Contacts of the helix formed by residues 330 - 355 (chain A) in PDB entry 1X7X
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 ASP 330 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.8 13.2 - - - -
329A TRP* 1.3 79.2 - - - +
331A GLU* 1.3 64.0 + - - +
332A GLU* 3.2 11.4 + - - +
333A GLN* 2.9 43.5 + - - +
334A GLU* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.8 1.4 - - - +
330A ASP* 1.3 74.4 - - - +
332A GLU* 1.3 60.6 + - + +
334A GLU* 3.2 17.2 + - - +
335A LYS* 3.0 54.7 + - + +
338A ARG* 4.9 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASP* 3.2 11.5 + - - +
331A GLU* 1.3 77.8 - - + +
333A GLN* 1.3 57.9 + - + +
335A LYS* 3.6 22.5 + - - +
336A ALA* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 5.8 1.0 - - - +
327A GLY 5.5 1.4 + - - -
328A TRP 4.2 5.2 + - - +
329A TRP* 3.5 44.5 - - + +
330A ASP* 2.9 46.8 + - - +
332A GLU* 1.3 72.5 - - + +
334A GLU* 1.3 60.1 + - - +
336A ALA* 3.9 5.7 - - - +
337A TRP* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 2.5 33.0 + - - -
65A THR* 5.5 1.5 - - - +
320A ARG* 3.8 15.9 + - - +
329A TRP* 2.8 26.0 + - + +
330A ASP 3.0 15.0 + - - +
331A GLU* 3.2 17.5 + - - +
333A GLN* 1.3 77.9 - - - +
335A LYS* 1.3 57.6 + - + +
337A TRP* 3.3 4.2 + - - +
338A ARG* 2.9 74.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLU* 3.0 39.2 + - + +
332A GLU* 3.7 24.3 + - - +
334A GLU* 1.3 72.9 - - + +
336A ALA* 1.3 66.0 + - - +
338A ARG* 3.4 14.7 + - - +
339A LYS* 3.1 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLU 3.1 15.5 + - - +
333A GLN* 3.9 6.7 - - - +
335A LYS* 1.3 78.7 - - - +
337A TRP* 1.3 57.4 + - - +
339A LYS* 3.6 6.4 + - - +
340A GLN* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.7 4.9 - + - -
62A LYS* 3.5 58.7 - - + +
65A THR* 2.7 31.3 + - + -
66A LEU* 4.2 11.2 - - + +
329A TRP* 3.8 23.8 - + + -
333A GLN 2.8 23.3 + - - +
334A GLU* 3.8 3.8 - - - +
335A LYS 3.2 0.2 - - - -
336A ALA* 1.3 70.6 - - - +
338A ARG* 1.3 58.1 + - + +
340A GLN* 3.6 34.8 - - + -
341A SER* 2.7 57.9 + - - -
344A LYS* 4.6 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 5.3 2.2 + - - -
320A ARG* 4.6 12.3 - - - +
331A GLU* 4.9 6.3 + - - -
334A GLU* 2.9 54.8 + - - +
335A LYS* 3.4 12.6 + - - +
337A TRP* 1.3 77.6 - - + +
339A LYS* 1.3 58.1 + - - +
341A SER* 3.3 5.6 + - - -
342A ARG* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LYS 3.1 14.4 + - - +
336A ALA* 3.8 7.2 - - - +
338A ARG* 1.3 77.4 - - - +
340A GLN* 1.3 64.7 + - - +
342A ARG* 3.7 9.7 + - - +
343A ARG* 3.1 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 5.7 1.6 - - - +
336A ALA 3.0 19.1 + - - +
337A TRP* 3.3 29.8 + - + +
339A LYS* 1.3 78.0 - - - +
341A SER* 1.3 58.0 + - - +
343A ARG* 3.5 7.9 + - - +
344A LYS* 3.0 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 5.5 0.5 - - - -
66A LEU* 3.5 26.9 - - - -
69A THR* 3.8 15.8 + - - -
337A TRP* 2.7 45.5 + - - -
338A ARG* 3.3 8.3 + - - -
340A GLN* 1.3 75.4 - - - +
342A ARG* 1.3 68.2 + - - +
344A LYS* 3.9 3.4 - - - +
345A VAL* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 3.9 18.0 - - + +
73A ILE* 4.6 9.3 - - + +
338A ARG 3.0 20.1 + - - +
339A LYS* 3.7 11.3 + - - +
341A SER* 1.3 77.7 + - - +
343A ARG* 1.3 68.9 - - - +
345A VAL* 3.9 1.0 - - - +
346A MET* 3.0 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LYS* 3.1 38.3 + - - +
340A GLN* 3.8 6.5 - - - +
342A ARG* 1.3 86.2 - - - +
344A LYS* 1.3 60.9 + - + +
346A MET* 3.8 5.0 - - + +
