Contacts of the helix formed by residues 106 - 120 (chain B) in PDB entry 4BR6
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
----------------------------------------------------------
100B ILE* 3.6 14.5 - - - +
101B GLU* 4.3 10.3 - - - +
104B PHE* 3.1 5.5 + - - +
105B GLY* 1.3 78.3 - - - +
107B PHE* 1.3 62.9 + - - +
108B GLU* 3.6 9.3 + - - +
109B THR* 3.1 27.5 + - - -
110B PHE* 3.3 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY 4.3 3.1 - - - -
91B GLU* 3.6 41.7 - - + +
92B PRO* 3.4 33.2 - - + -
97B LYS* 6.1 6.3 - - + -
100B ILE* 3.6 15.9 - - + +
101B GLU* 4.8 4.4 - - + +
106B SER* 1.3 71.3 - - - +
108B GLU* 1.3 67.6 + - + +
110B PHE* 3.2 16.7 + + - +
111B ARG* 2.8 52.9 + - - +
182B TRP* 4.1 15.5 - + + -
187B TRP* 3.6 31.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 5.6 2.3 - - - +
106B SER* 3.9 8.2 - - - +
107B PHE* 1.3 85.7 - - + +
109B THR* 1.3 57.9 + - - +
111B ARG* 3.2 14.5 + - + +
112B LYS* 2.9 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE 3.1 26.4 + - - +
105B GLY* 5.3 0.5 - - - -
106B SER* 3.1 18.3 + - - -
108B GLU* 1.3 73.1 - - - +
110B PHE* 1.3 60.4 + - - +
112B LYS* 3.2 18.8 + - - +
113B GLN* 2.9 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 4.2 10.5 - - + -
104B PHE* 3.7 36.3 - + + +
106B SER 3.3 11.8 + - - +
107B PHE* 3.2 21.9 + + - +
109B THR* 1.3 79.3 - - - +
111B ARG* 1.3 60.3 + - - +
113B GLN* 3.4 0.8 + - - -
114B MET* 2.9 48.4 + - - +
129B LEU* 3.8 37.0 - - + -
140B ILE* 3.7 24.5 - - + +
157B MET* 4.2 4.3 - - + -
182B TRP* 3.7 24.0 - + - -
187B TRP* 3.9 13.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY 5.5 3.4 + - - -
107B PHE* 2.8 40.0 + - + +
108B GLU* 3.3 17.9 - - - +
110B PHE* 1.3 74.1 - - + +
112B LYS* 1.3 63.7 + - - +
115B ASN* 3.1 36.3 + - - +
179B GLU* 3.2 47.2 + - - +
182B TRP* 3.5 56.4 + - + +
183B ASN* 5.3 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLU* 2.9 15.0 + - + +
109B THR* 3.4 23.1 + - - +
111B ARG* 1.3 75.2 - - - +
113B GLN* 1.3 85.4 + - - +
115B ASN* 3.4 8.9 + - - +
116B ALA* 3.0 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 3.3 30.2 - - - +
109B THR* 2.9 34.2 + - - +
112B LYS* 1.3 91.8 - - - +
114B MET* 1.3 58.1 + - - +
116B ALA* 3.3 7.8 + - - +
117B ALA* 2.9 27.5 + - - +
140B ILE* 3.7 12.9 - - + +
134C ASP* 3.4 34.2 + - - +
152C GLN* 3.8 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 2.9 34.7 + - + +
113B GLN* 1.3 74.4 - - - +
115B ASN* 1.3 62.3 + - - +
117B ALA* 3.1 2.4 + - - +
118B LEU* 2.9 37.2 + - + +
127B ALA* 3.2 42.0 - - + +
128B TRP* 3.5 12.6 - - - +
129B LEU 4.1 5.2 - - - -
140B ILE* 3.6 19.7 - - + +
157B MET* 3.7 32.5 - - + +
159B ILE* 4.2 8.5 - - + -
182B TRP* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ARG* 3.1 30.2 + - - +
112B LYS* 3.6 7.7 - - - +
113B GLN 3.3 0.2 - - - -
114B MET* 1.3 79.6 - - - +
116B ALA* 1.3 61.6 + - - +
118B LEU* 3.4 9.7 + - - +
119B THR* 3.0 26.2 + - - -
178B PHE* 3.3 21.8 + - + +
179B GLU* 3.5 23.0 + - - +
182B TRP* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 3.0 14.9 + - + +
113B GLN* 3.5 11.0 - - - +
115B ASN* 1.3 74.1 - - - +
117B ALA* 1.3 59.0 + - - +
119B THR* 3.0 9.8 + - - +
120B GLY* 2.9 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLN 2.9 14.0 + - - +
114B MET 3.4 8.1 - - - +
116B ALA* 1.3 75.8 - - - +
118B LEU* 1.3 62.3 + - - +
120B GLY* 3.4 7.8 + - - +
121B ILE* 3.3 19.7 + - - +
127B ALA* 4.7 2.5 - - + -
140B ILE* 3.7 24.2 - - + -
142B THR* 3.9 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B MET* 2.9 23.5 + - + +
115B ASN* 3.6 16.6 - - - +
117B ALA* 1.3 75.2 - - - +
119B THR* 1.3 63.9 + - - +
121B ILE* 3.3 25.1 + - + +
127B ALA* 3.3 28.7 - - + +
159B ILE* 3.6 51.1 - - + +
161B ALA* 4.1 14.1 - - + +
174B LYS* 5.0 1.2 + - - -
178B PHE* 3.7 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN 3.0 15.4 + - - -
116B ALA* 3.0 12.3 + - - +
118B LEU* 1.3 77.2 - - - +
120B GLY* 1.3 57.9 - - - +
121B ILE 3.3 0.7 - - - +
174B LYS* 3.2 30.2 + - - +
175B ALA* 5.1 7.8 - - - +
178B PHE* 3.7 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA 2.9 14.0 + - - -
117B ALA* 3.4 5.1 + - - -
118B LEU 3.2 0.4 - - - -
119B THR* 1.3 76.4 - - - +
121B ILE* 1.3 62.9 + - - +
122B GLN* 3.3 16.7 + - - +
----------------------------------------------------------
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