Contacts of the strand formed by residues 373 - 380 (chain A) in PDB entry 1TUB
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 ARG 373 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PRO* 3.5 6.8 - - - +
285A GLN* 2.6 38.8 + - - +
286A LEU 4.1 9.3 + - - +
288A VAL* 2.4 46.2 - - + +
291A ILE* 2.7 34.4 - - + +
320A ARG 4.0 1.2 + - - -
321A GLY 3.5 13.2 - - - +
322A ASP* 3.8 22.0 + - - +
323A VAL* 4.7 1.3 - - - -
371A VAL* 3.1 21.2 + - + +
372A GLN* 1.3 115.3 + - - +
374A ALA* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 4.5 7.6 - - + +
274A PRO* 3.7 16.4 - - + -
291A ILE* 3.5 2.1 - - - +
318A LEU 4.7 2.0 - - - +
319A TYR* 3.1 33.5 - - - +
320A ARG* 3.2 44.1 + - + +
323A VAL* 4.6 1.8 - - - +
360A PRO* 5.3 3.6 - - + -
373A ARG* 1.3 73.9 - - - +
375A VAL* 1.4 64.5 + - - +
376A CYS* 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR 2.6 21.2 - - - +
272A TYR* 3.2 2.9 - - - -
273A ALA* 3.1 14.5 + - + -
274A PRO* 3.7 3.9 - - - +
291A ILE* 2.5 52.1 - - + +
292A THR* 3.2 4.7 - - - +
295A CYS* 1.6 46.9 - - - -
317A LEU* 4.8 2.0 - - + -
318A LEU 3.9 1.6 - - - -
319A TYR* 3.2 33.4 - - + +
374A ALA* 1.4 68.5 - - - +
376A CYS* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 5.8 3.8 - - + -
237A SER* 2.9 40.4 - - - +
271A THR 2.9 7.6 - - - +
272A TYR* 4.7 13.7 - - - -
316A CYS 3.1 2.1 - - - +
317A LEU* 2.9 27.4 - - - +
318A LEU* 3.1 31.0 + - + +
320A ARG* 4.9 6.3 - - - -
374A ALA* 5.1 0.2 - - - -
375A VAL* 1.3 83.5 - - - +
377A MET* 1.3 61.0 + - - +
378A LEU* 3.7 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 2.3 23.3 - - - +
270A ALA* 3.0 13.5 - - - -
271A THR* 2.3 48.3 + - + +
295A CYS* 3.9 22.0 - - + +
296A PHE* 3.8 14.6 - - + -
312A TYR* 2.3 56.1 - - + +
315A CYS* 4.0 4.0 - - - -
317A LEU* 3.5 20.4 - - + -
376A CYS* 1.3 71.5 - - - +
378A LEU* 1.2 56.5 + - - +
379A SER* 3.4 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 3.0 49.4 - - + -
234A ILE* 4.7 1.3 - - + -
238A ILE* 3.8 22.4 - - + -
255A PHE* 4.1 15.0 - - + -
259A LEU* 3.8 16.3 - - + +
268A PRO* 4.8 0.2 - - - -
269A LEU 2.6 16.2 - - - +
270A ALA* 3.9 14.6 - - + -
314A ALA 3.5 0.9 - - - +
315A CYS* 3.5 0.2 - - - -
316A CYS* 2.7 51.4 + - + +
318A LEU* 4.8 8.1 - - + -
376A CYS* 4.8 7.4 - - + +
377A MET* 1.2 80.3 - - - +
379A SER* 1.3 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE 3.6 0.3 - - - +
268A PRO* 2.9 6.9 - - - +
269A LEU* 2.9 45.3 + - - +
312A TYR* 3.8 10.7 - - - -
314A ALA 2.7 11.4 - - - -
315A CYS* 3.9 3.6 - - - -
377A MET* 3.4 33.0 - - - +
378A LEU* 1.3 73.9 - - - +
380A ASN* 1.1 69.9 - - - +
381A THR* 3.8 8.7 + - - +
384A ILE* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 2.4 54.7 + - - +
261A PRO* 4.6 6.1 - - + -
266A HIS* 4.3 3.5 - - + -
267A PHE 2.2 42.3 + - - +
268A PRO* 3.6 2.4 - - - +
313A MET* 2.3 58.5 + - + +
314A ALA* 2.6 18.7 + - - +
379A SER* 1.1 80.5 - - - +
381A THR* 1.2 54.9 + - - +
384A ILE* 5.5 0.7 - - - -
432A TYR* 5.4 5.2 - - + +
----------------------------------------------------------
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