Contacts of the helix formed by residues 107 - 118 (chain E) in PDB entry 2OHI
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 107 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E GLN 5.7 0.2 - - - +
106E CYS* 1.3 84.2 - - - +
108E GLU* 1.3 63.1 + - - +
109E VAL* 3.8 3.2 + - - +
110E ALA* 3.1 23.6 + - - +
111E VAL* 3.2 13.5 + - - +
128E THR* 3.1 5.6 + - - -
129E VAL 3.6 13.7 - - - +
146E GLU* 4.7 14.1 - - + -
154E ASP* 3.3 21.9 + - - +
155E SER 4.1 6.3 - - - +
156E MET* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E THR* 1.3 70.5 - - - +
109E VAL* 1.4 83.0 + - + +
111E VAL* 2.9 24.9 + - + +
112E LYS* 4.0 18.3 + - - +
128E THR* 3.2 25.0 + - + +
129E VAL 4.6 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D TYR* 4.7 9.5 + - - +
107E THR* 3.6 2.7 + - - +
108E GLU* 1.4 90.6 - - + +
110E ALA* 1.3 62.5 + - - +
111E VAL 3.2 1.0 + - - -
112E LYS* 3.4 17.2 + - - +
113E GLY* 3.6 6.9 + - - -
153E PRO* 3.4 32.5 - - + +
154E ASP* 3.9 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E GLN 5.2 2.2 - - - +
84E VAL* 3.4 19.5 - - + +
106E CYS* 4.2 17.7 - - + -
107E THR* 3.1 24.8 + - - +
108E GLU 3.1 0.2 - - - -
109E VAL* 1.3 77.9 - - - +
111E VAL* 1.3 62.9 + - - +
113E GLY* 3.3 2.3 + - - +
114E LEU* 3.0 27.0 + - + +
154E ASP* 3.4 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E CYS* 3.9 15.0 - - - -
107E THR 3.2 18.6 - - - +
108E GLU* 2.9 12.7 + - + +
110E ALA* 1.3 76.3 - - - +
112E LYS* 1.3 73.5 + - - +
114E LEU* 3.2 7.2 + - - +
115E LEU* 3.0 48.5 + - + +
126E PHE* 4.0 27.4 - - + -
128E THR* 3.8 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D TYR* 4.2 11.9 - - + +
108E GLU* 4.7 18.7 + - - +
109E VAL* 3.4 10.2 + - - +
110E ALA 3.4 0.2 - - - -
111E VAL* 1.3 91.9 - - + +
113E GLY* 1.3 61.1 + - - +
115E LEU* 3.4 10.2 + - + +
116E LYS* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D TYR* 3.8 17.1 + - - -
381D TYR* 4.1 14.8 - - - -
84E VAL* 5.1 6.1 - - - -
109E VAL 3.6 6.4 + - - -
110E ALA* 3.3 5.6 + - - -
111E VAL 3.3 0.8 - - - -
112E LYS* 1.3 76.3 - - - +
114E LEU* 1.3 57.0 + - - +
116E LYS* 3.1 3.5 + - - +
117E HIS* 2.7 40.6 + - - -
154E ASP* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E GLN* 4.2 15.3 - - + +
84E VAL* 3.6 38.4 - - + +
89E SER* 4.2 14.4 - - - +
92E LEU* 3.8 22.2 - - + -
104E ILE* 4.8 0.4 - - + -
106E CYS* 4.0 16.8 - - + -
110E ALA 3.0 18.9 + - - +
111E VAL 3.5 4.9 - - - +
113E GLY* 1.3 74.8 - - - +
115E LEU* 1.3 57.9 + - - +
117E HIS* 4.1 4.0 - - - +
118E TYR* 3.2 33.2 + - + +
121E LEU* 3.7 8.7 - - + +
126E PHE* 4.0 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E VAL* 3.0 39.6 + - + +
112E LYS* 3.7 11.7 - - + +
113E GLY 3.2 0.4 - - - -
114E LEU* 1.3 74.9 - - - +
116E LYS* 1.3 65.5 + - - +
117E HIS 3.3 0.4 - - - -
118E TYR 3.3 19.9 - - - +
119E PRO* 3.4 12.1 - - + +
121E LEU* 3.6 35.0 - - + +
122E ARG* 3.8 10.3 - - + +
126E PHE* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D VAL* 4.1 0.2 - - - +
380D TYR* 2.4 61.9 + - + +
381D TYR* 4.0 8.7 - - + -
382D VAL* 2.6 34.1 + - - +
384D THR* 4.0 17.2 - - + +
387D GLU* 3.1 30.5 + - - -
112E LYS 3.1 13.3 + - - +
113E GLY 3.5 9.4 - - - +
115E LEU* 1.3 79.6 - - - +
117E HIS* 1.3 60.2 + - - +
119E PRO* 4.3 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D TYR* 3.3 49.7 - + - +
382D VAL* 3.8 28.0 - - + +
84E VAL* 4.6 20.8 + - + +
85E GLU* 5.4 1.0 - - - -
86E LYS* 5.2 17.6 + - + +
113E GLY 2.7 28.8 + - - +
114E LEU* 4.5 1.1 - - + -
116E LYS* 1.3 78.1 - - - +
118E TYR* 1.3 97.7 + + + +
119E PRO* 3.4 7.9 - - - +
152E TRP* 5.6 1.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E LYS* 4.7 7.8 - - - +
89E SER* 3.0 50.7 + - - -
90E GLY* 3.6 14.9 - - - -
92E LEU* 4.7 6.1 - - + -
93E VAL* 4.6 21.3 - - + -
114E LEU* 3.2 30.5 + - + +
115E LEU* 3.3 8.9 - - - +
117E HIS* 1.3 105.5 - + + +
119E PRO* 1.3 66.8 - - - +
120E SER* 3.2 3.8 - - - +
121E LEU* 3.0 41.7 + - + +
----------------------------------------------------------
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