Contacts of the helix formed by residues 428 - 443 (chain B) in PDB entry 5FHH
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 HIS 428 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B CYS* 3.4 3.8 - - - +
427B THR* 1.3 121.8 + - + +
429B GLN* 1.3 64.4 + - - +
430B ASP* 3.3 3.1 - - + +
431B ASP* 3.3 19.4 + - + +
432B VAL* 3.2 15.1 + - - +
553B SER* 5.9 0.4 - - - -
574B ALA* 6.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B THR 4.3 0.4 + - - -
428B HIS* 1.3 70.0 - - - +
430B ASP* 1.3 67.0 + - - +
432B VAL* 2.9 34.1 + - + +
433B ALA* 3.3 5.5 + - - +
553B SER* 4.7 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B HIS* 3.3 2.4 - - + -
429B GLN* 1.3 80.0 - - - +
431B ASP* 1.3 62.1 + - - +
433B ALA* 3.3 14.0 + - - +
434B LEU* 3.4 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B CYS* 5.4 7.6 - - - -
428B HIS* 3.3 15.8 + - + +
429B GLN 3.2 0.4 - - - -
430B ASP* 1.3 77.1 - - - +
432B VAL* 1.3 64.9 + - + +
434B LEU* 3.0 18.9 + - + +
435B THR* 3.0 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B CYS* 3.4 27.4 - - + +
428B HIS 3.2 18.4 - - - +
429B GLN* 2.9 29.9 + - + +
431B ASP* 1.3 76.7 - - - +
433B ALA* 1.3 63.0 + - + +
436B ASN* 3.7 7.3 + - - +
551B ALA* 3.1 30.8 - - + +
552B MET* 3.5 31.6 - - - +
553B SER* 4.0 8.5 - - - +
----------------------------------------------------------
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 GLN 4.1 5.4 - - - +
430B ASP* 3.3 10.5 + - - +
431B ASP 3.1 0.6 - - - -
432B VAL* 1.3 84.9 - - + +
434B LEU* 1.3 62.4 + - - +
436B ASN* 3.2 22.9 - - - +
437B GLU* 4.0 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ASP 3.4 10.2 + - - +
431B ASP* 3.0 14.3 + - + +
433B ALA* 1.3 76.0 - - - +
435B THR* 1.3 55.8 + - - +
436B ASN 2.7 23.5 - - - +
437B GLU* 4.2 4.1 - - - +
438B ARG* 3.9 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ASP 3.0 12.4 + - - -
434B LEU* 1.3 70.5 - - - +
436B ASN* 1.3 65.1 + - - +
438B ARG* 4.4 4.9 - - - +
439B ARG* 4.2 11.4 + - - +
550B TRP* 4.2 11.0 - - - +
551B ALA* 3.6 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL 3.7 9.8 + - - +
433B ALA* 3.2 16.5 + - - +
434B LEU 2.7 14.1 - - - +
435B THR* 1.3 81.3 - - - +
437B GLU* 1.3 57.0 - - - +
438B ARG* 2.2 24.3 + - - -
439B ARG 4.0 2.9 - - - -
548B LEU* 4.1 16.6 - - + -
550B TRP* 3.4 25.6 - - + -
551B ALA* 4.4 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ALA 4.2 9.2 - - - +
434B LEU* 4.2 4.3 - - - +
436B ASN* 1.3 73.0 - - - +
438B ARG* 1.3 57.0 + - - +
439B ARG 3.2 0.9 - - - -
440B LEU* 2.9 7.8 + - - +
441B GLN* 2.4 40.9 + - - +
548B LEU* 4.8 2.8 - - - +
550B TRP* 3.9 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU 3.9 8.7 + - - +
435B THR* 4.4 4.7 - - - +
436B ASN 2.2 20.9 + - - +
437B GLU* 1.3 71.6 - - - +
439B ARG* 1.3 59.8 + - - +
441B GLN* 3.5 6.4 + - - +
442B GLU* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B THR 4.3 6.3 - - - +
436B ASN 3.4 2.8 + - - -
437B GLU 3.2 0.6 - - - -
438B ARG* 1.3 79.6 - - - +
440B LEU* 1.3 57.3 + - - +
442B GLU* 3.0 21.2 - - + +
443B LEU* 2.9 20.7 - - - +
550B TRP* 3.7 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLU* 2.9 11.2 + - - +
439B ARG* 1.3 76.5 - - - +
441B GLN* 1.3 63.7 + - - +
442B GLU 3.1 1.9 + - - -
443B LEU* 3.5 18.8 + - + +
447B VAL* 4.0 24.6 - - + +
474B GLN* 5.9 7.0 - - + +
475B LEU 6.2 0.2 - - - -
476B LYS* 4.9 7.2 - - + +
479B ALA* 5.2 1.3 - - + -
548B LEU* 4.9 5.6 - - + -
550B TRP* 3.4 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLU* 2.4 32.4 + - + +
438B ARG* 3.9 7.6 - - - +
440B LEU* 1.3 68.4 - - - +
442B GLU* 1.3 60.6 + - - +
443B LEU 3.5 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ARG 3.3 12.2 + - - +
439B ARG* 3.0 30.9 - - - +
441B GLN* 1.3 77.8 - - - +
443B LEU* 1.3 80.3 + - - +
444B PRO* 3.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ARG 2.9 27.6 - - - +
440B LEU* 3.5 13.4 + - + +
441B GLN 3.5 6.5 - - - +
442B GLU* 1.3 94.2 - - - +
444B PRO* 1.3 80.2 - - + +
445B GLY* 4.6 0.2 - - - -
447B VAL* 4.0 5.9 - - - +
476B LYS* 3.5 29.6 - - + -
477B LEU* 5.4 0.9 - - + +
478B GLY* 3.7 36.3 - - - +
479B ALA* 4.4 7.0 - - - +
550B TRP* 4.8 2.0 - - + -
----------------------------------------------------------
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