Contacts of the helix formed by residues 415 - 431 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414I LEU* 1.3 73.5 - - - +
416I ARG* 1.3 63.7 + - - +
417I PHE* 3.6 4.6 + - - +
418I GLU* 2.8 43.3 + - - +
419I THR* 2.8 27.6 + - - -
17J ASN* 4.4 12.0 + - - -
18J VAL* 4.1 14.1 - - - +
21J GLU* 3.4 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 416 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415I SER* 1.3 70.6 - - - +
417I PHE* 1.3 56.0 + - - +
419I THR* 3.3 7.9 + - - -
420I LYS* 3.0 29.9 + - - +
18J VAL 5.2 2.8 + - - -
21J GLU* 2.8 61.8 + - - +
22J LYS 3.1 21.0 + - - -
23J ALA* 3.9 19.8 + - - +
25J THR* 6.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 417 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I ASN* 6.1 1.6 - - - -
239I ALA* 4.6 13.0 - - + -
415I SER* 3.2 4.2 - - - +
416I ARG* 1.3 74.3 - - - +
418I GLU* 1.3 58.1 + - + +
420I LYS* 3.3 7.8 + - + +
421I ALA* 3.0 30.6 + - + +
21J GLU* 2.7 20.4 + - - +
26J PRO* 4.2 19.1 - - + -
92J VAL 3.5 25.6 - - - -
93J ILE* 4.0 7.0 - - + -
94J PHE* 3.5 48.9 - + + -
97J ASN* 3.4 30.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 418 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I ALA* 5.1 4.3 - - + -
240I HIS* 3.8 25.8 + - - +
241I THR* 2.9 40.5 + - + +
365I PRO* 4.9 0.2 - - - -
414I LEU* 3.5 11.3 - - + +
415I SER* 2.8 41.6 + - - +
417I PHE* 1.3 75.7 - - + +
419I THR* 1.3 65.1 + - - +
421I ALA* 4.9 0.9 - - - -
422I LEU* 3.1 14.4 + - - +
15J ARG* 2.9 38.3 + - - -
17J ASN* 3.7 9.3 - - - +
94J PHE* 6.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 419 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408I ALA* 5.8 2.8 - - + +
414I LEU* 3.8 19.8 + - + +
415I SER 2.8 17.2 + - - -
416I ARG* 3.6 10.5 - - - -
418I GLU* 1.3 75.4 - - - +
420I LYS* 1.3 58.3 + - - +
422I LEU* 3.3 11.1 + - + +
423I ALA* 3.0 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416I ARG 3.0 17.2 + - - +
417I PHE* 3.6 9.2 - - + +
419I THR* 1.3 75.6 - - - +
421I ALA* 1.3 60.5 + - - +
422I LEU 3.2 0.2 + - - -
423I ALA* 3.3 8.3 + - + +
424I ASP* 2.9 63.9 + - - +
27J GLU* 4.9 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I ASN* 5.6 3.4 - - - +
239I ALA* 3.8 27.4 - - + -
241I THR* 3.8 5.4 - - - +
242I ILE* 4.0 17.8 - - + +
417I PHE* 3.0 22.4 + - + +
420I LYS* 1.3 75.8 - - - +
422I LEU* 1.3 56.2 + - - +
424I ASP* 3.4 9.8 + - - +
425I ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241I THR* 3.8 17.2 + - + +
244I VAL* 5.8 0.2 - - + -
245I ILE* 4.7 7.6 - - + -
400I CYS* 6.1 0.2 - - - -
401I CYS* 4.0 33.4 - - + +
404I ILE* 3.8 30.1 - - + -
405I GLU* 3.8 29.8 - - + +
408I ALA* 5.7 0.4 - - + -
414I LEU* 4.3 13.5 - - + -
418I GLU 3.1 17.4 + - - +
419I THR* 3.5 10.3 - - + +
420I LYS 3.1 0.6 - - - -
421I ALA* 1.3 74.4 - - - +
423I ALA* 1.3 60.3 + - - +
425I ALA* 3.2 5.6 + - - +
426I LYS* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405I GLU* 4.7 11.2 + - - +
419I THR* 3.0 19.5 + - + +
420I LYS* 3.9 8.7 - - + +
422I LEU* 1.3 72.6 - - - +
424I ASP* 1.3 66.8 + - - +
426I LYS* 3.8 8.1 - - + +
427I ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 424 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420I LYS* 2.9 52.8 + - - +
421I ALA* 3.5 8.6 - - - +
423I ALA* 1.3 77.4 - - - +
425I ALA* 1.3 62.4 + - - +
427I ALA* 3.4 6.0 + - - +
428I ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I ILE* 3.8 30.6 - - + +
242I ILE* 5.0 3.6 - - + -
245I ILE* 3.5 28.7 - - + -
401I CYS* 4.7 0.2 - - - -
421I ALA 2.9 18.7 + - - +
422I LEU 3.7 2.0 - - - +
424I ASP* 1.3 74.3 - - - +
426I LYS* 1.3 65.8 + - - +
428I ALA* 3.5 3.0 + - - +
429I LEU* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I ILE* 5.0 5.5 - - + +
401I CYS* 3.9 27.0 - - + -
402I ASN* 2.8 28.9 + - - +
405I GLU* 3.3 32.4 + - - +
422I LEU 2.9 16.4 + - - +
423I ALA* 3.8 7.0 - - - +
425I ALA* 1.3 76.8 - - - +
427I ALA* 1.3 61.0 + - - +
429I LEU* 3.2 6.0 + - - +
430I GLU* 2.8 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 427 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I ALA 3.0 18.0 + - - +
424I ASP* 3.6 6.5 - - - +
425I ALA 3.3 0.2 - - - -
426I LYS* 1.3 76.1 - - - +
428I ALA* 1.3 62.5 + - - +
430I GLU* 3.2 7.2 + - - +
431I ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I ILE* 4.4 8.7 - - + -
182I PRO* 4.2 24.6 - - + +
424I ASP 3.1 13.7 + - - +
425I ALA* 3.8 8.1 - - - +
426I LYS 3.4 0.2 - - - -
427I ALA* 1.3 77.0 - - - +
429I LEU* 1.3 61.9 + - - +
431I ALA* 3.5 12.8 + - - +
432I LEU* 3.5 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I ILE* 3.8 27.1 - - + +
185I LEU* 4.0 29.4 - - + -
245I ILE* 4.6 4.0 - - + -
249I ILE* 5.8 0.7 - - + -
394I LYS* 4.3 8.3 + - + +
397I ALA* 3.5 42.6 - - + +
398I ILE* 3.7 22.5 - - + +
401I CYS* 4.2 12.6 - - - -
425I ALA 3.1 21.2 + - - +
426I LYS* 3.2 4.5 + - - +
428I ALA* 1.3 77.1 - - - +
430I GLU* 1.3 61.7 + - - +
432I LEU* 3.2 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 430 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394I LYS* 5.5 0.9 + - - +
398I ILE* 4.1 27.6 - - + +
426I LYS* 2.8 57.8 + - + +
427I ALA* 3.2 6.0 + - - +
429I LEU* 1.3 71.2 - - - +
431I ALA* 1.3 62.5 + - - +
432I LEU 3.0 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427I ALA 3.0 16.4 + - - +
428I ALA* 3.7 9.0 - - - +
429I LEU 3.3 0.4 - - - -
430I GLU* 1.3 75.7 - - - +
432I LEU* 1.3 62.0 + - + +
433I PRO* 3.9 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