Contacts of the helix formed by residues 399 - 415 (chain B) in PDB entry 3E0D
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 PHE 399 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR* 4.9 14.4 - + - -
295B ILE* 4.4 18.4 - - + -
394B ILE* 3.5 16.8 + - + +
397B MET* 3.9 38.6 - - + -
398B GLY* 1.3 84.0 - - - +
400B PRO* 1.4 69.7 - - - +
401B GLY 3.2 2.7 - - - +
402B TYR* 3.3 22.5 + + + +
403B PHE* 3.2 26.3 + - + -
454B LEU* 4.3 9.9 - - + -
459B VAL* 5.1 3.6 - - + -
460B SER 3.7 19.7 - - - -
461B MET* 3.6 33.4 - - + -
462B PRO* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLU* 3.3 26.5 - - + +
307B ALA* 3.6 31.6 - - + +
310B LEU* 3.5 26.2 - - + +
394B ILE* 4.0 8.9 - - + +
395B GLU* 4.7 6.1 - - + +
398B GLY* 3.3 10.3 - - - -
399B PHE 1.4 89.5 - - - +
401B GLY* 1.3 57.1 + - - +
403B PHE* 3.2 4.5 + - - +
404B LEU* 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 4.8 5.8 - - - -
296B PRO 5.3 0.7 - - - -
298B PHE* 4.3 2.9 - - - +
306B GLU* 3.3 35.2 + - - +
398B GLY 5.3 0.4 + - - -
399B PHE* 3.2 0.8 - - - +
400B PRO* 1.3 81.0 - - - +
402B TYR* 1.3 64.2 + - - +
404B LEU* 3.3 6.9 + - - +
405B ILE* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 4.3 20.2 - - + +
399B PHE* 3.3 24.3 + + + +
401B GLY* 1.3 76.5 - - - +
403B PHE* 1.3 72.9 + + - +
405B ILE* 3.5 8.8 + - - +
406B VAL* 3.3 29.3 + - + +
461B MET* 4.3 4.0 - - + +
462B PRO* 3.0 51.0 + - + -
463B ASP* 3.8 0.9 - - - -
464B ILE* 3.0 39.4 + - + +
615B LEU* 3.0 41.5 - - + +
616B LYS 4.5 2.1 + - - -
617B MET* 3.3 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU* 3.7 18.8 - - + -
394B ILE* 3.7 36.1 - - + -
399B PHE* 3.2 28.9 + - + -
400B PRO 3.2 8.3 + - - +
402B TYR* 1.3 90.3 - + - +
404B LEU* 1.3 61.3 + - - +
406B VAL* 3.1 4.4 + - - +
407B GLN* 2.8 33.2 + - - +
430B SER* 4.7 5.2 - - - -
432B VAL* 4.5 15.7 - - + -
433B ALA* 4.7 5.2 - - + -
438B ILE* 3.7 22.9 - - + +
453B PHE* 3.4 37.7 - + - -
454B LEU* 4.5 5.4 - - + -
462B PRO* 4.7 2.5 - - + -
464B ILE* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 3.6 25.9 - - + -
300B LEU* 4.1 4.9 - - + -
306B GLU* 3.5 37.5 - - + +
309B TYR* 3.3 35.2 - - + -
310B LEU* 3.8 18.8 - - + +
313B LEU* 3.5 22.4 - - + -
400B PRO 3.0 16.5 + - - +
401B GLY* 3.3 6.5 + - - +
403B PHE* 1.3 76.0 - - - +
405B ILE* 1.3 63.5 + - - +
407B GLN* 2.8 19.6 - - - +
408B ASP* 2.9 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 5.2 0.2 - - + -
296B PRO* 3.9 30.7 - - + +
297B ARG 5.1 0.4 - - - +
298B PHE* 3.3 28.5 - - + -
401B GLY 3.1 16.7 + - - +
402B TYR* 3.6 7.2 - - - +
404B LEU* 1.3 77.3 - - - +
406B VAL* 1.3 65.0 + - + +
408B ASP* 3.3 8.7 + - - +
409B TYR* 3.1 25.0 + - + -
484B TYR* 3.4 24.4 + - + +
581B ILE* 3.9 22.7 - - + -
615B LEU* 3.8 27.1 - - + -
617B MET* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B TYR* 3.3 25.5 + - + +
403B PHE 3.1 6.7 + - - +
405B ILE* 1.3 73.8 - - + +
407B GLN* 1.3 67.8 + - - +
408B ASP 3.3 0.5 + - - -
409B TYR* 3.4 22.2 + - - +
410B ILE* 3.3 40.4 + - + +
438B ILE* 4.0 11.9 - - + -
464B ILE* 4.0 26.5 - - + -
466B THR* 4.8 0.2 - - - +
