Contacts of the strand formed by residues 349 - 359 (chain A) in PDB entry 5X61
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 GLY 349 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASN* 3.7 1.2 + - - -
270A ALA 3.5 11.0 - - - -
272A VAL* 3.7 15.3 - - - -
303A ILE* 3.9 6.7 - - - +
344A ILE* 2.8 16.4 + - - -
345A HIS* 3.2 29.8 + - - +
347A PHE 3.6 1.0 - - - -
348A GLY* 1.3 79.3 - - - +
350A ASP* 1.3 60.0 + - - -
351A PRO* 3.5 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASN* 3.0 31.4 + - - +
270A ALA 2.8 17.1 + - - +
272A VAL* 3.8 3.9 - - - +
344A ILE* 4.1 2.0 - - - -
349A GLY* 1.3 72.5 - - - -
351A PRO* 1.3 62.2 - - - +
352A SER* 2.9 27.2 + - - -
353A ARG* 2.8 59.0 + - + -
354A VAL* 3.8 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASN* 4.7 1.1 - - - +
341A ARG* 3.5 59.8 + - - +
344A ILE* 3.8 17.5 - - + -
345A HIS* 4.1 21.3 - - + +
349A GLY 3.5 9.4 - - - +
350A ASP* 1.3 87.9 - - - +
352A SER* 1.3 55.9 + - - +
353A ARG 3.5 0.4 - - - -
354A VAL* 4.0 13.0 + - + +
378A LEU 4.7 3.5 - - - +
379A PHE* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG* 5.1 5.8 - - - +
350A ASP* 2.8 23.7 + - - -
351A PRO* 1.3 78.2 - - - +
353A ARG* 1.3 63.3 + - - +
354A VAL 3.5 2.7 - - - -
379A PHE 5.2 0.6 - - - -
380A GLN* 3.3 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASN* 4.6 4.8 + - - -
270A ALA* 4.0 6.7 - - - +
271A ALA* 3.8 25.9 - - + +
272A VAL 3.2 20.0 + - - +
350A ASP* 2.8 39.4 + - + +
352A SER* 1.3 85.1 - - - +
354A VAL* 1.3 60.2 + - - +
355A THR* 3.6 5.5 + - - -
380A GLN* 3.4 23.7 + - - +
381A ARG* 5.7 0.4 - - - +
637A ALA 4.5 3.0 + - - +
638A LYS* 3.0 38.8 + - - +
802A SO4 2.9 42.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 3.5 16.6 - - + +
274A LEU* 4.2 19.7 - - + -
337A LEU* 5.4 0.9 - - + -
340A VAL* 4.0 21.5 - - + -
341A ARG* 5.7 1.1 - - - +
350A ASP 3.9 13.7 - - - +
351A PRO* 4.0 15.9 - - + +
352A SER 3.5 3.2 + - - -
353A ARG* 1.3 74.4 - - - +
355A THR* 1.3 60.9 + - - +
356A LEU* 4.0 22.7 - - + -
378A LEU 4.6 6.7 - - - +
379A PHE* 3.5 17.6 - - + +
380A GLN* 2.7 28.2 + - - +
381A ARG 3.3 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL 2.7 12.3 + - - -
273A MET* 3.5 5.1 - - + -
274A LEU 2.9 26.7 + - - -
353A ARG 3.6 2.6 + - - -
354A VAL* 1.3 71.6 - - - +
356A LEU* 1.3 71.6 + - - +
357A PHE* 3.6 2.1 + - + -
380A GLN* 5.1 0.2 + - - -
381A ARG* 3.4 31.2 + - + +
383A ILE* 4.1 22.0 - - + -
636A PHE* 4.6 0.9 - - + -
637A ALA* 3.3 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 3.6 22.2 - - + +
276A ILE* 4.5 4.9 - - + -
337A LEU* 3.6 28.5 - - + -
354A VAL* 4.0 11.9 - - + -
355A THR* 1.3 72.9 - - - +
357A PHE* 1.3 53.4 + - - +
366A VAL* 3.7 20.7 - - + +
369A HIS* 3.8 33.7 - - + -
379A PHE* 3.7 37.5 - - + -
381A ARG 3.0 9.8 + - - +
382A ALA* 3.2 2.4 - - - -
383A ILE 2.7 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A MET* 3.7 44.0 - - + -
274A LEU 2.8 51.0 + - - +
275A TRP* 3.1 50.5 - + + -
276A ILE 3.1 21.5 + - - -
296A LEU* 3.9 17.7 - - + -
304A VAL* 5.2 1.3 - - + -
355A THR* 4.1 2.9 - - + +
356A LEU* 1.3 75.2 - - - +
358A GLY* 1.3 57.7 + - - +
366A VAL* 3.8 4.5 - - - +
383A ILE* 3.2 29.4 - - + -
385A GLN* 4.4 4.7 - - - +
607A VAL* 5.1 5.2 - - + -
608A PHE* 3.9 12.6 - + - -
633A TRP* 4.2 14.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TRP* 3.6 9.3 - - - -
276A ILE 3.2 16.4 - - - -
357A PHE* 1.3 75.7 - - - +
359A GLU* 1.3 59.2 + - - -
362A GLY 3.8 10.3 - - - -
363A ALA* 3.4 10.0 - - - +
366A VAL* 3.6 3.4 - - - +
383A ILE 3.3 5.3 + - - -
384A LEU 3.9 0.2 - - - -
385A GLN* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TRP* 3.6 23.4 - - + -
276A ILE 4.0 1.0 + - - -
278A GLY* 3.4 16.3 + - - +
358A GLY* 1.3 73.7 - - - -
360A SER* 1.3 83.7 + - - +
361A ALA 3.2 0.2 + - - -
362A GLY* 2.9 17.7 + - - -
363A ALA 3.5 1.0 - - - +
385A GLN* 3.2 28.3 - - + +
386A SER* 3.8 5.9 + - - -
600A HIS* 3.3 27.5 + - - -
601A GLY* 3.4 17.6 + - - -
603A GLU* 4.0 4.5 - - - +
604A ILE* 3.6 25.6 - - + +
----------------------------------------------------------
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