Contacts of the helix formed by residues 107 - 118 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I GLN 4.7 0.4 + - - -
106I CYS* 1.3 79.2 - - - +
108I GLU* 1.3 66.1 + - - +
109I VAL* 3.9 6.4 + - - +
110I ALA* 3.2 22.1 + - - +
111I VAL* 3.4 12.1 + - - +
128I THR* 4.8 0.2 - - - -
129I VAL 3.5 14.6 - - - +
146I GLU* 4.1 17.9 - - + +
153I PRO 5.9 0.2 - - - -
154I ASP* 3.2 21.8 + - - +
155I SER 3.7 10.8 - - - +
156I MET* 3.7 36.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I THR* 1.3 72.1 - - - +
109I VAL* 1.3 68.5 + - + +
111I VAL* 3.1 20.6 + - + +
112I LYS* 4.0 4.5 + - - +
128I THR* 3.4 38.8 + - + +
129I VAL 4.3 4.1 + - - -
130I LYS* 5.8 3.8 - - - +
146I GLU* 5.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I THR* 4.2 7.2 - - - +
108I GLU* 1.3 80.3 - - + +
110I ALA* 1.3 63.0 + - - +
111I VAL 3.0 1.9 + - - -
112I LYS* 3.3 14.7 + - - +
113I GLY* 3.4 8.3 + - - -
153I PRO* 4.1 37.7 - - + +
154I ASP* 4.3 4.5 - - + +
380J TYR* 5.1 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I GLN* 5.2 3.4 - - + +
83I HIS* 5.9 1.3 - - - -
84I VAL* 3.6 14.5 - - + +
106I CYS* 3.9 18.8 - - + -
107I THR* 3.2 24.3 + - - +
109I VAL* 1.3 77.0 - - - +
111I VAL* 1.3 53.3 + - - +
112I LYS 3.6 0.2 - - - -
113I GLY* 4.7 0.9 - - - +
114I LEU* 2.8 37.4 + - + +
154I ASP* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I CYS* 3.8 16.6 - - - -
107I THR 3.4 14.7 + - - +
108I GLU* 3.4 10.5 - - + +
109I VAL 3.0 2.4 + - - -
110I ALA* 1.3 75.7 - - - +
112I LYS* 1.3 57.8 + - + +
114I LEU* 3.2 5.8 + - - +
115I LEU* 2.8 57.5 + - + +
126I PHE* 4.3 23.1 - - + -
128I THR* 4.0 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I GLU 4.0 3.8 + - - +
109I VAL* 3.3 8.3 + - - +
111I VAL* 1.3 78.7 - - + +
113I GLY* 1.3 64.1 + - - +
115I LEU* 3.9 7.3 - - + +
116I LYS* 3.1 23.7 + - - +
380J TYR* 4.2 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I VAL* 4.5 7.2 - - - -
109I VAL 3.4 9.3 + - - -
110I ALA* 4.0 2.7 - - - -
111I VAL 3.3 0.6 - - - -
112I LYS* 1.3 74.5 - - - +
114I LEU* 1.3 61.3 + - - +
116I LYS* 3.3 4.2 + - - +
117I HIS* 2.8 35.9 + - - -
154I ASP* 6.3 0.7 - - - -
380J TYR* 3.4 18.3 + - - -
381J TYR* 4.1 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I GLN* 4.1 18.2 - - + +
84I VAL* 3.8 25.2 - - + +
89I SER* 4.3 16.8 - - - +
92I LEU* 3.7 30.3 - - + -
104I ILE* 4.3 1.1 - - + -
106I CYS* 4.2 9.6 - - - -
110I ALA* 2.8 22.8 + - + +
111I VAL* 3.2 5.4 + - - +
113I GLY* 1.3 72.4 - - - +
115I LEU* 1.3 62.6 + - - +
117I HIS* 3.1 16.7 + - - +
118I TYR* 3.1 24.6 + - + +
121I LEU* 5.0 2.0 - - + -
126I PHE* 3.5 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I VAL* 2.8 39.6 + - + +
112I LYS* 3.9 10.1 - - + +
114I LEU* 1.3 73.6 - - - +
116I LYS* 1.3 62.1 + - - +
118I TYR 3.3 28.4 - - - +
119I PRO* 3.4 12.6 - - + +
121I LEU* 3.4 37.0 - - + +
122I ARG* 3.7 9.0 - - + +
126I PHE* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I LYS 3.1 17.7 + - - +
113I GLY 3.6 5.8 - - - +
114I LEU 3.2 0.2 - - - -
115I LEU* 1.3 77.4 - - - +
117I HIS* 1.3 62.1 + - - +
119I PRO* 4.2 9.1 - - - +
380J TYR* 2.7 56.1 + - + +
381J TYR* 4.0 10.5 - - + -
382J VAL* 2.7 35.1 + - - +
384J THR* 4.1 15.8 - - + +
387J GLU* 2.9 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I VAL* 4.1 24.9 + - + +
86I LYS* 5.2 12.0 + - + +
113I GLY 2.8 21.9 + - - -
114I LEU* 3.1 10.4 + - + +
116I LYS* 1.3 78.6 - - - +
118I TYR* 1.3 92.5 + + + +
119I PRO* 3.8 4.9 - - - +
152I TRP* 5.3 1.8 - + - -
267J HIS* 6.2 2.2 - - - -
381J TYR* 3.3 47.8 - + - +
382J VAL* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I VAL 4.7 0.5 + - - -
86I LYS* 4.6 8.3 - - - +
89I SER* 2.7 47.3 + - - -
90I GLY* 3.6 13.7 + - - -
92I LEU* 4.8 5.2 - - + -
93I VAL* 4.9 18.6 - - + -
114I LEU* 3.1 26.3 + - + -
115I LEU* 3.3 10.9 - - - +
117I HIS* 1.3 108.0 - + + +
119I PRO* 1.4 66.0 - - - +
120I SER* 3.1 8.8 + - - +
121I LEU* 3.1 41.1 + - + +
----------------------------------------------------------
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