Contacts of the helix formed by residues 415 - 431 (chain A) in PDB entry 2I2X
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 SER 415 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 1.3 73.6 - - - +
416A ARG* 1.3 63.6 + - - +
417A PHE* 3.5 5.2 + - - +
418A GLU* 2.9 39.6 + - - +
419A THR* 2.9 26.3 + - - -
17B ASN* 4.3 12.2 + - - -
18B VAL* 3.8 19.3 - - - +
21B GLU* 3.4 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU 4.0 0.4 + - - -
415A SER* 1.3 69.3 - - - +
417A PHE* 1.3 60.2 + - - +
419A THR* 3.1 7.5 + - - -
420A LYS* 3.0 26.2 + - - +
18B VAL 5.4 1.6 + - - -
21B GLU* 2.7 42.4 + - - +
22B LYS 2.8 31.7 + - - -
23B ALA* 3.8 17.0 + - - +
25B THR* 6.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASN* 6.1 1.3 - - - -
239A ALA* 4.4 13.2 - - + -
415A SER* 3.1 4.0 - - - +
416A ARG* 1.3 77.5 - - - +
418A GLU* 1.3 64.2 + - + +
420A LYS* 3.6 5.7 + - + +
421A ALA* 3.2 25.4 + - + +
21B GLU* 2.9 19.5 + - - +
26B PRO* 4.2 19.3 - - + -
92B VAL 3.7 24.2 - - - -
93B ILE* 4.1 6.3 - - + -
94B PHE* 3.5 48.7 - + + -
97B ASN* 3.7 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU 5.5 0.5 - - - +
239A ALA* 4.9 3.4 - - + -
240A HIS* 3.7 27.7 + - - +
241A THR* 2.7 44.2 + - + +
365A PRO* 5.0 1.3 - - - -
414A LEU* 3.6 10.2 - - + -
415A SER* 2.9 41.3 + - - +
417A PHE* 1.3 78.8 - - + +
419A THR* 1.3 57.6 + - - +
421A ALA* 3.6 1.1 + - - -
422A LEU* 3.1 13.9 + - - +
15B ARG* 2.9 38.3 + - - -
17B ASN* 3.8 6.8 - - - +
94B PHE* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA* 5.7 2.8 - - + +
414A LEU* 3.5 25.5 + - + +
415A SER 2.9 18.2 + - - -
416A ARG* 3.1 12.1 + - - -
418A GLU* 1.3 75.0 - - - +
420A LYS* 1.3 60.5 + - - +
422A LEU* 3.5 7.0 + - + +
423A ALA* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG 3.0 15.2 + - - +
417A PHE* 4.0 6.5 - - + +
419A THR* 1.3 76.5 - - - +
421A ALA* 1.3 57.5 + - - +
423A ALA* 3.2 8.1 + - + +
424A ASP* 2.8 67.0 + - - +
27B GLU* 5.2 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASN* 5.9 1.8 - - - +
239A ALA* 4.0 17.3 - - + -
241A THR* 3.9 11.9 - - - +
242A ILE* 4.2 17.4 - - + +
417A PHE* 3.2 21.1 + - + +
419A THR 3.3 0.2 - - - -
420A LYS* 1.3 77.7 - - - +
422A LEU* 1.3 63.3 + - - +
424A ASP* 3.4 8.9 + - - +
425A ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A THR* 3.5 28.5 + - + +
245A ILE* 4.3 4.3 - - + -
401A CYS* 3.9 35.2 - - - +
404A ILE* 3.6 36.6 - - + -
405A GLU* 4.0 29.6 - - + +
408A ALA* 6.1 0.4 - - + -
414A LEU* 4.8 5.6 - - + -
418A GLU 3.1 15.1 + - - +
419A THR* 3.6 10.1 - - + +
421A ALA* 1.3 75.2 - - - +
423A ALA* 1.3 56.4 + - - +
425A ALA* 3.1 6.9 + - - +
426A LYS* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLU* 5.1 6.5 - - - +
419A THR* 3.0 15.2 + - + +
420A LYS* 3.5 13.0 - - + +
422A LEU* 1.3 72.3 - - - +
424A ASP* 1.3 68.2 + - - +
426A LYS* 3.5 6.9 + - - +
427A ALA* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LYS* 2.8 56.7 + - - +
421A ALA* 3.7 8.0 - - - +
423A ALA* 1.3 73.3 - - - +
425A ALA* 1.3 56.9 + - - +
427A ALA* 3.4 6.6 + - - +
428A ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.6 31.8 - - + +
242A ILE* 5.0 2.2 - - + -
245A ILE* 3.5 30.7 - - + -
421A ALA 2.9 17.8 + - - +
422A LEU 3.6 1.1 - - - +
424A ASP* 1.3 75.2 - - - +
426A LYS* 1.3 65.2 + - - +
428A ALA* 3.3 2.8 + - - +
429A LEU* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE* 5.4 4.0 - - + -
401A CYS* 3.9 29.9 - - + -
402A ASN* 3.6 15.3 + - - +
405A GLU* 3.1 40.2 + - - +
422A LEU 2.8 15.4 + - - +
423A ALA* 3.9 5.6 - - - +
424A ASP 3.3 0.2 - - - -
425A ALA* 1.3 76.8 - - - +
427A ALA* 1.3 57.4 + - - +
429A LEU* 3.2 5.1 + - - +
430A GLU* 2.9 65.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ALA 3.1 17.6 + - - +
424A ASP* 3.8 6.3 - - - +
426A LYS* 1.3 76.2 - - - +
428A ALA* 1.3 57.9 + - - +
430A GLU* 3.3 9.6 + - - +
431A ALA* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.6 5.4 - - + -
182A PRO* 4.5 23.9 - - + +
424A ASP 3.0 16.5 + - - +
425A ALA* 3.7 7.2 - - - +
427A ALA* 1.3 75.7 - - - +
429A LEU* 1.3 63.1 + - - +
431A ALA* 3.5 11.9 + - - +
432A LEU* 3.5 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.8 25.8 - - + -
185A LEU* 4.4 25.8 - - + -
245A ILE* 4.5 4.9 - - + -
249A ILE* 5.0 1.1 - - + -
394A LYS* 3.9 14.9 + - + +
397A ALA* 3.8 37.2 - - + +
398A ILE* 3.8 17.4 - - + +
401A CYS* 4.0 24.0 - - - -
425A ALA 2.9 22.3 + - - +
426A LYS* 3.7 3.6 - - - +
428A ALA* 1.3 76.8 - - - +
430A GLU* 1.3 61.8 + - - +
431A ALA 3.4 0.3 + - - -
432A LEU* 3.5 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 6.1 0.2 - - - +
398A ILE* 4.1 28.9 - - + +
426A LYS* 2.9 58.2 + - + +
427A ALA* 3.3 7.7 + - - +
429A LEU* 1.3 78.6 - - - +
431A ALA* 1.3 59.7 + - - +
432A LEU 3.3 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ALA 3.1 16.9 + - - +
428A ALA* 4.0 7.6 - - - +
429A LEU 3.2 0.4 - - - -
430A GLU* 1.3 75.9 - - - +
432A LEU* 1.3 64.9 + - + +
433A PRO* 3.9 1.6 - - - +
----------------------------------------------------------
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