Contacts of the helix formed by residues 112 - 126 (chain E) in PDB entry 5ZRV
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 THR 112 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E LYS* 1.3 77.1 - - - +
113E LEU* 1.3 64.9 + - - +
114E GLN 3.4 2.2 - - - -
115E GLU* 3.2 6.7 + - - +
116E VAL* 3.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E THR* 1.3 70.8 - - - +
114E GLN* 1.3 58.1 + - - +
116E VAL* 3.3 1.9 + - - +
117E THR* 2.9 26.3 + - - -
328E GLY* 5.3 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E THR 3.4 0.4 - - - -
113E LEU* 1.3 76.1 - - - +
115E GLU* 1.3 56.8 + - - +
117E THR* 3.8 1.0 - - - +
118E GLN* 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E THR 3.2 8.0 + - - -
114E GLN* 1.3 75.5 - - - +
116E VAL* 1.3 59.4 + - - +
118E GLN* 3.7 2.2 - - - +
119E LEU* 2.9 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E LYS* 5.3 2.8 - - - +
112E THR 3.0 14.5 + - - -
113E LEU* 3.3 3.1 + - - +
115E GLU* 1.3 76.1 - - - +
117E THR* 1.3 59.7 + - - +
119E LEU* 5.4 0.4 - - - +
120E SER* 3.5 15.4 + - - -
327E PHE 5.8 0.7 - - - -
328E GLY* 5.2 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E LEU 2.9 16.4 + - - -
114E GLN 3.8 1.1 - - - -
116E VAL* 1.3 77.3 - - - +
118E GLN* 1.3 57.8 + - - +
120E SER* 3.6 2.0 - - - +
121E GLN* 2.9 25.5 + - - -
324E SER* 4.3 22.4 - - - +
328E GLY* 5.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E GLN 2.9 18.2 + - - -
115E GLU* 3.2 3.5 + - - +
117E THR* 1.3 75.2 - - - +
119E LEU* 1.3 58.2 + - - +
121E GLN* 3.3 2.1 + - - +
122E GLU* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E GLU 2.9 15.5 + - - -
116E VAL* 4.6 0.7 - - - +
118E GLN* 1.3 75.7 - - - +
120E SER* 1.3 56.4 + - - +
121E GLN 3.2 0.2 - - - -
122E GLU* 3.2 2.1 + - - +
123E ALA* 2.8 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E VAL 3.5 13.2 + - - -
117E THR* 3.5 7.1 + - - +
118E GLN 3.3 0.2 - - - -
119E LEU* 1.3 75.0 - - - +
121E GLN* 1.3 55.8 + - - +
123E ALA* 4.2 5.2 + - - +
124E GLN 5.0 2.8 + - - -
181E GLY 5.4 7.0 - - - +
182E ALA* 5.8 2.9 - - - -
323E GLU 6.0 0.2 - - - -
324E SER* 5.1 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E THR 2.9 15.5 + - - -
118E GLN* 3.7 1.8 - - - +
119E LEU 3.2 0.2 - - - -
120E SER* 1.3 78.5 - - - +
122E GLU* 1.3 61.1 + - - +
123E ALA 3.3 1.6 - - - -
124E GLN* 4.0 2.1 + - - -
125E ARG* 3.8 13.0 + - - -
324E SER* 5.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLN 2.9 14.1 + - - -
119E LEU* 3.2 3.6 + - - +
121E GLN* 1.3 77.0 - - - +
123E ALA* 1.3 64.1 + - - +
125E ARG* 3.1 12.2 + - - +
126E ILE* 3.6 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E LEU 2.8 16.6 + - - -
120E SER* 5.0 2.2 - - - +
121E GLN 3.3 1.8 - - - +
122E GLU* 1.3 77.4 - - - +
124E GLN* 1.3 57.2 + - - +
126E ILE* 4.4 2.2 + - - -
127E VAL* 4.4 5.9 + - - -
181E GLY 4.7 15.1 - - - +
182E ALA* 4.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E SER 5.0 3.4 + - - -
121E GLN 4.0 4.7 + - - -
122E GLU 3.2 0.2 - - - -
123E ALA* 1.3 75.0 - - - +
125E ARG* 1.3 60.0 + - - +
126E ILE 3.2 2.5 - - - -
127E VAL* 2.9 6.2 + - - +
128E GLU* 2.8 25.8 + - - -
182E ALA* 4.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E GLN 3.8 8.4 + - - -
122E GLU* 3.1 11.1 + - - +
124E GLN* 1.3 77.9 - - - +
126E ILE* 1.3 55.6 + - - +
128E GLU* 3.4 3.6 + - - +
129E LYS* 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E GLU 3.6 9.7 + - - -
123E ALA 4.4 2.4 + - - -
124E GLN 3.2 0.8 - - - +
125E ARG* 1.3 75.1 - - - +
127E VAL* 1.3 59.8 + - - +
129E LYS* 3.7 7.9 + - - +
130E LEU* 3.8 7.1 + - - -
----------------------------------------------------------
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