Contacts of the helix formed by residues 106 - 122 (chain B) in PDB entry 2IK8
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 SER 106 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.5 1.0 - - - +
105B ARG* 1.3 73.1 - - - +
107B ALA* 1.3 59.5 + - - +
108B THR* 3.3 15.8 + - - -
109B LYS* 3.6 14.9 + - - +
110B LEU* 3.1 30.5 + - - +
302B SO4 2.8 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG 3.5 2.9 + - - +
106B SER* 1.3 71.8 + - - +
108B THR* 1.3 60.1 + - - +
110B LEU* 4.1 12.4 - - + +
111B ALA* 3.3 23.2 + - - +
147B ALA 4.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B SER* 3.3 7.7 + - - -
107B ALA* 1.3 77.7 - - - +
109B LYS* 1.3 61.8 + - - +
110B LEU 3.3 0.2 - - - -
111B ALA* 2.9 9.8 - - + +
112B SER* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.6 23.1 - - + -
106B SER* 3.6 11.9 + - - +
108B THR* 1.3 76.0 - - - +
110B LEU* 1.3 57.9 + - - +
112B SER* 2.9 8.8 + - - -
113B ARG* 2.7 39.9 + - - +
302B SO4 4.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.4 50.2 - - + +
104B ILE* 3.5 25.3 - - + +
105B ARG 4.2 4.3 - - - +
106B SER 3.1 26.3 + - - +
107B ALA* 4.1 8.3 - - + +
109B LYS* 1.3 78.2 - - - +
111B ALA* 1.3 64.7 + - - +
113B ARG* 4.6 0.4 - - - -
114B ALA* 2.8 27.5 + - - +
147B ALA* 3.7 24.7 - - - +
148B THR* 4.4 1.8 - - - -
149B ALA* 4.2 19.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
107B ALA 3.3 15.8 + - - +
108B THR* 2.9 19.8 + - + +
110B LEU* 1.3 78.3 - - - +
112B SER* 1.3 58.9 + - - +
114B ALA* 3.8 3.3 - - - +
115B HIS* 3.6 19.4 + - - -
144B LEU* 5.6 0.2 - - - +
147B ALA* 4.1 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B THR* 2.9 16.0 + - - +
109B LYS* 2.9 14.7 + - - -
111B ALA* 1.3 71.0 - - - +
113B ARG* 1.3 72.7 + - - +
115B HIS* 2.9 19.6 + - - +
116B GLN* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.6 25.6 - - + -
104B ILE* 4.1 14.1 - - + -
109B LYS 2.7 24.0 + - - +
110B LEU 3.9 0.2 - - - +
112B SER* 1.3 73.2 + - - +
114B ALA* 1.3 56.0 + - - +
116B GLN* 3.1 29.1 + - - +
117B ILE* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.5 16.2 - - + -
110B LEU 2.8 21.2 + - - +
111B ALA 3.8 3.4 - - - +
113B ARG* 1.3 73.1 - - - +
115B HIS* 1.3 55.6 + - - +
118B PHE* 3.0 31.7 + - - +
144B LEU* 3.3 26.4 - - + +
147B ALA* 3.5 19.5 - - + -
151B CYS* 4.5 0.7 - - - -
152B PHE* 3.7 10.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA 3.6 10.7 + - - +
112B SER* 2.9 11.0 + - - +
114B ALA* 1.3 78.9 - - - +
116B GLN* 1.3 54.3 + - + +
118B PHE* 4.0 4.6 - - - +
119B GLU* 2.7 45.5 + - + +
144B LEU* 4.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B SER* 3.1 28.0 + - - +
113B ARG* 3.1 30.4 + - - +
115B HIS* 1.3 75.0 - - + +
117B ILE* 1.3 67.4 + - + +
119B GLU* 3.3 6.1 + - - +
120B GLU* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PHE* 3.4 35.9 - - + -
97B ALA* 3.4 38.6 - - + +
98B CYS* 4.4 1.3 - - - +
101B PHE* 3.6 30.5 - - + -
113B ARG* 2.9 29.5 + - + +
116B GLN* 1.3 71.4 - - + +
118B PHE* 1.3 62.3 + - - +
120B GLU* 3.3 1.1 + - - -
121B PHE* 3.1 34.5 + - + +
122B ILE* 4.1 0.3 + - - +
152B PHE* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ALA 3.0 18.9 + - - +
115B HIS* 4.0 3.4 - - - +
117B ILE* 1.3 78.1 - - - +
119B GLU* 1.3 64.2 + - + +
122B ILE* 3.3 39.8 + - + -
123B CYS* 3.0 53.4 + - + -
137B ARG* 4.3 6.7 - - + -
140B THR* 4.2 9.9 - - + -
141B ARG* 3.8 46.7 - - + -
144B LEU* 3.7 24.5 - - + -
152B PHE* 3.8 5.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
115B HIS* 2.7 33.3 + - + +
116B GLN* 3.3 7.4 + - - +
118B PHE* 1.3 81.8 - - + +
120B GLU* 1.3 58.9 + - - +
123B CYS* 4.3 8.8 - - - +
126B ALA* 3.6 7.6 - - - +
127B PRO* 3.4 16.8 - - - +
316C THR* 5.4 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN 3.1 15.9 + - - +
117B ILE* 5.8 0.2 - - - -
118B PHE 3.2 0.4 - - - -
119B GLU* 1.3 78.8 - - + +
121B PHE* 1.3 82.2 + - + +
126B ALA* 3.3 8.8 - - - +
127B PRO* 3.4 15.2 - - + +
128B LYS* 2.9 73.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU 3.9 7.6 - - - -
93B GLU* 4.0 11.9 - - + -
94B PHE* 3.5 57.9 - + + -
97B ALA* 3.9 21.5 - - + -
117B ILE* 3.1 25.7 + - + +
120B GLU* 1.3 103.5 - - + +
122B ILE* 1.3 59.4 + - + +
126B ALA* 4.2 0.4 - - - -
128B LYS* 3.4 43.5 - - + -
129B GLU* 3.3 4.2 - - - -
130B VAL* 2.7 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PHE* 3.4 37.2 - - + -
117B ILE 4.3 0.4 - - - +
118B PHE* 3.3 37.3 + - + +
121B PHE* 1.3 82.7 - - + +
123B CYS* 1.3 70.4 + - - +
124B SER* 3.6 0.7 + - - -
129B GLU* 4.4 6.6 - - - +
130B VAL* 4.3 2.2 - - + +
132B ILE* 3.8 28.3 - - + +
137B ARG* 3.7 32.0 + - + +
140B THR* 4.5 3.8 - - + -
152B PHE* 3.8 21.3 - - + -
155B ALA* 4.2 6.3 - - + -
----------------------------------------------------------
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