 1.3 76.4 + - - +
388A PRO* 1.3 74.3 - - + +
389A ILE* 4.1 21.2 + - + +
409A THR* 3.1 6.2 - - - -
410A ALA* 2.7 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PHE* 4.0 13.9 - - - -
386A SER* 3.7 9.0 - - - +
387A LEU* 1.3 91.6 - - + +
389A ILE* 1.3 69.2 + - - +
408A MET 3.5 6.1 - - - +
409A THR* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 4.5 2.0 - - + -
338A TYR* 3.7 32.1 - - + -
340A LEU* 3.5 30.7 - - + -
359A SER* 4.2 11.9 - - - +
362A PHE* 4.8 5.8 - - + -
378A LEU* 3.8 18.4 - - + -
387A LEU* 4.3 19.1 - - + +
388A PRO* 1.3 80.6 - - + +
390A THR* 1.3 65.1 + - - +
391A VAL* 4.3 4.5 - - + -
407A SER* 3.3 4.8 - - - -
408A MET* 2.9 52.7 + - + +
410A ALA* 5.3 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL 4.0 0.2 - - - +
359A SER* 3.3 27.3 + - - -
360A GLU 4.3 2.0 + - - +
361A ALA* 5.6 0.4 + - - +
362A PHE* 5.9 0.6 - - - -
389A ILE* 1.3 73.5 + - - +
391A VAL* 1.3 69.7 + - - +
392A ARG* 4.4 3.3 + - + +
405A THR* 4.4 9.4 - - - +
406A LYS 3.8 4.7 - - - +
407A SER* 2.7 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 3.4 20.6 - - + +
325A PHE* 4.2 17.2 - - + -
340A LEU* 3.8 29.2 - - + -
342A VAL* 3.8 24.7 - - + -
357A VAL* 4.1 9.4 - - + -
358A VAL 3.5 11.9 - - - +
359A SER* 4.3 6.5 - - - -
376A LEU* 5.4 2.0 - - + -
389A ILE* 4.4 1.3 - - + -
390A THR* 1.3 81.7 - - - +
392A ARG* 1.3 70.1 + - - +
405A THR* 3.5 2.6 + - - -
406A LYS 3.2 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 3.7 6.7 - - - -
357A VAL* 3.5 3.2 - - - -
358A VAL* 3.0 45.9 + - + +
360A GLU* 3.1 32.6 + - + +
390A THR* 5.0 3.3 - - + +
391A VAL* 1.3 75.6 - - - +
393A THR* 1.3 87.0 + - - +
394A ASN* 3.2 23.8 + - - +
400A ARG* 3.6 44.4 - - - +
403A GLN* 4.4 8.9 - - + +
404A ALA 3.0 15.5 - - - +
405A THR* 4.2 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A TYR* 4.2 16.4 - - + -
323A ILE* 4.4 11.7 - - + -
344A VAL* 4.4 8.7 - - + -
355A VAL* 3.5 29.8 - - + -
356A PRO 3.5 4.5 - - - +
357A VAL* 4.2 9.6 - - + +
392A ARG* 1.3 96.4 + - - +
394A ASN* 1.3 62.1 + - - +
395A HIS 4.7 0.4 - - - -
403A GLN* 3.2 20.2 + - - +
404A ALA* 2.7 36.6 + - + +
----------------------------------------------------------
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