Contacts of the strand formed by residues 430 - 437 (chain B) in PDB entry 3DBL
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
----------------------------------------------------------
152B ARG* 4.7 1.8 + - - +
153B TRP* 4.3 4.0 - - - -
156B GLY* 3.8 18.2 - - - +
201B GLU* 4.6 12.1 + - + -
345B ALA* 6.3 2.0 - - + -
376B MET* 5.9 2.0 - - - +
426B ALA* 5.4 0.2 - - - -
427B ASP* 3.0 22.2 + - - +
428B VAL 3.3 1.0 + - - -
429B THR* 1.3 96.6 + - - +
431B PRO* 1.3 77.9 - - + +
432B GLN* 3.2 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B TRP* 3.1 65.7 - - + +
156B GLY* 3.9 4.5 - - - -
157B MET* 3.6 26.5 - - + +
160B SER* 5.3 1.6 - - - +
430B THR* 1.3 95.5 - - + +
432B GLN* 1.3 59.5 + - + +
433B THR* 5.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLY* 3.5 32.8 - - - +
159B ILE* 3.6 28.9 - - - +
160B SER* 4.1 18.4 - - - -
344B PRO 5.3 0.6 + - - -
345B ALA* 3.8 21.9 + - - +
425B VAL 4.1 3.8 - - - +
426B ALA* 4.2 9.9 - - - +
427B ASP 4.5 0.7 + - - -
430B THR* 3.1 29.8 - - + +
431B PRO* 1.3 79.2 - - - +
433B THR* 1.3 69.8 + - - +
434B VAL* 4.0 2.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ALA* 3.9 18.2 - - + -
425B VAL 3.1 28.5 - - - +
426B ALA* 4.8 7.5 - - + +
431B PRO 5.1 1.0 + - - -
432B GLN* 1.3 80.4 + - - +
434B VAL* 1.3 60.8 + - - +
435B LEU* 3.8 12.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B PRO* 3.3 42.4 - - + +
351B GLN* 5.0 1.1 - - + +
376B MET* 3.6 26.2 - - + -
423B LEU 3.8 0.2 - - - +
424B ALA* 4.0 0.2 - - - -
425B VAL* 2.9 37.9 + - + +
432B GLN* 4.0 2.5 + - + +
433B THR* 1.3 72.5 - - - +
435B LEU* 1.3 72.2 + - - +
436B PHE* 3.3 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLN 5.4 4.9 - - - +
350B PRO* 3.4 23.6 - - + +
351B GLN* 2.7 28.8 + - - +
422B GLU* 3.7 30.3 - - + +
423B LEU 3.3 16.4 - - - +
424B ALA* 4.5 10.3 - - + -
433B THR* 3.8 11.6 + - + +
434B VAL* 1.3 78.0 - - - +
436B PHE* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B PRO* 4.0 4.3 - - - -
351B GLN* 2.9 43.5 - - + +
353B ILE* 3.4 21.5 - - + -
368B LEU* 3.3 30.5 - - + -
374B LEU* 4.0 12.1 - - + -
376B MET* 4.7 2.2 - - + -
422B GLU* 3.3 7.1 - - - +
423B LEU* 2.9 50.0 + - + +
425B VAL* 3.3 31.6 - - + -
434B VAL* 3.3 37.0 - - + -
435B LEU* 1.3 77.3 - - - +
437B LYS* 1.3 60.2 + - - +
438B LEU 3.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LEU* 6.4 0.4 - - - -
350B PRO* 3.4 31.1 - - + +
351B GLN 3.0 9.7 + - - -
352B ASN* 3.3 22.2 - - - +
353B ILE* 3.0 22.0 + - - -
420B GLY 5.3 8.5 - - - +
421B GLN 3.6 9.2 - - - +
422B GLU* 4.3 12.1 - - + +
436B PHE* 1.3 68.6 - - - +
438B LEU* 1.3 65.6 + - - +
439B HIS* 3.2 17.6 - - + +
----------------------------------------------------------
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