Contacts of the strand formed by residues 318 - 322 (chain K) 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 LEU 318 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J MET* 4.7 10.8 - - + +
42J PHE* 4.1 19.1 - - + +
45J ASN* 3.9 26.2 - - + +
314K TRP* 3.5 10.6 - - - -
315K LEU* 3.2 31.1 + - + +
317K ASP* 1.3 81.5 - - + +
319K ILE* 1.3 65.3 + - - +
330K CYS* 3.6 18.6 - - - -
331K TRP 3.8 3.8 - - - +
332K LYS* 3.6 26.9 - - + -
353K LEU* 3.3 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252K MET* 3.5 22.7 - - + -
260K LEU* 4.5 0.4 - - + -
312K VAL* 3.7 26.5 - - + -
313K ARG 3.8 3.1 - - - +
314K TRP* 3.3 45.3 - - + -
318K LEU* 1.3 75.2 - - - +
320K LEU* 1.3 67.1 + - - +
321K SER* 4.4 0.4 - - - -
329K VAL 3.4 0.9 - - - +
330K CYS* 3.2 7.0 - - - -
331K TRP* 2.9 81.5 + - + +
333K PRO* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312K VAL* 3.3 3.5 - - - +
313K ARG* 3.0 34.8 + - + +
315K LEU* 3.6 24.2 - - + +
319K ILE* 1.3 74.1 - - - +
321K SER* 1.3 62.1 + - - +
328K ILE* 4.0 8.1 - - + -
329K VAL 3.4 2.0 - - - -
330K CYS* 3.6 33.7 - - + +
356K PHE* 3.8 21.3 - - + -
368K PHE* 3.7 21.8 - - + -
370K MET* 3.5 37.7 - - + -
377K LEU* 4.8 7.2 - - + -
391K LEU* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 321 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260K LEU* 3.6 25.0 - - - +
305K HIS* 2.5 34.2 + - - -
309K VAL* 4.0 2.9 - - - -
311K CYS 3.4 12.8 - - - -
312K VAL* 4.0 1.3 - - - -
320K LEU* 1.3 76.3 - - - +
322K LYS* 1.3 60.7 + - - +
328K ILE* 3.6 1.8 - - - +
329K VAL 3.0 27.9 + - - +
331K TRP* 3.0 21.7 + - - -
368K PHE* 4.3 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305K HIS* 3.7 6.3 - - - -
309K VAL* 3.4 6.3 - - - +
310K ASP* 3.1 54.7 + - - +
311K CYS* 3.4 7.3 + - + -
321K SER* 1.3 76.0 - - - +
323K SER* 1.3 69.9 + - - +
327K ALA 3.7 13.9 - - - +
328K ILE* 3.9 11.0 - - + -
358K TYR* 3.3 23.6 - - - -
361K CYS* 3.8 21.8 - - - -
363K ILE 4.3 3.4 + - - -
366K MET* 3.4 24.9 + - - +
368K PHE* 3.9 22.2 - - + -
379K LEU* 4.2 12.8 - - + -
----------------------------------------------------------
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