Contacts of the helix formed by residues 113 - 120 (chain B) in PDB entry 2E2I
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 TYR 113 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA* 3.8 26.7 + - + +
112B LEU* 1.3 81.2 - - - +
114B PRO* 1.3 83.1 - - + +
115B GLN* 3.1 4.8 + - + +
116B GLU* 3.3 18.7 + - + +
117B ALA* 3.4 6.6 + - - +
124B TYR* 4.0 3.4 - - - -
180B TYR* 3.6 47.2 - + + -
192B LEU* 3.9 35.7 - - + +
53L HIS* 5.6 11.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 1.3 92.3 - - + +
115B GLN* 1.3 66.8 + - - +
117B ALA* 2.8 14.0 + - - +
118B ARG* 3.2 37.3 + - - +
124B TYR* 3.8 30.5 - - + +
174B LEU* 4.5 10.3 - - + -
180B TYR* 5.2 0.4 - - + -
181B LEU* 3.6 40.6 - - + -
192B LEU* 5.6 2.5 - - + +
194B GLU* 3.9 8.3 - - + -
204B ILE* 5.1 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 3.3 3.2 - - + +
114B PRO* 1.3 81.1 - - - +
116B GLU* 1.3 66.6 + - - +
118B ARG* 3.0 35.9 + - - +
119B LEU* 2.9 51.6 + - + +
192B LEU 3.7 19.3 - - - +
193B LYS* 3.3 37.4 - - + +
194B GLU* 5.1 0.2 - - + -
784B ASN* 4.3 5.4 + - - -
787B VAL* 3.6 19.7 + - + -
788B ARG* 3.6 18.2 - - - +
789B MET 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLU* 4.3 2.8 - - - +
110B HIS* 4.3 24.0 + - - -
111B ALA 4.6 3.8 - - - +
112B LEU* 3.6 24.8 - - + +
113B TYR* 3.3 12.3 + - + +
114B PRO 3.2 0.2 + - - -
115B GLN* 1.3 77.4 - - - +
117B ALA* 1.3 57.0 + - - +
119B LEU* 3.3 7.4 + - - +
120B ARG* 2.9 75.1 + - + +
122B LEU* 4.5 0.7 - - + -
33L GLU* 5.8 2.7 - - - +
53L HIS* 4.2 22.4 + - + +
54L ARG 5.1 5.5 + - - -
55L ILE* 5.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.8 19.6 - - + +
113B TYR 3.4 2.4 + - - +
114B PRO 2.8 13.0 + - - +
116B GLU* 1.3 71.0 - - - +
118B ARG* 1.3 65.8 + - - +
121B ASN 3.2 3.3 + - - -
122B LEU* 2.8 56.9 + - + +
124B TYR* 4.2 8.3 - - + +
204B ILE* 4.0 11.2 - - + -
207B GLY* 3.4 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PRO* 3.2 33.3 + - - +
115B GLN* 3.0 39.9 + - - +
117B ALA* 1.3 78.8 - - - +
119B LEU* 1.3 62.1 + - - +
121B ASN* 3.5 7.4 + - - -
174B LEU* 3.7 15.6 - - - +
194B GLU* 3.2 21.6 + - - +
202B TYR* 3.0 28.3 + - - -
204B ILE* 4.1 14.9 - - + +
207B GLY* 3.8 21.4 - - - +
209B GLU* 3.1 25.9 + - + -
485B ARG* 4.9 0.2 - - - +
788B ARG* 4.3 13.9 - - + +
789B MET 6.4 0.2 - - - +
790B ASP* 5.7 1.1 - - - -
965B LYS* 3.2 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 2.9 48.7 + - + +
116B GLU* 3.5 10.5 - - - +
118B ARG* 1.3 73.8 - - - +
120B ARG* 1.3 58.9 + - - +
121B ASN 3.3 1.4 + - - -
193B LYS* 5.5 4.3 - - + -
787B VAL* 4.4 11.4 - - + +
789B MET* 3.8 24.9 - - + +
953B LEU* 3.2 36.6 - - + +
963B PHE* 3.4 11.4 - - - -
965B LYS* 3.3 24.1 + - + +
55L ILE* 4.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLU* 2.7 41.4 + - - -
116B GLU* 2.9 57.8 + - + +
119B LEU* 1.3 73.2 - - + +
121B ASN* 1.3 70.7 + - - +
122B LEU* 3.3 34.1 + - + +
955B THR* 3.4 25.1 - - + +
956B THR* 2.9 46.8 + - - +
957B ASN* 4.0 12.4 + - - +
958B GLN* 5.3 0.2 - - - +
963B PHE* 3.7 14.8 - - + -
54L ARG* 3.9 12.0 - - - +
55L ILE* 4.5 6.5 - - + -
----------------------------------------------------------
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