Contacts of the strand formed by residues 511 - 520 (chain B) in PDB entry 4M5X
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 THR 511 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B VAL* 3.8 17.9 - - + -
456B HIS 3.5 2.7 - - - -
457B SER* 2.6 25.1 + - - +
468B TYR* 6.2 0.7 - - + +
496B HIS 3.7 18.3 - - - +
497B ASN* 3.9 8.1 - - - +
499B GLY* 3.9 8.3 - - - -
509B HIS* 2.9 29.0 + - - +
510B CYS* 1.3 75.2 - - - +
512B ASN* 1.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ARG* 3.3 31.0 - - - +
420B LYS* 2.8 28.4 + - - -
422B ASN* 2.9 34.7 + - - +
455B VAL* 3.3 7.0 - - - -
456B HIS* 2.8 30.5 + - - +
497B ASN* 3.5 14.1 - - - +
499B GLY* 3.8 5.3 - - - -
509B HIS 3.7 7.3 + - - -
510B CYS 3.7 6.7 - - - -
511B THR* 1.3 81.7 - - - +
513B ALA* 1.3 61.5 + - - +
514B TYR* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LEU* 3.8 13.2 - - + +
408B ARG* 2.8 24.7 + - - +
427B PHE* 4.0 20.9 - - + -
453B VAL* 3.6 29.2 - - + -
454B LEU 3.3 7.2 - - - +
455B VAL* 4.2 2.5 - - + -
497B ASN* 3.2 6.4 + - - +
512B ASN* 1.3 75.9 - - - +
514B TYR* 1.3 60.1 + - - +
515B MET 4.5 0.7 - - - +
516B LEU* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TYR* 3.2 30.1 - + + +
227B SER* 4.3 4.2 + - - -
296B VAL* 3.9 29.6 - - + -
405B GLN* 3.6 3.6 - - - +
406B LEU* 2.7 45.6 + - - +
408B ARG* 4.6 4.7 - - - +
409B PHE* 4.0 26.2 - + + -
420B LYS* 6.0 0.4 - - - -
454B LEU* 2.9 40.8 + - + +
455B VAL 3.7 13.5 - - - -
456B HIS* 3.8 18.4 - - + -
465B TYR* 3.7 16.0 - + - -
512B ASN 5.2 0.2 - - - +
513B ALA* 1.3 74.2 - - - +
515B MET* 1.3 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 4.3 13.2 - - + -
231B THR* 5.0 0.9 - - + -
296B VAL* 3.8 24.2 - - - -
300B CYS* 5.6 1.6 - - + -
403B HIS* 3.7 38.4 - - + +
404B LEU 3.3 12.6 - - - +
405B GLN* 3.5 24.5 - - + +
406B LEU* 4.4 1.5 - - - +
453B VAL* 3.6 2.1 - - - -
454B LEU* 2.7 53.1 + - + +
513B ALA 3.6 0.6 - - - -
514B TYR* 1.3 94.3 - - + +
516B LEU* 1.3 69.2 + - - +
517B VAL* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ILE* 3.8 21.8 - - + -
402B LEU 3.6 1.2 - - - +
403B HIS* 3.7 1.7 - - - -
404B LEU* 2.8 44.8 + - + +
406B LEU* 4.1 15.5 - - + -
427B PHE* 3.6 60.1 - - + -
450B LEU* 4.3 2.5 - - + -
452B ALA 3.4 3.4 - - - +
453B VAL* 3.8 20.0 - - + -
513B ALA* 4.1 4.0 - - + -
515B MET* 1.3 83.1 - - - +
517B VAL* 1.3 63.8 + - - +
518B TYR* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B THR* 3.6 25.1 - - + -
235B THR* 5.8 2.0 - - - +
401B VAL* 3.9 16.4 - - + -
402B LEU 3.4 2.2 - - - -
403B HIS* 3.5 32.5 - - + +
450B LEU* 3.6 4.0 - - - +
451B HIS* 2.7 49.0 + - + +
452B ALA* 2.9 25.3 + - + -
454B LEU* 4.7 2.2 - - + -
515B MET* 3.7 11.0 - - + -
516B LEU* 1.3 76.2 - - - +
518B TYR* 1.3 61.0 + - - +
519B ILE* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ILE* 5.0 0.8 - - + +
401B VAL* 3.6 0.3 - - - -
402B LEU* 2.8 39.4 + - + +
404B LEU* 3.8 26.9 - - + -
427B PHE* 3.7 11.4 - - - +
428B PRO* 2.6 43.4 + - - +
429B GLU 4.1 2.0 - - - -
431B LEU* 3.6 30.7 - - + +
448B TYR* 3.7 27.8 - - + -
449B ILE 3.3 6.5 - - - -
450B LEU* 3.4 31.2 - - + -
516B LEU* 3.9 20.4 - - + -
517B VAL* 1.3 77.7 - - - +
519B ILE* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B THR* 6.1 0.7 - - + -
400B PRO 3.3 11.0 - - - +
401B VAL* 4.5 9.9 - - + -
448B TYR* 3.5 3.4 - - - -
449B ILE* 2.8 36.4 + - - +
451B HIS* 3.5 38.4 - - + +
517B VAL* 4.8 0.9 - - + -
518B TYR* 1.3 80.0 - - - +
520B ARG* 1.3 77.3 + - - +
521B GLU 3.2 0.7 + - - -
523B LYS 4.4 0.2 - - - -
524B LEU* 3.7 31.6 - - + +
527B VAL* 4.0 23.3 - - + -
528B LEU* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 3.2 32.4 + - - +
399B PRO 5.0 0.4 - - - -
400B PRO* 2.8 22.5 + - + +
437B LEU* 5.0 5.7 - - - +
441B ASP* 5.8 0.6 - - - +
444B ASP* 2.8 53.5 + - - -
445B PRO 3.7 12.3 + - - +
446B ALA* 3.8 10.6 - - - +
447B ASN 3.7 7.4 - - - +
448B TYR* 3.3 38.5 + - + +
519B ILE* 1.3 70.0 - - - +
521B GLU* 1.3 60.5 + - - +
522B SER* 3.8 13.5 - - - +
523B LYS* 2.8 39.1 + - + +
524B LEU 3.1 9.2 + - - -
----------------------------------------------------------
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