Contacts of the helix formed by residues 4 - 15 (chain 3) 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 4 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23 SER* 3.5 12.2 + - - -
33 ALA* 1.3 88.4 - - - +
53 ALA* 1.3 58.7 + - - +
63 GLN* 2.9 16.3 + - - -
73 GLN* 2.8 43.5 + - - +
83 LEU* 3.6 2.6 + - - +
283 VAL* 4.4 1.9 - - - +
383 GLU* 4.5 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 5 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33 ALA 3.9 0.2 - - - -
43 SER* 1.3 71.8 - - - +
63 GLN* 1.3 54.8 + - + +
83 LEU* 3.7 4.0 - - - +
93 ALA* 2.7 37.9 + - - +
243 ILE* 3.5 27.0 - - + +
253 GLU* 4.4 12.3 - - + -
283 VAL* 3.6 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 6 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43 SER* 2.9 11.6 + - - +
53 ALA* 1.3 81.1 - - + +
73 GLN* 1.3 59.2 + - + +
93 ALA* 4.1 6.5 - - - -
103 GLU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 7 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33 ALA 3.1 17.5 - - - +
43 SER* 2.8 23.9 + - - +
63 GLN* 1.3 79.6 - - + +
83 LEU* 1.3 60.3 + - - +
103 GLU* 4.0 14.9 - - - +
113 GLU* 4.6 6.4 - - - +
383 GLU* 3.6 28.4 - - + +
393 GLU* 5.4 2.0 - - - +
548C ARG* 4.8 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33 ALA* 5.9 0.4 - - + -
43 SER 3.6 1.9 + - - +
53 ALA* 3.2 11.3 + - - +
73 GLN* 1.3 76.0 - - - +
93 ALA* 1.3 66.2 + - - +
103 GLU 3.2 2.2 - - - -
113 GLU* 3.3 15.1 + - - +
123 LEU* 3.4 24.7 - - + +
243 ILE* 4.6 4.9 - - + +
273 LEU* 3.5 41.1 - - + +
283 VAL* 4.5 3.1 - - + +
313 CYS* 3.6 29.2 - - - -
383 GLU* 3.7 20.4 - - + -
413 MET* 4.5 7.0 - - + -
423 VAL* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53 ALA 2.7 20.1 + - - +
63 GLN* 4.3 7.6 - - - +
73 GLN 3.5 0.2 - - - -
83 LEU* 1.3 76.0 - - - +
103 GLU* 1.3 59.6 + - - +
123 LEU* 2.8 31.5 + - - +
133 GLN* 3.2 24.9 + - + +
243 ILE* 3.9 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63 GLN* 3.0 26.1 - - - +
73 GLN* 4.0 9.9 - - - +
83 LEU 3.2 0.4 - - - -
93 ALA* 1.3 79.4 - - - +
113 GLU* 1.3 66.4 + - - +
133 GLN* 3.1 37.2 + - - +
143 ILE* 3.1 19.3 + - + +
399C PRO* 5.3 12.0 - - + +
548C ARG* 3.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73 GLN 4.6 8.5 - - - +
83 LEU 3.3 4.6 + - - +
93 ALA 3.2 0.6 - - - -
103 GLU* 1.3 79.3 - - - +
123 LEU* 1.3 60.6 + - - +
133 GLN 3.3 0.4 + - - -
143 ILE* 3.6 26.1 + - - +
153 PHE* 3.1 38.8 - - - -
173 LEU* 4.2 0.3 - - - +
383 GLU 4.2 9.6 - - - +
393 GLU* 5.1 13.8 - - + +
423 VAL* 3.5 37.8 - - + +
548C ARG* 5.4 3.6 + - - -
550C LYS* 4.6 9.0 - - - +
552C TYR* 3.5 29.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 LEU* 3.4 29.8 - - + +
93 ALA* 2.8 24.0 + - + +
113 GLU* 1.3 80.6 - - - +
133 GLN* 1.3 58.7 + - + +
143 ILE 3.3 0.9 - - - -
163 GLY* 3.6 0.9 - - - -
173 LEU* 2.7 72.8 + - + +
193 CYS* 4.2 16.8 - - + -
243 ILE* 3.8 28.3 - - + -
273 LEU* 5.8 4.7 - - + -
423 VAL* 4.7 7.0 - - + -
453 LEU* 6.3 2.2 - - + -
573 LEU* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 13 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 ALA* 3.4 21.9 + - + +
103 GLU* 3.1 35.2 + - - +
123 LEU* 1.3 78.5 - - + +
143 ILE* 1.3 63.9 + - + +
153 PHE 3.7 0.2 - - - -
163 GLY* 4.0 7.0 + - - +
399C PRO* 5.6 7.5 - - + +
400C LYS* 5.6 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 GLU* 3.1 20.4 - - + +
113 GLU* 3.6 37.5 - - - +
123 LEU 3.3 0.4 - - - -
133 GLN* 1.3 82.7 - - - +
153 PHE* 1.3 80.0 + - + +
163 GLY 3.2 1.6 + - - -
395C HIS* 4.2 36.3 + - + +
396C CYS* 4.3 12.1 - - - -
398C LEU 5.4 3.8 - - - +
399C PRO* 4.7 22.2 - - + -
400C LYS 5.9 1.1 - - - +
550C LYS* 4.2 11.9 - - - +
552C TYR* 4.1 10.8 - - - +
616C LYS* 4.6 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 15 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 GLU* 3.1 40.0 + - - -
123 LEU 4.4 0.2 + - - -
143 ILE* 1.3 88.6 - - + +
163 GLY* 1.3 63.2 + - - +
173 LEU* 3.9 18.8 - - + +
423 VAL* 4.0 10.1 - - + -
463 ILE* 3.5 30.5 - - + -
396C CYS* 4.0 27.1 - - + -
552C TYR* 4.7 9.9 - + - -
616C LYS* 4.4 15.3 - - + +
617C PHE* 6.3 0.2 - - - -
620C ALA* 3.7 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