Contacts of the strand formed by residues 371 - 379 (chain A) in PDB entry 1TFZ
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 PHE 371 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN* 3.1 37.2 + - + -
287A HIS* 3.1 47.8 - + + +
288A LEU 3.4 3.5 + - - -
314A MET* 5.7 0.9 - - + -
360A PHE* 3.6 26.5 - + + -
361A THR* 3.6 22.4 - - - +
362A LYS 4.0 4.9 - - - +
363A PRO* 4.1 9.0 - - + -
364A LEU* 3.9 9.2 - - - -
369A THR 3.5 13.5 - - - -
370A ILE* 1.3 77.4 - - - +
372A ILE* 1.3 75.3 + - - +
551A 869 4.0 37.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.5 0.7 - - + -
47A LEU* 3.9 32.3 - - + -
76A PHE* 4.3 10.8 - - + -
287A HIS* 5.1 0.4 - - - -
288A LEU* 3.6 16.8 - - + +
290A LEU* 3.8 15.7 - - + -
311A PHE* 5.3 1.6 - - + -
360A PHE* 3.4 3.8 - - - -
361A THR* 2.9 46.4 + - + +
364A LEU* 3.7 28.7 - - + +
371A PHE* 1.3 84.4 - - - +
373A GLU* 1.3 72.6 + - - +
374A ILE* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A HIS* 3.3 6.2 + - - -
287A HIS* 3.3 6.9 + - + -
288A LEU 2.9 6.3 + - - +
289A ALA* 3.4 16.7 - - + +
290A LEU* 2.7 33.4 + - - -
358A GLN* 2.8 34.1 + - + +
359A ILE 3.3 7.2 - - - +
360A PHE* 3.4 24.0 - - + -
372A ILE* 1.3 78.6 - - - +
374A ILE* 1.3 68.0 + - - +
375A ILE* 3.9 10.3 - - + +
398A PHE 4.7 0.3 - - - +
425A FE 2.0 32.5 - - - -
551A 869 3.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ILE* 4.0 16.8 - - + -
290A LEU* 3.5 11.2 - - + +
292A SER* 4.0 15.5 - - - -
295A ILE* 3.7 7.4 - - + +
298A THR* 3.9 19.5 - - + -
299A LEU* 4.0 10.8 - - + -
302A MET* 4.0 27.8 - - + -
313A PHE* 4.5 7.0 - - + -
358A GLN* 3.2 5.9 - - - +
359A ILE* 3.0 46.9 + - + -
361A THR* 5.2 1.1 - - + -
372A ILE* 3.8 18.8 - - + -
373A GLU* 1.3 80.4 - - - +
375A ILE* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 4.0 22.4 - - + +
205A HIS* 4.5 6.3 - - + -
289A ALA* 4.5 5.4 - - + -
290A LEU 3.0 15.7 + - - +
291A MET* 3.3 10.7 - - + -
292A SER* 2.8 30.0 + - - -
295A ILE* 4.4 3.4 - - - -
356A LEU* 4.0 21.3 - - + -
357A LEU 3.2 13.7 - - - +
358A GLN* 4.3 2.2 - - + +
373A GLU* 3.9 20.2 - - + +
374A ILE* 1.3 78.1 - - - +
376A GLN* 1.3 72.7 + - - +
377A ARG* 3.7 34.1 - - + +
397A GLY 4.9 0.4 - - - +
398A PHE* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A MET* 5.2 4.5 - - + -
292A SER 3.1 17.6 + - - +
293A GLU* 3.0 28.7 + - - +
294A ASP* 3.6 2.2 - - - +
295A ILE* 2.9 42.2 + - + +
356A LEU* 3.4 1.0 - - - -
357A LEU* 2.7 46.5 + - + +
375A ILE* 1.3 76.6 - - - +
377A ARG* 1.3 70.2 + - - +
378A VAL* 4.8 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ARG* 5.7 2.7 - - - +
204A ASP* 2.9 41.5 + - - +
291A MET* 5.8 2.9 - - + +
355A THR 3.4 3.8 - - - -
356A LEU* 3.6 11.6 - - + +
375A ILE* 3.7 17.9 - - + +
376A GLN* 1.3 84.3 - - - +
378A VAL* 1.3 60.9 + - - +
391A GLN* 3.0 34.0 + - - +
392A SER 5.1 0.7 - - - -
393A GLY* 5.8 0.4 - - - -
394A GLY* 3.5 15.3 - - - +
395A CYS* 3.0 46.8 + - - +
397A GLY 2.7 31.1 + - - +
398A PHE* 3.6 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL* 4.3 18.6 - - + +
333A LEU* 5.2 6.7 - - + -
354A GLY* 3.1 5.2 - - - -
355A THR* 2.7 57.7 + - + +
357A LEU* 4.9 13.0 - - + -
376A GLN* 4.8 8.1 - - + +
377A ARG* 1.3 77.9 - - - +
379A GLY* 1.3 61.2 + - - +
391A GLN* 3.8 1.3 - - - -
395A CYS* 4.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLN 3.5 8.3 - - - -
378A VAL* 1.3 77.5 - - - +
380A CYS* 1.3 69.3 + - - -
381A MET* 3.1 15.3 + - - +
391A GLN* 3.0 22.7 + - - +
395A CYS* 3.4 3.4 - - - -
----------------------------------------------------------
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