Contacts of the helix formed by residues 117 - 129 (chain B) in PDB entry 3ER8
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 ASP 117 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 4.5 1.3 + - - -
115B PHE 4.2 4.6 - - - +
116B VAL* 1.3 83.7 - - - +
118B GLU* 1.3 73.3 + - + +
119B GLU* 3.3 34.4 + - - +
120B TYR* 3.0 10.1 + - - +
121B LEU* 2.9 22.8 + - - +
159B LEU* 4.8 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LYS* 4.4 8.8 + - - -
117B ASP* 1.3 77.3 - - + +
119B GLU* 1.3 68.2 + - - +
121B LEU* 2.9 15.6 + - - +
122B ARG* 3.0 46.9 + - - +
159B LEU* 5.5 2.0 - - - +
162B VAL* 4.7 20.0 - - + +
166B ILE* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 3.3 31.7 + - - -
117B ASP* 3.3 22.3 + - - +
118B GLU* 1.3 78.4 - - - +
120B TYR* 1.3 73.7 + - - +
122B ARG* 3.5 8.3 + - - +
123B SER* 3.2 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 4.0 26.0 - - + -
112B VAL* 3.4 28.9 - - - +
114B ARG* 3.3 43.1 - - - +
116B VAL* 4.2 19.1 - - + -
117B ASP* 3.0 22.6 + - - +
119B GLU* 1.3 84.3 - - - +
121B LEU* 1.3 69.3 + - + +
123B SER* 2.8 21.4 + - - -
124B ILE* 3.0 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 4.2 19.1 - - + -
116B VAL* 4.5 14.8 - - + -
117B ASP 2.9 18.7 + - - +
118B GLU 2.9 7.9 + - - +
120B TYR* 1.3 74.4 - - + +
122B ARG* 1.3 60.7 + - - +
124B ILE* 3.4 22.6 - - + +
125B LYS* 3.2 18.7 + - - +
159B LEU* 5.4 4.3 - - + -
162B VAL* 3.9 8.3 - - + -
163B MET* 3.3 41.7 - - + +
166B ILE* 3.0 33.6 - - + +
167B LEU* 3.6 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LYS* 3.2 50.4 - - - +
187A ASP 4.8 4.8 + - - -
118B GLU* 3.0 48.2 + - - +
119B GLU* 3.7 10.1 - - - +
121B LEU* 1.3 75.5 - - - +
123B SER* 1.3 57.9 + - - +
125B LYS* 4.1 2.9 - - - +
126B LYS* 3.2 44.0 + - - +
166B ILE* 3.1 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 3.2 18.2 + - - -
120B TYR* 2.8 24.7 + - - -
122B ARG* 1.3 76.4 - - - +
124B ILE* 1.3 61.9 + - - -
126B LYS* 3.5 12.1 + - - +
127B GLN* 3.3 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 4.8 9.9 - - + -
67B ILE* 5.4 0.2 - - + -
92B MET* 4.6 9.6 - - - -
94B ILE* 4.1 15.7 - - + -
120B TYR* 3.0 53.0 + - + +
121B LEU* 3.4 23.1 - - + +
123B SER* 1.3 70.8 - - - +
125B LYS* 1.3 65.5 + - - +
126B LYS 3.1 1.8 - - - -
127B GLN* 2.9 19.0 + - - +
128B LEU* 2.7 47.6 + - + +
133B ILE* 6.3 0.2 - - + -
167B LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG* 5.0 4.4 - - - +
121B LEU 3.2 17.6 + - - +
122B ARG* 4.1 4.9 - - - +
124B ILE* 1.3 77.0 - - - +
126B LYS* 1.3 64.4 + - - +
128B LEU* 4.8 2.0 - - - -
129B HIS* 2.9 51.9 + - + +
131B SER 5.5 2.7 - - - -
133B ILE* 3.6 23.3 - - + -
166B ILE* 3.8 17.7 + - + +
167B LEU* 2.9 33.2 + - + +
168B ASN* 3.5 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.2 33.5 + - - +
123B SER* 3.5 11.9 + - - +
124B ILE 3.1 0.2 - - - -
125B LYS* 1.3 80.9 - - + +
127B GLN* 1.3 62.8 + - - +
129B HIS* 3.9 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS* 6.2 0.4 - - - +
92B MET* 3.6 28.5 - - - +
123B SER 3.3 8.8 + - - +
124B ILE* 2.9 20.2 + - - +
126B LYS* 1.3 82.4 - - - +
128B LEU* 1.3 73.0 + - - +
129B HIS 3.7 5.0 + - - +
466C ARG* 3.9 7.3 + - - -
902H U 5.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 4.2 17.5 - - + +
65B VAL* 3.7 23.3 - - + -
92B MET* 4.2 12.8 - - + -
124B ILE* 2.7 48.6 + - + +
125B LYS 4.1 0.4 - - - +
127B GLN* 1.3 93.0 - - - +
129B HIS* 1.3 69.4 + - - +
131B SER* 2.6 30.0 + - - +
133B ILE* 3.5 35.4 - - + -
466C ARG* 3.2 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 2.9 42.9 + - + +
126B LYS* 3.9 11.2 - - - +
127B GLN 3.5 4.0 - - - +
128B LEU* 1.3 73.5 - - - +
130B PRO* 1.3 88.2 - - + +
131B SER 3.8 3.1 + - - +
466C ARG* 2.7 18.2 + - - -
----------------------------------------------------------
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