Contacts of the helix formed by residues 107 - 117 (chain B) in PDB entry 4IRX
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 LEU 107 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 4.2 13.5 - - - +
82B GLN* 3.6 30.7 - - + +
83B ILE* 3.9 20.9 - - + -
86B LEU* 3.9 26.9 - - + -
99B VAL* 5.0 2.2 - - + -
101B PRO* 3.8 16.2 - - + -
102B THR* 3.8 13.0 - - - +
103B ASP 3.3 16.0 + - - +
104B SER 4.3 0.4 + - - +
105B LYS 3.1 1.0 - - - -
106B ALA* 1.3 82.4 - - + +
108B ALA* 1.3 65.9 + - - +
109B GLY 3.2 2.7 - - - -
110B ALA* 3.3 8.2 + - + +
111B ALA* 3.0 22.2 + - - +
128B ILE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LYS 3.2 16.4 + - - +
107B LEU* 1.3 77.2 - - - +
109B GLY* 1.3 57.7 + - - +
111B ALA* 3.3 2.1 + - - +
112B ASP* 3.0 34.7 + - - -
128B ILE* 3.7 17.5 - - + +
129B ALA 3.5 20.0 - - - +
130B GLY 4.1 2.5 - - - +
131B GLY* 3.7 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LYS 4.8 0.6 + - - -
106B ALA 4.5 3.4 + - - -
107B LEU 3.2 0.8 - - - -
108B ALA* 1.3 79.0 - - - +
110B ALA* 1.3 60.7 - - - +
112B ASP* 3.4 8.1 + - - +
113B ASP* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 4.1 37.5 - - + +
86B LEU* 4.4 14.1 - - + -
87B GLN* 5.7 4.9 - - + +
106B ALA 5.1 1.0 + - - -
107B LEU* 3.3 18.1 + - + +
109B GLY* 1.3 74.6 - - - +
111B ALA* 1.3 57.9 + - - +
113B ASP* 3.2 7.1 + - - +
114B LEU* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 5.5 1.9 - - + +
107B LEU 3.0 16.7 + - - +
108B ALA 3.7 4.0 - - - +
110B ALA* 1.3 78.0 - - - +
112B ASP* 1.3 63.4 + - - +
114B LEU* 3.3 4.6 + - - +
115B VAL* 3.0 28.9 + - - +
121B VAL* 4.2 15.0 - - + +
128B ILE* 4.0 17.7 - - + -
133B THR* 4.7 0.9 - - - -
135B VAL* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 3.0 19.2 + - - +
109B GLY* 3.7 6.6 - - - +
110B ALA 3.3 0.2 - - - -
111B ALA* 1.3 77.1 - - - +
113B ASP* 1.3 57.2 + - - +
115B VAL* 3.3 2.1 + - - +
116B GLU* 3.0 44.5 + - - +
131B GLY* 3.4 7.8 - - - -
132B LYS* 2.7 33.1 + - - +
133B THR* 2.4 45.0 + - + +
135B VAL* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLN* 4.7 18.4 + - - +
109B GLY 3.0 18.1 + - - +
110B ALA* 3.5 7.2 - - - +
112B ASP* 1.3 74.9 - - - +
114B LEU* 1.3 66.2 + - + +
116B GLU* 3.4 13.2 + - - +
117B GLN* 3.2 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.7 40.6 - - + +
87B GLN* 4.7 4.5 - - + +
90B ALA* 3.6 30.1 - - + -
97B VAL* 4.3 22.4 - - + -
110B ALA* 2.9 21.6 + - + +
111B ALA* 3.3 4.0 + - - +
113B ASP* 1.3 78.4 - - - +
115B VAL* 1.3 60.4 + - - +
117B GLN* 3.1 17.8 + - - +
118B GLY 3.2 0.2 + - - -
119B VAL* 2.9 33.2 + - + +
121B VAL* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA 3.0 20.1 + - - +
112B ASP 3.8 3.6 - - - +
114B LEU* 1.3 74.1 - - - +
116B GLU* 1.3 60.4 + - + +
118B GLY* 2.9 20.4 + - - -
119B VAL 3.4 16.6 - - - +
120B ALA* 5.0 1.6 - - - -
121B VAL* 4.2 16.8 - - + +
133B THR* 4.2 31.6 - - + +
135B VAL* 5.7 4.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
112B ASP* 3.0 29.6 + - - +
113B ASP* 3.9 12.5 - - - +
114B LEU 3.3 0.2 - - - -
115B VAL* 1.3 78.5 - - + +
117B GLN* 1.3 57.9 + - + +
118B GLY 3.2 0.8 + - - -
132B LYS* 4.4 18.9 - - - +
133B THR* 5.8 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLN* 5.6 3.6 + - - +
90B ALA* 3.5 32.7 - - - +
91B VAL* 4.7 4.0 + - - +
95B LYS* 4.5 6.2 + - - -
113B ASP* 3.2 41.2 + - - +
114B LEU* 3.1 13.7 + - - +
116B GLU* 1.3 75.5 - - - +
118B GLY* 1.3 59.5 + - - +
119B VAL* 4.5 6.6 - - + +
----------------------------------------------------------
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