Contacts of the helix formed by residues 426 - 435 (chain B) in PDB entry 1T9A
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 ASP 426 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY 5.0 0.5 - - - +
312B ASN 4.7 1.0 - - - +
313B HIS* 3.3 27.5 - - - +
408B VAL* 4.2 5.0 - - + +
425B GLY* 1.3 70.5 - - - -
427B ALA* 1.3 65.4 + - - +
428B THR* 3.5 4.5 + - - -
429B THR* 2.8 41.0 + - - +
430B ASN* 3.1 25.0 + - - -
1701B FAD 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY 5.0 5.6 - - - +
310B ILE* 4.7 5.2 - - + -
373B VAL* 3.8 28.0 - - + -
374B GLY* 4.6 2.7 - - - +
406B PHE* 4.2 17.7 - - + +
425B GLY 4.2 0.9 - - - -
426B ASP* 1.3 69.5 - - - +
428B THR* 1.3 62.2 + - - +
430B ASN* 3.1 3.3 + - - +
431B LEU* 2.8 35.0 + - - +
1701B FAD 2.9 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY 5.1 1.1 + - - -
310B ILE* 3.8 8.0 + - - +
313B HIS* 3.2 46.7 - - + +
315B ASP* 3.5 4.0 - - + -
316B GLY* 3.1 31.6 - - - +
319B LEU* 3.2 32.9 - - + +
426B ASP* 3.5 3.6 + - - -
427B ALA* 1.3 77.6 - - - +
429B THR* 1.3 63.2 + - - +
431B LEU* 3.3 9.7 + - - +
432B GLY 3.1 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B HIS* 4.3 9.4 + - - -
426B ASP* 2.8 34.8 + - - +
427B ALA 3.2 0.2 - - - -
428B THR* 1.3 77.3 - - - +
430B ASN* 1.3 68.6 + - - +
432B GLY* 3.2 10.9 + - - -
433B LYS* 3.2 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 4.2 4.0 - - - +
289B ILE* 4.1 7.1 - - + +
406B PHE* 4.0 9.3 - - + -
423B VAL* 3.5 30.7 + - + +
424B GLU 2.9 31.3 + - - +
425B GLY* 3.7 5.3 + - - -
426B ASP 3.1 18.0 + - - +
427B ALA 3.1 4.9 + - - +
429B THR* 1.3 76.9 - - - +
431B LEU* 1.3 64.3 + - - +
433B LYS* 3.3 26.9 + - - +
434B MET* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 4.0 16.6 - - + -
319B LEU* 4.7 25.6 - - + +
320B LEU* 4.9 5.4 - - + -
323B LEU* 3.9 27.1 - - + -
373B VAL* 4.0 26.9 - - + -
406B PHE* 3.7 33.7 - - + -
427B ALA 2.8 20.3 + - - +
428B THR* 3.7 6.5 - - - +
430B ASN* 1.3 77.2 - - - +
432B GLY* 1.3 58.9 + - - +
434B MET* 4.0 8.6 - - + +
435B MET* 3.1 34.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
319B LEU* 4.1 16.6 - - - +
428B THR 3.1 12.7 + - - -
429B THR 3.2 4.9 + - - -
430B ASN 3.1 0.6 - - - -
431B LEU* 1.3 80.9 - - - +
433B LYS* 1.3 59.3 + - - +
434B MET 3.2 1.2 + - - -
435B MET* 3.7 15.7 + - - +
436B SER* 4.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 4.8 6.5 - - - +
286B MET* 3.8 24.5 - - + +
289B ILE* 3.6 17.8 - - + +
429B THR* 3.2 26.0 + - + +
430B ASN* 3.3 27.8 + - - +
432B GLY* 1.3 77.6 - - - +
434B MET* 1.3 57.4 + - - +
436B SER* 4.5 6.4 + - - -
437B LYS* 3.9 19.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE* 3.4 26.7 - - + +
292B ALA* 4.0 21.1 - - - -
293B ALA* 4.1 9.6 - - + -
296B ILE* 3.5 25.4 - - + -
323B LEU* 4.3 12.1 - - + -
371B ILE* 5.8 0.2 - - + -
406B PHE* 3.9 26.9 - - + -
430B ASN 3.2 12.3 + - - +
431B LEU* 3.6 17.0 + - + +
433B LYS* 1.3 80.2 - - - +
435B MET* 1.3 65.7 + - - +
436B SER 3.3 2.2 - - - -
437B LYS* 3.0 17.1 + - - +
438B ILE* 3.2 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.4 37.9 - - + +
322B GLU* 2.8 50.3 - - + +
323B LEU* 3.7 27.4 - - + +
326B ARG* 3.1 37.6 + - - +
431B LEU* 3.1 20.8 + - + +
432B GLY* 3.8 11.2 - - - +
433B LYS 3.6 0.2 - - - -
434B MET* 1.3 76.0 - - - +
436B SER* 1.3 65.0 + - - +
438B ILE* 3.0 16.8 + - - +
----------------------------------------------------------
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