347A GLU* 2.9 66.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.9 12.1 - - + -
126A LEU* 3.8 19.1 - - + +
337A TRP* 4.6 15.0 - - - -
340A GLN* 3.0 49.4 + - + +
341A SER* 3.5 6.0 + - - +
343A ARG* 1.3 75.0 - - + +
345A VAL* 1.3 61.6 + - - +
347A GLU* 3.4 13.1 + - - +
348A ALA* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.7 20.2 - - + -
69A THR* 3.9 11.2 - - + -
70A MET* 3.9 25.1 - - + +
73A ILE* 3.5 29.2 - - + -
126A LEU* 4.1 12.6 - - + -
130A MET* 3.8 21.0 - - + +
341A SER 3.0 22.2 + - - +
342A ARG 4.0 2.9 - - - +
344A LYS* 1.3 73.0 - - - +
346A MET* 1.3 59.1 + - - +
348A ALA* 3.3 4.5 + - - +
349A PHE* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.8 36.6 - - + -
342A ARG* 3.0 45.5 + - - +
343A ARG* 4.0 5.6 - - + +
345A VAL* 1.3 72.9 - - - +
347A GLU* 1.3 66.0 + - + +
349A PHE* 4.0 22.2 - - + -
350A GLU* 3.1 54.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 2.9 50.6 + - + +
344A LYS* 3.7 12.6 - - - +
346A MET* 1.3 76.5 - - + +
348A ALA* 1.3 61.1 + - - +
350A GLU* 4.1 5.9 - - - +
351A GLN* 3.2 32.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
126A LEU* 3.7 34.8 - - + -
127A GLU* 4.1 8.3 - - + +
130A MET* 4.0 14.0 - - + +
344A LYS 3.2 10.1 + - - +
345A VAL* 3.6 7.6 - - - +
346A MET 3.3 0.2 - - - -
347A GLU* 1.3 77.6 - - - +
349A PHE* 1.3 52.8 + - - +
351A GLN* 3.5 4.8 + - - +
352A ALA* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.8 23.6 - - + -
74A LEU* 4.0 14.6 - - + -
77A SER* 3.5 24.0 - - - -
82A ARG* 3.9 15.0 - - - -
130A MET* 4.0 14.6 - - + +
134A TYR* 2.9 30.0 - + - -
345A VAL 2.9 17.6 + - - +
346A MET* 3.7 28.3 - - + +
347A GLU 3.3 0.2 - - - -
348A ALA* 1.3 76.0 - - - +
350A GLU* 1.3 64.9 + - + +
352A ALA* 3.3 3.3 + - - +
353A GLU* 3.0 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A MET* 3.1 37.4 + - + +
347A GLU* 4.2 5.7 - - - +
349A PHE* 1.3 88.7 - - + +
351A GLN* 1.3 68.5 + - - +
353A GLU* 3.5 6.2 + - - +
354A ARG* 3.2 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 5.9 1.1 - - - +
347A GLU* 3.2 21.1 + - + +
348A ALA* 4.0 4.3 - - - +
350A GLU* 1.3 79.2 - - - +
352A ALA* 1.3 61.3 + - - +
354A ARG* 3.3 26.6 + - - +
355A LYS* 3.2 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 5.2 1.6 - - - +
130A MET* 3.3 27.6 - - + -
131A ALA 4.4 0.2 - - - +
134A TYR* 3.9 18.6 - - + +
136A ASN* 3.0 35.5 + - - +
348A ALA 2.9 19.4 + - - +
349A PHE 3.5 5.2 - - - +
350A GLU 3.2 0.2 - - - -
351A GLN* 1.3 77.0 - - - +
353A GLU* 1.3 60.6 + - - +
354A ARG 3.4 0.7 + - - -
355A LYS* 3.6 9.3 + - - +
357A LYS* 5.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 2.8 48.7 + - - +
134A TYR* 3.0 43.6 + - + +
349A PHE* 3.0 29.2 + - + +
350A GLU* 3.8 8.2 - - - +
351A GLN 3.3 0.2 - - - -
352A ALA* 1.3 75.0 - - - +
354A ARG* 1.3 64.8 + - + +
355A LYS 3.5 5.1 + - - +
357A LYS* 5.3 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A GLU* 3.2 50.7 + - - +
351A GLN* 3.3 22.7 + - - +
353A GLU* 1.3 80.1 + - + +
355A LYS* 1.3 66.0 + - - +
356A PRO* 3.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 2.7 38.9 + - - +
136A ASN* 3.5 36.9 - - + +
137A ILE* 4.1 9.9 - - + -
138A SER* 2.7 30.3 + - - +
351A GLN* 3.2 28.8 + - - +
352A ALA* 4.3 2.3 - - - +
353A GLU 3.5 7.1 - - - +
354A ARG* 1.3 79.4 - - - +
356A PRO* 1.3 74.1 - - + +
357A LYS* 4.5 8.0 + - - +
----------------------------------------------------------
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