Contacts of the helix formed by residues 430 - 444 (chain B) in PDB entry 1B0P
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 430 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PHE* 3.9 10.8 - - + -
424B GLY* 3.7 10.9 - - - -
428B ASP* 2.6 28.5 + - - -
429B GLY* 1.3 75.8 - - - +
431B VAL* 1.3 58.0 + - - +
433B ALA* 3.2 6.3 + - - +
434B ASN* 2.8 50.4 + - - +
464B THR* 4.5 10.5 - - + -
466B SER* 4.0 5.4 - - - +
490B HIS* 3.0 38.3 + - + +
560B ASN* 4.8 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A SER* 4.1 4.9 - - - +
1209A GLY* 4.1 10.1 + - - -
429B GLY 3.3 1.0 - - - -
430B THR* 1.3 78.5 - - - +
432B GLY* 1.3 58.4 + - - +
434B ASN* 3.1 7.9 + - - +
435B LYS* 2.8 58.7 + - - +
453B PHE* 3.9 24.2 - - + -
455B TYR* 4.2 19.5 - - + +
464B THR* 3.7 32.8 - - + +
466B SER* 4.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A SER 4.0 9.0 - - - -
1209A GLY 3.1 27.9 + - - -
1210A GLU* 4.4 4.0 - - - -
429B GLY 3.8 0.4 - - - -
431B VAL* 1.3 76.2 - - - +
433B ALA* 1.3 57.0 + - - +
435B LYS* 3.3 7.7 + - - +
436B GLN* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B GLY 2.9 18.9 + - - +
430B THR* 3.5 7.0 - - - +
432B GLY* 1.3 76.6 - - - +
434B ASN* 1.3 57.2 + - - +
436B GLN* 3.1 3.0 + - - -
437B ALA* 2.8 23.6 + - - +
560B ASN* 4.2 20.2 - - + +
564B GLN* 3.0 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PHE* 3.5 36.4 - - - -
430B THR* 2.8 29.9 + - - +
431B VAL 3.1 5.8 + - - +
433B ALA* 1.3 75.3 - - - +
435B LYS* 1.3 59.2 + - - +
437B ALA* 2.8 25.4 + - - +
438B ILE* 3.0 19.1 + - - +
453B PHE* 3.6 14.1 - - + -
466B SER* 2.7 36.3 + - - -
468B LEU* 4.1 8.6 - - + +
490B HIS* 5.6 0.5 - - - -
564B GLN* 5.1 2.8 - - - +
567B PHE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205A ARG 2.7 30.3 + - - -
1206A PRO* 3.2 19.1 + - + +
1207A ASP* 5.2 0.2 - - - -
1208A SER* 2.9 28.7 + - - +
180B ILE* 5.1 10.7 - - + +
431B VAL* 2.8 35.1 + - - +
432B GLY* 3.6 6.1 - - - +
434B ASN* 1.3 76.1 - - - +
436B GLN* 1.3 62.0 + - - +
438B ILE* 3.5 10.6 + - - +
439B LYS* 3.2 36.5 + - - +
453B PHE* 3.7 24.9 - - + -
455B TYR* 4.4 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B GLY 2.8 18.0 + - - +
433B ALA* 3.6 6.3 - - - +
435B LYS* 1.3 76.5 - - - +
437B ALA* 1.3 59.6 + - - +
439B LYS* 3.2 28.0 + - - +
440B ILE* 2.9 51.2 + - + +
564B GLN* 4.1 9.2 - - - +
586B SER* 4.6 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ALA 2.8 14.0 + - - +
434B ASN* 2.8 13.2 + - - +
436B GLN* 1.3 78.5 - - - +
438B ILE* 1.3 55.6 - - - +
440B ILE* 3.4 1.4 + - - +
441B ILE* 2.9 36.3 + - + +
468B LEU* 4.5 6.1 - - + -
564B GLN* 3.9 9.4 - - - +
567B PHE* 3.7 31.0 - - + -
568B PHE* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 4.3 7.1 + - - +
180B ILE* 4.0 32.1 - - + -
434B ASN 3.0 17.0 + - - +
435B LYS* 3.8 14.4 - - - +
437B ALA* 1.3 75.4 - - - +
439B LYS* 1.3 58.7 + - - +
441B ILE* 4.1 0.2 - - - +
442B GLY* 2.8 28.4 + - - -
449B ALA* 3.6 26.6 - - + +
450B GLN 4.3 3.4 - - - +
451B GLY* 3.7 16.4 - - - -
453B PHE* 4.3 6.5 - - + -
468B LEU* 3.5 35.9 - - + -
470B PHE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206A PRO* 5.1 7.5 + - - +
1207A ASP* 4.8 11.3 + - - +
7B THR* 3.7 35.8 + - - +
8B THR* 5.8 2.2 - - - +
180B ILE* 4.5 9.9 - - - +
435B LYS* 3.2 24.0 + - - +
436B GLN* 3.2 34.5 + - - +
438B ILE* 1.3 78.7 - - - +
440B ILE* 1.3 62.8 + - - +
443B ASP* 2.9 42.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
436B GLN* 2.9 31.7 + - + +
437B ALA 3.7 3.6 - - - +
439B LYS* 1.3 76.6 - - - +
441B ILE* 1.3 62.6 + - - +
443B ASP* 4.8 0.4 - - - -
444B ASN* 2.7 45.7 + - - +
564B GLN* 4.9 2.0 - - - +
568B PHE* 4.2 29.6 - - + -
582B LEU* 3.8 26.7 - - + -
583B LEU* 4.6 12.1 - - + -
586B SER* 3.4 32.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
437B ALA 2.9 20.0 + - - +
438B ILE 4.1 0.4 - - - +
440B ILE* 1.3 76.0 - - - +
442B GLY* 1.3 61.9 + - - +
445B THR* 2.4 50.2 + - + +
447B LEU* 4.0 17.0 - - + -
449B ALA* 5.1 1.3 - - + -
470B PHE* 3.4 47.8 - - + -
567B PHE* 3.9 15.7 - - + -
568B PHE* 4.2 10.8 - - + -
573B VAL* 3.7 27.4 - - + -
574B LEU* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 4.2 8.5 - - - -
182B LYS* 2.8 41.9 + - - -
438B ILE 2.8 21.4 + - - -
439B LYS 4.0 0.4 - - - -
441B ILE* 1.3 74.2 - - - +
443B ASP* 1.3 61.9 + - - +
445B THR* 3.3 6.4 - - - +
447B LEU 4.7 2.0 - - - -
449B ALA* 4.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B MET* 5.9 0.9 - - - -
7B THR* 4.2 14.0 + - - +
439B LYS* 2.9 32.3 + - - +
440B ILE* 4.0 2.2 - - - +
442B GLY* 1.3 82.1 - - - +
444B ASN* 1.3 68.5 + - - +
445B THR 3.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ILE* 2.7 44.8 + - - +
443B ASP* 1.3 88.3 - - - +
445B THR* 1.3 61.4 + - + +
578B LYS* 2.9 24.6 + - - -
582B LEU* 3.6 33.5 - - + +
----------------------------------------------------------
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