Contacts of the strand formed by residues 341 - 351 (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 SER 341 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334K MET 3.3 11.9 - - - -
335K SER* 2.7 21.9 + - - +
339K GLY 4.9 2.1 + - - -
340K SER* 1.3 79.7 + - - +
342K VAL* 1.3 69.3 + - - +
343K TYR* 4.5 17.1 + - - -
368K ASN* 4.3 6.2 + - - -
460K TRP* 4.3 1.5 - - - -
468K ARG* 5.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332K PHE 3.9 0.2 - - - +
333K ASP* 3.8 0.3 - - - -
334K MET* 3.0 51.0 + - + +
341K SER* 1.3 78.0 - - - +
343K TYR* 1.3 70.7 + - - +
368K ASN* 2.9 34.5 - - + +
369K ALA* 3.4 17.5 - - + -
460K TRP* 3.4 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 343 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266K HIS* 3.1 42.6 - + + +
331K LEU* 4.2 5.6 - - + -
332K PHE 3.2 10.5 - - - +
333K ASP* 3.9 15.7 - - + -
341K SER* 4.5 18.2 + - - -
342K VAL* 1.3 82.6 - - - +
344K ALA* 1.3 58.6 - - - +
345K GLN* 5.1 3.1 - - - +
367K GLY* 4.4 7.4 - - - -
368K ASN* 2.7 31.4 + - - +
369K ALA* 2.7 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331K LEU* 4.3 0.4 - - - +
332K PHE* 2.8 40.6 + - + -
343K TYR* 1.3 82.3 - - - +
345K GLN* 1.3 60.0 + - - +
346K TYR* 4.2 6.1 - - + -
365K TYR* 3.8 16.2 - - + -
366K SER 3.5 11.6 + - - -
369K ALA* 3.8 13.2 - - + -
457K TRP* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 345 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266K HIS* 3.8 24.7 + - - +
270K TRP* 4.1 16.5 - - - -
329K GLN* 4.2 10.3 - - + +
330K VAL 3.0 17.3 - - - +
331K LEU* 3.6 27.2 - - + +
343K TYR* 5.1 2.6 - - + +
344K ALA* 1.3 75.7 - - - +
346K TYR* 1.3 65.0 + - - +
347K ALA 4.3 0.2 + - - -
364K ASP 3.3 10.2 - - - +
365K TYR* 3.6 1.6 - - - -
366K SER* 3.1 39.1 + - - +
475K ARG* 4.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 346 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329K GLN* 3.5 3.7 - - - +
330K VAL* 2.9 41.4 + - + +
332K PHE* 4.6 3.4 - + - -
344K ALA* 4.2 13.9 - - + -
345K GLN* 1.3 80.7 - - - +
347K ALA* 1.3 64.7 + - - +
348K SER 3.1 2.2 + - - +
362K VAL* 3.5 20.0 - - + -
363K GLU 3.4 15.0 - - - +
364K ASP 3.2 4.0 - - - -
365K TYR* 3.5 31.6 - + + -
370K GLY 4.3 0.5 + - - -
371K ASN* 3.3 18.4 - - - -
372K ALA 3.5 1.2 + - - -
373K LEU* 3.2 55.5 + - + +
374K LEU* 3.8 24.9 - - + -
457K TRP* 4.9 2.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329K GLN* 3.4 23.5 - - - +
345K GLN 4.2 0.2 - - - -
346K TYR* 1.3 70.6 - - - +
348K SER* 1.3 58.1 + - - +
363K GLU 2.7 6.3 + - - -
364K ASP* 3.2 32.9 + - + +
477K LYS* 3.6 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327K THR* 3.3 22.6 - - - +
328K GLN 3.3 3.4 - - - -
346K TYR* 3.1 4.9 - - - +
347K ALA* 1.3 81.0 - - - +
349K PHE* 1.3 60.2 + - - +
350K ARG* 5.3 0.9 - - - +
361K TRP 4.1 3.1 + - - -
362K VAL* 3.0 9.5 - - - +
363K GLU* 2.9 49.0 + - - +
364K ASP* 5.4 0.9 - - - -
477K LYS* 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 349 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319K VAL* 3.8 24.5 - - + -
323K THR* 3.6 19.2 - - + +
327K THR* 3.4 1.8 - - - +
328K GLN 2.4 42.8 + - - +
330K VAL* 3.4 36.8 - - + +
332K PHE* 5.4 2.9 - + - -
348K SER* 1.3 75.3 + - - +
350K ARG* 1.3 65.1 + - - +
351K PRO* 4.4 8.1 - - + -
360K LEU* 3.6 23.3 - - + -
361K TRP 3.7 2.0 - - - -
362K VAL* 3.8 11.0 - - + -
423K TRP* 4.5 14.1 - + - -
472K MET* 3.6 28.7 - - + -
474K LEU* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 350 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323K THR* 3.3 27.2 + - - -
324K LYS* 4.2 18.2 + - - +
326K HIS* 5.1 0.6 - - - +
327K THR* 3.0 33.7 + - + +
348K SER* 5.3 1.1 - - - +
349K PHE* 1.3 82.4 - - - +
351K PRO* 1.3 78.4 + - + +
352K GLU* 5.7 2.3 + - - +
360K LEU* 4.9 1.1 - - - -
361K TRP* 2.8 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 351 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316K THR* 5.4 2.2 - - + +
319K VAL* 4.7 7.2 - - + -
320K HIS* 3.0 42.3 + - + +
323K THR* 2.8 35.4 + - + +
324K LYS* 5.8 0.3 + - - +
349K PHE* 4.4 8.3 - - + -
350K ARG* 1.3 92.2 + - - +
352K GLU* 1.3 62.5 + - - +
358K TYR* 3.5 18.2 - - + +
359K ARG 2.8 13.0 - - - +
360K LEU* 4.4 4.0 - - - -
423K TRP* 4.8 11.0 - - + -
----------------------------------------------------------
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