Contacts of the strand formed by residues 350 - 357 (chain H) in PDB entry 5LS6
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 VAL 350 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G PHE* 4.9 5.2 - - + -
167G ASN* 2.7 40.3 + - - +
169G GLU* 4.5 3.3 - - - +
299H PHE* 3.5 23.3 - - + -
301H THR* 3.9 21.3 - - + +
303H ASP* 4.5 17.5 - - + +
304H ILE* 3.8 22.7 - - + -
331H TRP* 4.2 5.2 - - + -
332H LYS 3.4 9.4 - - - +
334H GLY 3.0 11.5 - - - +
335H LYS* 5.0 0.3 - - - -
348H SER 5.5 0.9 - - - +
349H ASN* 1.3 82.0 - - - +
351H THR* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 351 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ARG* 4.2 23.3 - - - +
167G ASN* 4.7 1.8 - - - +
169G GLU* 4.7 9.8 + - - +
331H TRP* 3.1 5.4 - - - -
332H LYS* 2.8 50.3 + - - +
334H GLY 2.8 16.9 + - - -
335H LYS* 3.4 1.4 - - - -
336H MET* 3.3 25.4 + - - -
350H VAL* 1.3 74.0 + - - +
352H ILE* 1.3 66.7 + - - +
353H LEU* 3.6 17.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 352 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ARG* 5.6 2.0 - - - +
34G ARG* 5.5 2.4 - - - -
38G VAL* 5.3 1.9 - - - +
165G PHE* 3.5 39.2 - - + -
167G ASN* 5.6 0.2 - - - +
304H ILE* 3.5 35.2 - - + +
329H VAL* 3.7 20.0 - - + -
331H TRP* 3.9 2.9 - - + -
350H VAL* 5.3 0.7 - - + -
351H THR* 1.3 78.9 - - - +
353H LEU* 1.3 61.2 + - - +
354H GLY 3.4 22.0 - - - +
355H ARG* 3.3 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL* 4.3 19.5 - - + +
41G MET* 4.5 13.0 - - + -
42G PHE* 3.5 31.0 - - + -
318H LEU* 3.7 38.6 - - + -
330H CYS* 2.8 19.2 + - - +
331H TRP* 4.6 2.0 - - - -
332H LYS* 4.3 3.6 - - + -
336H MET* 3.5 35.0 - - + -
351H THR* 3.6 20.1 + - + +
352H ILE* 1.3 80.7 - - - +
354H GLY* 1.3 56.5 + - - +
396H PRO* 5.3 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G PHE* 4.3 0.9 - - - -
329H VAL* 3.6 1.4 - - - +
330H CYS* 3.0 27.5 + - - +
352H ILE* 3.4 14.5 - - - +
353H LEU* 1.3 78.1 - - - +
355H ARG* 1.3 68.8 + - - +
356H PHE* 5.5 0.4 - - - -
396H PRO* 5.6 4.9 - - - -
397H HIS* 4.3 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 355 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ARG* 3.5 25.0 - - - +
164G GLY 5.3 2.2 + - - -
165G PHE* 4.1 26.7 - - - +
304H ILE 5.3 3.0 + - - -
327H ALA* 4.3 12.1 - - + +
328H ILE 3.7 6.1 - - - -
329H VAL* 4.3 19.5 - - + +
352H ILE* 3.3 29.8 - - - +
354H GLY* 1.3 77.1 - - - +
356H PHE* 1.3 63.9 + - - +
357H ASP* 4.0 15.2 + - - +
396H PRO* 6.1 0.2 - - - +
397H HIS* 2.7 37.5 + - - +
398H LYS 4.1 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G PHE* 6.1 2.2 - + - -
315H LEU* 5.6 1.1 - - + -
320H LEU* 4.0 21.1 - - + -
327H ALA* 3.2 3.5 - - - -
328H ILE* 2.9 55.0 + - + +
330H CYS* 4.6 9.9 - - + -
355H ARG* 1.3 73.3 - - - +
357H ASP* 1.3 65.5 + - - +
358H TYR* 3.7 4.3 - - - -
377H LEU* 4.2 13.0 - - + -
389H TRP* 3.5 52.5 - + + +
390H ASP 4.5 9.4 - - - -
391H LEU* 4.0 18.6 - - + -
397H HIS* 3.4 45.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 357 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H ASN 3.8 7.9 - - - +
327H ALA* 4.2 4.1 - - - +
355H ARG* 4.0 20.0 + - - +
356H PHE* 1.3 74.2 - - - +
358H TYR* 1.3 64.2 + - - +
387H TYR* 4.4 4.5 - - - -
389H TRP* 3.3 20.3 + - - +
398H LYS* 5.2 18.2 + - - +
401H CYS* 5.5 1.0 - - - +
----------------------------------------------------------
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