Contacts of the helix formed by residues 346 - 360 (chain A) in PDB entry 1XTB
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 346 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.4 6.8 - - + +
164A LEU* 4.6 20.9 - - + -
165A MET* 3.4 28.8 - - + +
168A GLU* 4.6 10.1 - - + -
343A TYR 4.8 0.8 + - - -
344A LEU 3.1 1.0 - - - -
345A HIS* 1.3 114.9 + - + +
347A PHE* 1.3 59.5 + - - +
348A ALA 3.5 2.2 - - - -
349A ALA* 3.4 25.3 + - - +
350A TYR* 3.0 23.4 + - - +
381A GLU* 4.7 7.3 + - - -
1346B ARG* 3.9 20.8 - - - +
1381B GLU* 3.4 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A MET* 3.7 21.1 - - + +
337A VAL* 3.7 28.0 - - + -
339A PRO* 4.5 10.8 - - + -
344A LEU* 3.0 45.5 + - + +
346A ARG* 1.3 74.4 - - - +
348A ALA* 1.3 64.8 + - - +
350A TYR* 3.1 12.1 + - - +
351A PHE* 3.2 43.8 + + - -
406A LEU* 4.2 14.1 - - + -
486A LEU* 4.6 7.2 - - + -
489A LEU* 4.8 11.0 - - + -
490A ILE* 4.5 14.8 - - + -
493A TYR* 3.9 24.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 4.0 35.9 - - + +
339A PRO* 5.3 3.9 - - + +
344A LEU 4.5 0.8 + - - -
345A HIS 5.2 2.8 + - - +
346A ARG 3.5 0.4 - - - -
347A PHE* 1.3 78.5 - - - +
349A ALA* 1.3 57.5 + - - +
351A PHE* 3.2 4.5 + - - +
352A GLN* 2.9 28.1 + - - +
378A VAL* 4.1 4.9 - - + +
379A TRP* 4.4 3.1 - - - -
380A GLY 3.6 31.9 - - - +
381A GLU* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.3 21.0 - - + +
345A HIS 5.5 0.4 + - - -
346A ARG* 3.4 45.4 + - - +
347A PHE 3.3 0.8 - - - -
348A ALA* 1.3 78.2 - - - +
350A TYR* 1.3 64.9 + - - +
352A GLN* 3.2 27.2 + - - +
353A GLN 3.4 1.6 + - - -
1381B GLU* 4.2 10.5 - - + +
1389B ALA* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.7 16.8 - - + +
162A GLY* 3.4 40.4 - - - -
165A MET* 3.7 24.5 - - + -
272A ARG* 3.2 27.2 + - + -
273A TYR* 4.6 1.2 - - - -
274A SER 5.4 0.2 + - - -
275A LEU* 3.4 19.8 - - + +
346A ARG 3.0 13.4 + - - +
347A PHE 3.1 9.1 + - - +
349A ALA* 1.3 76.3 - - - +
351A PHE* 1.3 83.6 + + - +
353A GLN* 3.2 10.6 + - - +
354A GLY* 3.0 23.3 + - - -
490A ILE* 3.8 19.5 - - + +
494A GLU* 4.2 11.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 5.4 5.2 - - + -
347A PHE* 3.2 54.3 + + - +
348A ALA* 3.2 6.5 + - - +
350A TYR* 1.3 96.5 - + - +
352A GLN* 1.3 59.3 + - - +
353A GLN 3.1 1.6 - - - -
354A GLY* 3.6 5.2 - - - +
355A ASP* 2.7 38.5 + - + +
378A VAL* 4.2 10.8 - - + +
490A ILE* 3.5 32.8 - - + -
493A TYR* 3.3 37.2 - + + -
494A GLU* 4.2 8.7 - - + -
497A ILE* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ALA 2.9 12.7 + - - +
349A ALA* 3.2 19.6 - - - +
350A TYR 3.1 0.2 - - - -
351A PHE* 1.3 76.5 - - - +
353A GLN* 1.3 58.4 + - - +
356A MET* 2.9 45.2 + - - +
378A VAL* 2.9 36.4 + - - +
379A TRP* 4.1 9.7 - - - +
1379B TRP* 3.7 19.8 - - - +
1380B GLY 5.0 3.2 + - - +
1381B GLU* 3.6 17.4 + - - +
1389B ALA* 4.5 0.7 - - + -
1390B PHE* 3.5 32.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY* 3.6 20.6 + - - -
