Contacts of the strand formed by residues 333 - 347 (chain A) in PDB entry 1NQF
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 TYR 333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN 3.5 0.2 - - - +
321A MSE 3.7 1.2 - - - -
322A THR* 2.8 42.2 + - - +
331A ASP* 3.5 41.7 + - - -
332A GLY* 1.3 79.2 - - - -
334A ASP* 1.3 63.3 + - - +
335A GLN* 4.0 7.4 - - + -
398A LEU* 4.8 23.6 - - + -
402A TYR* 3.6 64.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A MSE 4.2 1.9 - - - +
320A GLN 3.1 6.0 - - - +
321A MSE 3.5 26.8 - - + +
333A TYR* 1.3 75.7 - - - +
335A GLN* 1.3 65.6 + - - +
336A ARG* 2.3 51.4 + - - +
363A SER* 4.4 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A MSE 4.3 2.8 - - - +
318A GLN 4.0 0.3 - - - +
319A MSE 3.5 2.4 - - - -
320A GLN* 2.8 68.8 + - + +
322A THR* 4.5 0.6 + - - +
333A TYR* 4.8 10.3 - - + -
334A ASP* 1.3 79.3 - - - +
336A ARG* 1.3 63.5 + - - +
362A ASN* 5.6 5.1 + - - +
363A SER* 4.1 5.4 - - - +
364A GLN* 5.7 5.2 + - + +
396A PRO 4.6 6.7 + - - -
398A LEU* 3.5 34.6 - - + +
401A LEU* 4.3 21.2 - - - +
402A TYR* 6.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A MSE 6.5 0.2 - - + -
318A GLN 3.5 2.5 - - - +
319A MSE 3.0 50.7 - - + +
321A MSE 4.7 3.2 - - - +
334A ASP* 2.3 40.5 + - - -
335A GLN* 1.3 74.2 - - - +
337A ASN* 1.3 61.4 + - - +
361A ASP 4.3 0.6 - - - +
362A ASN* 3.9 3.7 - - - +
363A SER* 2.9 43.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 5.9 0.6 - - - -
316A ASP 4.0 0.9 - - - +
317A MSE 3.5 1.2 - - - +
318A GLN* 2.8 56.0 + - + +
336A ARG* 1.3 76.2 - - - +
338A THR* 1.3 80.8 + - - +
358A ARG* 4.3 2.4 + - - -
360A ASP* 3.1 23.6 + - - +
361A ASP 3.5 4.4 + - - -
362A ASN* 3.1 37.8 + - - +
365A PHE* 4.6 2.0 - - - -
393A TYR* 4.3 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 5.1 8.7 - - + -
316A ASP 3.4 5.8 - - - +
317A MSE 3.6 25.6 - - + +
337A ASN* 1.3 83.2 + - - +
339A GLY* 1.3 65.0 + - - +
340A ILE* 6.0 0.9 - - + -
359A SER 4.0 0.3 - - - +
360A ASP* 3.5 0.5 - - - -
361A ASP* 2.6 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 3.5 6.4 - - - +
316A ASP* 2.7 44.6 + - - +
337A ASN* 4.2 1.0 + - - -
338A THR* 1.3 80.0 - - - +
340A ILE* 1.3 62.5 + - - +
341A TYR* 4.3 0.6 - - - -
358A ARG* 4.0 8.4 - - - +
359A SER 3.1 10.1 - - - -
360A ASP* 3.9 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLY 3.7 9.9 - - - +
315A VAL* 4.4 14.6 - - + -
338A THR* 6.0 0.7 - - + -
339A GLY* 1.3 76.1 - - - +
341A TYR* 1.3 61.0 + - - +
358A ARG* 3.4 2.2 - - - +
359A SER* 2.6 58.8 + - - +
800A C8E 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN 5.7 1.6 - - - -
14A ARG* 2.9 48.9 + - + +
15A PHE* 5.5 0.3 - - - -
116A ALA 3.8 4.5 - - - +
117A VAL* 3.7 18.4 - - + -
301A ALA* 3.5 18.7 - - - +
313A ALA* 3.1 10.5 - - - +
314A GLY 3.1 50.1 + - - +
315A VAL 4.4 0.7 - - - -
316A ASP* 5.0 4.3 - - + -
339A GLY 5.1 1.3 - - - -
340A ILE* 1.3 78.1 - - - +
342A LEU* 1.3 63.1 + - - +
343A THR* 3.8 28.3 - - + -
357A ALA 3.2 13.9 - - - +
358A ARG* 3.7 21.5 - - + -
800A C8E 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ILE* 4.5 4.0 - - + -
312A GLY 3.1 10.1 - - - +
313A ALA* 4.3 4.7 - - + -
341A TYR* 1.3 76.4 - - - +
343A THR* 1.3 74.6 + - - +
356A ALA* 3.3 2.6 - - - -
357A ALA* 3.0 34.0 + - + +
800A C8E 4.1 28.2 - - + +
803A C8E 2.9 57.9 - - + -
805A C8E 4.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 4.6 22.0 + - + +
117A VAL* 4.0 23.3 - - + -
303A ASN* 4.4 8.1 + - - -
311A ILE* 3.3 2.9 - - - +
312A GLY* 2.6 51.2 + - - +
313A ALA 4.5 0.2 + - - -
341A TYR* 3.8 24.5 - - + -
342A LEU* 1.3 89.2 - - - +
344A GLY* 1.3 56.8 - - - +
355A GLY 3.3 7.6 - - - -
356A ALA* 4.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A SER 3.6 10.3 - - - -
311A ILE* 4.3 1.8 - - - -
343A THR* 1.3 75.7 - - - +
345A LEU* 1.3 58.1 + - - -
354A GLU* 3.1 3.8 - - - +
355A GLY 2.7 41.4 + - - -
803A C8E 3.1 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 6.0 1.1 - - - +
17A GLN* 3.7 26.7 - - + +
21A THR* 2.9 38.8 - - - +
308A HIS 5.1 3.8 - - - +
309A GLY* 3.2 9.0 - - - -
310A SER* 2.8 51.5 + - - +
344A GLY* 1.3 71.5 - - - -
346A GLN* 1.3 70.3 + - - +
347A GLN* 4.8 2.9 - - + +
352A THR* 4.3 13.7 - - + +
353A PHE 3.2 11.2 - - - +
354A GLU* 4.3 12.6 - - + +
803A C8E 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A VAL* 3.3 22.8 + - - +
307A GLY* 5.1 0.2 - - - -
308A HIS* 3.0 38.4 + - - +
309A GLY 4.1 2.8 - - - +
310A SER 4.2 8.9 + - - +
345A LEU* 1.3 87.7 + - - +
347A GLN* 1.3 67.6 + - - +
348A VAL* 5.7 4.9 - - + -
352A THR* 3.7 1.4 - - - -
353A PHE* 2.8 46.1 + - + +
803A C8E 3.9 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A HIS* 3.2 44.2 + - + +
345A LEU* 5.5 2.9 - - + -
346A GLN* 1.3 83.7 + - - +
348A VAL* 1.3 62.8 + - - +
349A GLY 5.1 2.9 - - - +
350A ASP* 5.6 3.1 + - - +
351A PHE 3.3 17.0 + - - +
352A THR* 3.7 14.3 + - - +
384A ARG* 5.5 2.4 + - - -
----------------------------------------------------------
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