Contacts of the strand formed by residues 451 - 465 (chain T) in PDB entry 6O81
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 TRP 451 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP 5.4 2.2 + - - -
263A ASN* 4.8 4.2 - - - +
264A PHE* 4.7 4.5 - - + -
265A ASP* 3.5 43.1 - - + -
78T THR* 6.0 6.7 - - - -
79T ILE* 6.1 4.5 - - + -
139T ASP* 3.6 14.9 - - - +
140T ILE* 4.7 6.7 + - + +
403T VAL* 4.8 12.3 - - + -
404T LEU 4.7 1.8 - - - -
405T MET* 3.7 56.0 - - + +
444T SER* 4.5 6.1 - - - -
445T ARG* 3.9 12.1 - - - -
446T ARG* 3.1 55.6 - - + +
450T HIS* 1.3 70.8 - - - +
452T ARG* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 452 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139T ASP* 3.8 13.0 - - + -
381T LEU* 5.5 4.9 - - - +
384T VAL* 3.5 29.7 - - - +
444T SER* 3.8 3.4 - - - -
445T ARG* 2.8 40.1 + - - +
447T VAL* 4.4 20.0 - - + +
448T GLU 5.8 0.4 - - - +
450T HIS* 3.3 27.3 + - + +
451T TRP* 1.3 77.3 - - - +
453T LEU* 1.3 65.2 + - - +
454T ILE* 3.7 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139T ASP* 4.0 15.2 + - + +
142T MET* 5.8 3.6 - - + -
143T ALA* 4.6 22.2 - - + +
381T LEU* 5.8 4.7 - - - +
382T LEU 5.8 0.9 + - - -
442T ALA* 6.0 1.8 - - + -
443T LEU 4.6 2.7 - - - +
444T SER* 3.9 10.0 - - - -
452T ARG* 1.3 78.3 - - - +
454T ILE* 1.3 60.1 + - - +
455T GLY 4.9 4.5 - - - +
456T TRP* 5.5 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 454 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377T LEU* 3.5 9.1 - - + +
378T LEU* 2.9 31.6 + - - +
395T VAL* 4.6 18.8 - - + +
443T LEU* 2.9 12.6 + - + +
444T SER 4.6 0.4 - - - -
445T ARG* 4.6 26.7 - - + +
452T ARG 3.7 0.6 + - - +
453T LEU* 1.3 75.0 - - - +
455T GLY* 1.3 59.2 + - - +
456T TRP* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 455 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376T PHE 3.4 13.2 - - - -
377T LEU* 4.1 3.1 - - - -
378T LEU 4.5 1.1 - - - -
442T ALA* 3.6 2.4 - - - +
443T LEU* 2.9 34.5 + - - +
453T LEU* 4.9 2.8 - - - +
454T ILE* 1.3 80.8 + - - +
456T TRP* 1.3 79.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 456 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ASN* 6.2 4.3 - - + -
576A LEU* 6.0 8.3 - - + -
142T MET 5.1 2.0 + - - -
143T ALA* 5.4 3.2 - - - +
146T LEU* 3.4 40.1 - - + +
177T ILE* 4.5 23.3 - - + -
374T SER 3.6 0.7 - - - +
376T PHE* 3.1 36.6 + - - +
378T LEU* 5.1 15.0 - - + -
382T LEU* 6.1 4.7 - - + -
440T LYS* 6.2 3.1 - - + -
441T ILE 3.6 8.5 - - - +
442T ALA* 4.1 13.9 - - + +
443T LEU* 4.7 1.8 - - - +
453T LEU* 5.5 12.8 - - + +
454T ILE 6.0 0.9 - - - -
455T GLY* 1.3 88.8 + - - -
457T GLY* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 457 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373T ILE* 5.1 2.9 - - - -
374T SER* 3.3 17.7 - - - -
376T PHE* 5.1 1.8 - - - -
440T LYS* 3.4 8.2 - - - +
441T ILE* 2.9 34.0 + - - -
456T TRP* 1.3 78.6 - - - +
458T GLN* 1.3 60.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 458 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373T ILE* 4.0 2.9 - - - -
374T SER* 3.0 32.5 + - - -
438T GLY* 4.6 8.5 - - - +
439T GLU 3.8 7.2 - - - +
440T LYS* 5.4 1.1 - - - -
457T GLY* 1.3 73.7 - - - -
459T ILE* 1.3 66.9 + - - +
460T ARG* 3.2 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 459 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371T LEU* 5.5 7.9 - - + -
372T GLU 4.1 1.6 - - - +
373T ILE* 4.0 12.5 - - + +
436T GLU 5.2 3.4 - - - +
437T VAL 3.0 30.3 - - - +
438T GLY* 3.6 8.5 - - - -
439T GLU 3.4 16.9 + - - +
441T ILE* 5.3 6.6 - - + +
457T GLY 4.3 0.2 - - - -
458T GLN* 1.3 71.3 - - - +
460T ARG* 1.3 61.5 + - - +
461T ARG 5.0 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 460 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372T GLU* 2.8 15.0 + - + +
373T ILE* 4.7 4.3 - - - -
374T SER* 5.2 1.8 - - - +
437T VAL 4.9 3.2 - - - +
458T GLN 3.2 6.2 + - - +
459T ILE* 1.3 75.2 - - - +
461T ARG* 1.3 63.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 461 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371T LEU* 3.5 4.9 - - - +
372T GLU* 2.9 41.2 + - + +
437T VAL 5.5 2.2 - - - -
459T ILE* 3.7 4.9 - - - +
460T ARG* 1.3 79.8 + - + +
462T GLY* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 462 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368T PHE* 4.8 14.8 - - - -
370T GLU 3.3 10.1 - - - -
371T LEU* 4.3 3.6 - - - -
461T ARG* 1.3 77.8 - - - +
463T VAL* 1.3 61.2 + - - -
464T THR* 3.7 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 463 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368T PHE* 3.4 4.2 - - - +
369T THR* 3.0 28.8 + - - +
370T GLU* 2.9 29.5 + - + +
462T GLY* 1.3 69.4 - - - -
464T THR* 1.3 63.9 + - - +
465T ILE* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 464 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366T GLU* 4.0 12.6 - - - -
367T ILE 3.5 5.4 - - - -
368T PHE* 3.7 25.4 - - - -
462T GLY 3.7 4.1 + - - -
463T VAL* 1.3 75.6 - - - +
465T ILE* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 465 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309T LEU 5.1 10.5 - - - +
310T MET* 6.1 1.1 - - - -
311T CYS* 5.1 7.3 - - + +
366T GLU* 5.1 0.7 - - - -
367T ILE* 2.9 37.8 + - + +
369T THR* 6.2 3.6 - - - -
463T VAL 5.3 0.7 - - - +
464T THR* 1.3 77.1 - - - +
466T LYS* 1.3 62.9 + - - +
467T PRO 4.2 0.7 - - - -
----------------------------------------------------------
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