617B MET* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 4.7 3.0 - - - -
309B TYR* 5.1 4.1 + - - -
310B LEU* 6.3 1.3 - - + -
313B LEU* 3.3 31.0 - - + +
403B PHE 2.8 15.0 + - - +
404B LEU* 2.8 26.4 - - - +
406B VAL* 1.3 75.9 - - - +
408B ASP* 1.3 87.1 + - - +
410B ILE* 3.9 2.3 - - - +
411B ASN* 3.0 48.8 + - - +
436B VAL* 3.3 33.0 - - + +
438B ILE* 3.8 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 3.7 14.0 - - + -
404B LEU 2.9 18.2 + - - +
405B ILE 3.4 5.2 - - - +
406B VAL 3.2 0.2 - - - -
407B GLN* 1.3 91.5 + - - +
409B TYR* 1.3 58.8 + - - +
411B ASN* 3.8 2.5 - - - +
412B TRP* 3.0 26.7 + - - +
479B TYR* 2.9 33.6 + - - -
483B ARG* 3.6 27.1 + - - -
484B TYR* 3.8 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ILE* 3.1 26.1 + - + -
406B VAL* 3.4 31.5 - - + +
408B ASP* 1.3 81.0 - - - +
410B ILE* 1.3 76.4 + - + +
412B TRP* 3.6 2.3 - - - +
413B ALA* 3.1 26.5 + - - +
464B ILE 4.5 2.1 + - - -
466B THR* 4.3 8.9 + - - -
468B PHE* 4.2 7.2 - + - -
476B VAL* 4.1 10.0 - - + +
479B TYR* 3.9 28.9 - - + -
480B VAL* 4.1 17.0 - - + -
484B TYR* 5.3 2.9 - + + -
581B ILE* 4.8 2.2 - - + -
617B MET* 3.4 32.5 - - - +
618B ASP 5.3 0.2 + - - -
619B PHE* 3.5 37.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 3.3 36.8 + - + +
407B GLN* 3.9 3.8 - - - +
408B ASP 3.3 0.6 - - - -
409B TYR* 1.3 88.4 - - + +
411B ASN* 1.3 58.4 + - - +
413B ALA* 3.3 7.7 + - - +
414B ARG* 3.1 41.3 + - - +
420B VAL* 3.8 14.5 - - + +
437B GLY 3.4 22.7 - - - +
438B ILE* 3.6 26.9 - - + +
466B THR* 3.8 26.2 - - + +
468B PHE* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 5.8 2.2 - - - +
320B ARG* 5.4 4.4 - - - +
407B GLN* 3.0 46.7 + - - +
408B ASP 3.9 2.5 - - - +
410B ILE* 1.3 72.3 - - - +
412B TRP* 1.3 66.0 + - - +
414B ARG* 3.2 27.9 + - - +
415B GLY* 3.4 14.6 + - - -
436B VAL* 3.5 11.9 + - - +
437B GLY* 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP 3.0 17.1 + - - +
409B TYR* 3.6 7.0 - - - +
411B ASN* 1.3 75.8 - - - +
413B ALA* 1.3 90.7 + - + +
415B GLY 2.9 14.2 + - - -
416B HIS* 3.1 65.3 + + + -
418B VAL* 4.7 4.5 - - + -
475B ARG* 3.7 40.6 - - + -
476B VAL* 4.0 12.6 - - + -
479B TYR* 3.2 54.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TYR 3.1 15.4 + - - +
410B ILE 3.3 6.0 + - - +
412B TRP* 1.3 89.5 - - + +
414B ARG* 1.3 59.8 + - - +
416B HIS* 3.4 4.5 + - - -
418B VAL* 2.9 50.0 + - + +
420B VAL* 4.1 2.9 - - + -
468B PHE* 4.0 11.2 - - + -
476B VAL* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ILE* 3.1 27.2 + - - +
411B ASN* 3.2 25.7 + - - +
412B TRP 3.1 1.0 - - - -
413B ALA* 1.3 73.9 - - - +
415B GLY* 1.3 58.6 + - - +
416B HIS 2.9 9.8 + - - -
417B GLY* 3.5 9.0 + - - -
418B VAL 3.9 5.3 + - - +
420B VAL* 4.1 29.6 + - + +
421B GLY 4.8 1.4 + - - -
437B GLY* 2.7 37.2 + - - -
438B ILE 4.4 3.6 + - - -
440B ASN* 4.3 27.5 - - - +
646B ASP* 5.6 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ASN 3.4 7.7 + - - -
412B TRP 2.9 6.8 + - - -
414B ARG* 1.3 76.6 - - - +
416B HIS* 1.3 70.2 + - - +
417B GLY 3.8 0.9 - - - -
----------------------------------------------------------
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