Contacts of the strand formed by residues 328 - 335 (chain K) in PDB entry 1LWU
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 GLN 328 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K HIS* 2.9 34.1 + - - -
322K LEU* 3.5 25.3 + - + +
323K THR* 3.5 27.1 - - + -
326K HIS* 2.8 22.4 + - - +
327K THR* 1.3 77.7 + - - +
329K GLN* 1.3 57.0 + - - +
347K ALA 3.9 1.5 - - - +
348K SER* 3.3 5.7 - - - -
349K PHE* 2.4 39.1 + - + +
474K LEU* 4.0 19.6 - - + +
475K ARG 3.4 12.0 + - - +
476K PRO* 4.1 13.4 - - - +
477K LYS* 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 329 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270K TRP* 3.3 11.6 - - + -
328K GLN* 1.3 73.9 - - - +
330K VAL* 1.3 60.3 + - - +
345K GLN* 4.2 7.8 - - - +
346K TYR 3.5 11.2 - - - +
347K ALA* 3.4 23.0 - - - +
349K PHE* 4.1 1.6 - - - +
474K LEU* 3.5 1.8 - - - -
475K ARG* 2.6 90.5 + - + +
476K PRO 2.9 20.2 + - - +
477K LYS* 3.9 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 330 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270K TRP* 4.2 1.3 - - - -
329K GLN* 1.3 74.9 - - - +
331K LEU* 1.3 73.8 + - - +
332K PHE* 3.3 32.3 - - + -
345K GLN* 3.0 6.4 - - - +
346K TYR* 2.9 50.1 + - + +
349K PHE* 3.4 33.2 - - + +
362K VAL* 4.4 2.2 - - + -
472K MET* 3.6 22.9 - - + -
473K LYS 3.2 12.1 - - - +
474K LEU* 3.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265K SER* 5.1 0.7 - - - -
266K HIS* 3.5 26.2 - - + +
270K TRP* 3.5 47.1 - - + +
330K VAL* 1.3 77.4 - - - +
332K PHE* 1.3 72.4 + - - +
333K ASP* 3.0 25.5 - - - +
343K TYR* 4.2 6.5 - - + -
344K ALA 3.7 1.3 - - - +
345K GLN* 3.6 32.3 - - + +
471K ALA 3.7 1.7 - - - +
472K MET 3.8 0.2 - - - -
473K LYS* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330K VAL* 3.3 24.0 - - + -
331K LEU* 1.3 78.5 - - - +
333K ASP* 1.3 62.3 + - - +
334K MET* 3.9 17.2 - - + +
342K VAL 3.9 0.3 - - - +
343K TYR* 3.2 9.4 - - - -
344K ALA* 2.8 43.0 + - + +
346K TYR* 4.6 2.5 - + - -
349K PHE* 5.4 1.3 - + - -
373K LEU* 3.9 31.4 - - + -
422K TRP* 4.0 17.5 - + - -
432K PRO* 4.5 2.5 - - + -
457K TRP* 3.5 29.2 - + + -
470K MET* 4.5 8.7 - - - -
471K ALA 3.3 7.4 - - - +
472K MET* 3.3 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 333 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265K SER* 3.9 7.4 + - - -
266K HIS* 3.8 17.8 + - - -
331K LEU* 3.0 37.0 - - - +
332K PHE* 1.3 71.6 - - - +
334K MET* 1.3 61.3 + - - +
342K VAL 3.8 4.7 - - - +
343K TYR* 3.9 12.7 - - + -
469K GLN* 3.9 1.2 - - - +
470K MET* 3.4 3.7 + - - -
471K ALA* 3.0 31.7 + - + +
473K LYS* 3.2 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 334 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332K PHE* 3.9 20.9 - - + +
333K ASP* 1.3 75.5 - - - +
335K SER* 1.3 63.1 + - - +
341K SER* 3.3 5.2 - - - -
342K VAL* 3.0 53.7 + - + +
369K ALA* 3.7 11.7 - - + -
457K TRP* 3.3 68.6 - - + -
460K TRP* 4.3 9.9 - - + -
467K MET* 4.0 11.9 - - + +
469K GLN* 2.9 11.4 - - - +
470K MET* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334K MET* 1.3 75.7 + - - +
336K ASP* 1.3 61.2 + - - +
340K SER 3.3 6.3 - - - -
341K SER* 2.7 22.4 + - - +
460K TRP* 4.3 3.8 - - - -
467K MET* 3.6 2.7 - - - +
468K ARG* 2.8 44.4 + - - -
469K GLN* 2.7 43.2 + - - +
----------------------------------------------------------
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