158A GLY* 3.3 6.3 + - - +
161A LEU* 3.3 28.2 - - + +
272A ARG* 4.1 12.5 - - + +
349A ALA 3.4 1.0 + - - -
350A TYR* 3.2 10.6 + - + +
352A GLN* 1.3 79.1 - - - +
354A GLY* 1.3 63.6 + - - +
357A GLU* 2.8 46.4 + - - +
2002A S6P 3.1 16.8 + - - -
1388B HIS 3.0 22.3 - - - +
1389B ALA* 3.1 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 4.2 17.9 - - - -
273A TYR* 3.9 3.9 + - - -
350A TYR* 3.0 18.5 + - - -
351A PHE* 4.0 7.4 - - - -
353A GLN* 1.3 82.5 - - - +
355A ASP* 1.3 55.3 + - - +
358A SER* 2.6 29.1 + - - -
497A ILE* 3.5 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLN* 5.5 1.2 - - - +
351A PHE* 2.7 25.4 + - + +
354A GLY* 1.3 73.0 - - - +
356A MET* 1.3 59.6 + - - +
358A SER* 3.2 2.8 + - - -
359A ASN* 2.9 38.1 + - - +
376A PRO* 4.0 21.2 - - - +
378A VAL* 3.7 22.7 - - + +
496A LYS* 4.9 11.3 + - - +
497A ILE* 3.5 26.6 - - + +
500A GLN* 4.6 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLN* 2.9 38.3 + - - +
355A ASP* 1.3 77.0 - - - +
357A GLU* 1.3 56.4 + - - +
359A ASN 5.2 0.2 - - - -
360A GLY* 2.9 28.9 + - - +
375A GLY* 6.0 0.4 - - - -
376A PRO 3.4 17.0 - - - +
377A ILE* 4.0 10.1 - - + -
378A VAL* 3.5 24.9 - - + +
1379B TRP* 3.8 20.9 - - + -
1390B PHE* 3.7 23.6 - - + +
1392B GLN* 4.1 0.2 - - - +
1393B LEU* 3.7 43.0 + - + +
1394B ILE* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.1 32.0 + - - +
353A GLN* 2.8 29.9 + - - +
356A MET* 1.3 74.5 - - - +
358A SER* 1.3 59.2 + - - +
361A LYS* 3.4 20.1 + - - -
510A ASP 3.9 0.5 - - - +
511A GLN* 4.2 11.4 - - + +
514A VAL* 4.4 9.4 - - - +
2002A S6P 3.1 28.4 + - - -
1387B GLN 4.9 0.2 - - - +
1388B HIS* 3.1 26.1 - - - +
1389B ALA 3.2 12.7 + - - +
1392B GLN* 3.4 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 2.6 23.0 + - - +
273A TYR* 2.8 17.5 + - - -
354A GLY 2.6 22.6 + - - -
355A ASP 3.2 3.2 + - - -
356A MET 3.2 0.4 - - - -
357A GLU* 1.3 78.8 - - - +
359A ASN* 1.3 61.4 + - - +
360A GLY 3.5 0.2 - - - -
361A LYS* 2.8 25.8 + - - +
497A ILE* 3.7 12.3 - - - -
508A SER* 3.3 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASP* 2.9 17.6 + - - +
356A MET 4.8 0.2 - - - -
358A SER* 1.3 74.6 - - - +
360A GLY* 1.3 55.1 + - - +
361A LYS* 2.8 13.6 + - - -
374A THR* 3.4 4.5 + - - -
375A GLY* 2.9 27.4 + - - -
497A ILE* 3.1 35.5 + - - +
500A GLN* 3.9 7.5 + - - +
501A GLY* 3.7 3.6 - - - +
504A TRP* 3.5 30.8 - - + -
506A ILE* 3.7 11.3 - - + +
508A SER* 2.5 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A MET 2.9 21.3 + - - -
357A GLU 4.5 0.2 - - - -
358A SER 3.5 2.0 - - - -
359A ASN* 1.3 74.7 - - - +
361A LYS* 1.3 59.2 + - - -
374A THR* 4.7 0.9 - - - -
375A GLY* 4.8 0.2 - - - -
1392B GLN* 3.0 31.4 + - - +
1393B LEU* 3.7 25.8 - - - -
1396B GLN 3.4 9.2 - - - +
1397B GLY* 3.9 4.9 - - - -
----------------------------------------------------------
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