Contacts of the strand formed by residues 432 - 442 (chain B) in PDB entry 4LT6
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 TYR 432 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B SER* 3.3 3.3 - - - -
380B ALA 3.0 34.5 + - - +
381B SER 4.0 10.3 - - - -
382B THR* 3.0 29.2 - - - +
383B GLU* 3.4 34.3 - - + +
386B HIS* 3.3 27.0 + + + +
431B ASN* 1.3 87.8 + - - +
433B VAL* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B THR* 3.7 26.5 - - + -
378B ALA 3.5 2.5 - - - +
379B SER* 3.4 23.6 - - - +
386B HIS* 3.7 3.1 + - - -
421B PRO* 3.7 21.7 - - - +
422B GLY* 4.2 17.4 + - - +
431B ASN* 4.0 19.1 + - - +
432B TYR* 1.3 78.4 - - - +
434B SER* 1.3 69.9 + - - +
435B MET* 5.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B THR* 3.6 1.4 - - - -
378B ALA* 2.8 37.7 + - - -
386B HIS* 3.0 19.4 + - - -
390B VAL* 3.6 21.2 - - - +
419B SER* 4.6 10.8 - - - -
420B PHE 3.2 9.2 + - - -
421B PRO* 5.6 0.2 - - - +
433B VAL* 1.3 75.4 + - - +
435B MET* 1.3 63.3 + - - +
436B TRP* 4.4 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL* 3.5 17.3 - - + -
376B LEU 3.2 12.1 - - - +
377B THR* 4.4 12.8 - - + +
418B GLN 3.9 1.0 - - - +
419B SER* 3.4 8.0 - - - -
420B PHE* 2.7 54.6 + - + +
421B PRO 3.4 19.3 - - - +
422B GLY* 5.1 3.1 - - - -
433B VAL* 5.1 5.4 - - - -
434B SER* 1.3 76.4 - - - +
436B TRP* 1.3 64.7 + - - +
437B PHE* 4.2 9.0 - - + -
495B TYR* 3.4 51.4 - - + +
496B LEU* 4.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 5.2 2.4 - - + +
375B VAL* 3.5 3.3 - - - +
376B LEU* 2.9 63.8 + - + +
378B ALA* 3.7 25.6 - - + -
390B VAL* 4.1 35.9 - - + -
393B VAL* 4.0 12.6 - - + -
394B GLU* 4.0 29.1 + - + +
397B ILE* 3.7 19.7 - - + +
415B VAL* 5.5 2.7 - - + -
416B ASN 3.7 20.4 - - - +
417B PRO* 4.2 8.1 + - + -
418B GLN 3.8 11.2 - - - -
419B SER* 3.8 22.4 - - - +
434B SER* 4.4 8.1 - - - -
435B MET* 1.3 77.6 - - - +
437B PHE* 1.3 72.0 + - - +
438B LEU* 4.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B PHE* 3.5 24.3 - - + -
367B PHE* 3.7 18.8 - + + -
373B TYR* 4.6 5.2 - + + -
374B ILE 3.5 2.2 - - - -
375B VAL* 3.6 41.5 - - + -
415B VAL* 3.6 1.4 - - - +
416B ASN* 2.9 34.7 + - + +
418B GLN 5.1 0.2 + - - -
420B PHE* 3.9 22.2 - + - -
435B MET* 4.2 16.2 - - + -
436B TRP* 1.3 83.5 - - - +
438B LEU* 1.3 63.6 + - - +
492B LEU* 4.0 19.1 - - + -
495B TYR* 4.4 4.7 - - + -
496B LEU* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TYR* 3.0 10.9 - - - -
374B ILE* 2.9 48.9 + - + +
376B LEU* 4.8 14.4 - - + -
397B ILE* 4.8 4.9 - - + -
400B LEU* 3.4 35.2 - - + -
401B VAL* 4.2 22.7 - - + -
404B LEU* 3.9 17.5 - - + -
413B ALA* 4.9 4.5 - - + -
414B HIS 3.3 4.0 - - - +
415B VAL* 3.6 24.9 - - + +
436B TRP* 4.9 0.7 - - + -
437B PHE* 1.3 81.7 - - - +
439B GLY* 1.3 64.2 + - - +
440B ILE* 4.5 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B PHE* 3.9 3.4 - - - -
370B TYR* 3.4 33.0 - - - -
372B HIS 3.7 4.7 - - - -
373B TYR* 3.9 3.8 - - - -
412B LEU 3.8 0.5 - - - +
413B ALA* 3.5 1.7 - - - -
414B HIS* 2.9 34.9 + - - +
438B LEU* 1.3 74.9 - - - +
440B ILE* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B TYR* 3.9 8.9 - - - +
371B ARG* 4.3 3.3 + - - +
372B HIS* 3.2 33.4 + - + +
373B TYR* 4.5 4.0 - - - +
374B ILE* 3.5 43.1 - - + +
404B LEU* 4.0 18.4 - - + -
410B ILE* 4.2 11.9 - - + -
412B LEU 3.4 8.3 - - - +
413B ALA* 4.7 1.8 - - + -
438B LEU* 4.5 2.2 - - + +
439B GLY* 1.3 79.6 - - - +
441B ILE* 1.3 80.9 + - - +
442B PHE* 3.8 24.1 + - + -
455B LEU* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B TYR* 4.1 20.2 - - + -
410B ILE* 3.8 1.4 - - - -
411B THR* 3.2 30.5 + - + -
412B LEU* 3.2 42.1 + - + +
440B ILE* 1.3 88.0 - - - +
442B PHE* 1.3 75.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B HIS* 3.3 50.6 - + + -
409B PHE* 3.4 26.5 - - + +
410B ILE* 3.7 22.4 - - + -
411B THR* 4.0 5.1 + - - -
440B ILE* 3.8 16.2 - - + -
441B ILE* 1.3 89.1 - - - +
443B ARG* 1.3 68.1 + - - +
454B ASP 5.2 9.0 - - - -
455B LEU* 4.2 25.4 - - + -
486B HIS* 4.4 7.9 - + - -
----------------------------------------------------------
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