Contacts of the helix formed by residues 269 - 281 (chain I) in PDB entry 4E2I
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 269 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I GLN 3.9 2.3 + - - -
268I VAL* 1.3 73.0 - - - +
270I TRP* 1.3 61.9 + - - +
271I LYS* 3.7 6.6 + - - +
272I LEU* 3.3 42.6 + - - +
273I VAL* 3.3 10.0 + - - +
323I ASN* 2.6 32.3 + - - -
336I ILE* 4.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 270 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I VAL* 3.6 22.9 - - + +
269I SER* 1.3 73.2 + - - +
271I LYS* 1.3 57.7 + - - +
272I LEU 3.2 2.7 - - - -
273I VAL* 3.3 3.3 + - - +
274I THR* 2.8 37.0 + - - -
332I ASN* 5.1 7.9 - - + -
335I THR* 3.6 33.7 - - + -
336I ILE* 3.6 47.6 - - + +
339I GLN* 3.1 38.6 - - + +
328J ALA 5.3 3.1 - - - +
329J ASP* 5.7 3.8 - - - -
330J SER 4.8 5.4 - - - +
331J LYS* 2.9 71.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I SER* 3.5 5.8 + - - +
270I TRP* 1.3 79.8 - - - +
272I LEU* 1.3 57.4 - - + +
274I THR* 3.7 6.8 - - - -
275I GLU* 2.9 39.9 + - + +
296J GLN* 4.2 23.5 - - - +
297J TYR* 6.1 2.0 - - - -
328J ALA* 4.3 25.1 + - + +
329J ASP* 3.7 30.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I SER* 3.3 22.1 + - - +
270I TRP 3.2 0.4 - - - -
271I LYS* 1.3 77.6 - - + +
273I VAL* 1.3 60.9 + - - +
275I GLU* 3.1 20.1 + - - +
276I TYR* 3.0 24.6 + - - +
292I TYR* 4.1 0.7 - - - +
319I LYS* 4.9 7.4 - - + +
320I HIS* 3.2 29.3 - - + +
322I ALA* 5.8 3.1 - - + -
323I ASN* 3.5 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I SER 3.3 9.4 - - - +
270I TRP 3.3 4.7 + - - +
272I LEU* 1.3 76.0 - - - +
274I THR* 1.3 58.2 + - - +
276I TYR* 3.3 4.3 + - - +
277I ALA* 3.0 26.3 + - - +
288I LEU* 5.1 5.3 - - + +
292I TYR* 3.5 29.6 - - + -
323I ASN* 3.2 25.6 - - - +
327I PHE* 4.8 2.7 - - + -
336I ILE* 3.6 33.4 - - + +
337I CYS* 4.2 23.8 - - - -
340I ALA* 4.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 274 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I TRP 2.8 22.7 + - - -
271I LYS* 3.7 8.6 - - - -
273I VAL* 1.3 73.4 - - - +
275I GLU* 1.3 60.5 + - - +
277I ALA* 3.2 1.9 + - - +
278I MET* 2.9 30.7 + - + +
336I ILE 5.3 1.2 + - - -
339I GLN* 4.2 13.2 + - - -
340I ALA* 3.9 17.6 + - - +
343I THR* 3.6 41.0 + - + +
293J LEU* 6.4 0.2 - - + -
328J ALA 5.6 0.6 + - - -
333J GLN* 4.9 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271I LYS* 2.9 27.2 + - + +
272I LEU* 3.1 28.2 + - - +
274I THR* 1.3 78.1 - - - +
276I TYR* 1.3 62.5 + - - +
278I MET* 3.1 9.8 + - + +
279I GLU* 3.0 35.0 + - + +
319I LYS* 3.2 35.9 + - - -
320I HIS* 3.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 276 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I LEU 3.0 8.1 + - - +
273I VAL 3.3 7.4 + - - +
275I GLU* 1.3 77.9 - - - +
277I ALA* 1.3 61.9 + - - +
279I GLU* 3.2 6.4 + - - +
280I THR* 3.1 46.6 + - + +
288I LEU* 4.1 23.1 - - + -
291I MET* 3.8 23.2 - - + +
292I TYR* 3.6 21.5 - + + -
295I PHE* 3.8 19.8 - + - -
312I SER* 2.7 34.9 + - - -
316I TYR* 3.6 34.8 - + + -
320I HIS* 3.2 24.6 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273I VAL 3.0 14.0 + - - +
274I THR 3.3 9.6 - - - +
275I GLU 3.1 0.2 - - - -
276I TYR* 1.3 78.5 - - - +
278I MET* 1.3 52.0 + - - +
280I THR* 4.2 0.9 - - - -
281I LYS* 2.8 35.0 + - - -
282I CYS 3.3 3.9 + - - +
288I LEU* 3.8 19.3 - - + -
340I ALA* 3.5 24.9 - - + +
344I VAL* 3.7 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 278 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I THR* 2.9 23.0 + - + +
275I GLU* 3.1 10.1 + - + +
277I ALA* 1.3 76.5 - - - +
279I GLU* 1.3 66.1 + - - +
281I LYS* 3.6 16.6 - - - +
343I THR* 3.5 45.8 - - + +
344I VAL* 4.3 7.6 - - - +
347I LYS* 3.9 33.2 - - + +
293J LEU* 6.0 3.1 - - + -
297J TYR* 4.8 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I GLU* 3.0 31.8 + - + +
276I TYR* 3.3 9.6 - - - +
277I ALA 3.1 0.2 - - - -
278I MET* 1.3 80.9 - - - +
280I THR* 1.3 62.0 + - + +
281I LYS* 3.0 15.3 + - - +
316I TYR* 3.5 45.0 + - + +
319I LYS* 5.5 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 280 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I TYR* 3.1 40.7 + - + -
277I ALA* 3.8 1.0 + - - -
279I GLU* 1.3 78.1 - - - +
281I LYS* 1.3 70.2 + - - +
282I CYS* 3.1 20.5 + - - +
312I SER* 3.6 33.0 - - - -
316I TYR* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 281 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I ALA 2.8 12.9 + - - -
278I MET 3.6 11.9 - - - +
279I GLU 3.0 13.9 - - - +
280I THR* 1.3 79.2 - - - +
282I CYS* 1.3 63.3 + - - +
283I ASP* 3.1 11.4 + - - +
344I VAL* 3.6 14.6 - - + +
348I LYS* 3.7 18.2 + - - +
363I ASN* 5.7 3.6 - - - +
367I ASP* 3.5 30.4 + - - -
----------------------------------------------------------
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