Contacts of the helix formed by residues 108 - 121 (chain B) in PDB entry 3Q84
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 GLU 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN* 3.2 27.6 + - - +
107B ASN* 1.3 89.6 - - + +
109B ASP* 1.3 62.3 + - - +
110B LEU 3.5 0.2 - - - -
111B GLU* 3.7 3.8 + - - +
112B LYS* 2.9 32.9 + - - +
255B HIS* 4.0 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 4.9 5.7 - - + +
104B ASN 3.0 4.5 + - - +
105B LEU* 3.2 18.1 - - + +
108B GLU* 1.3 80.4 - - - +
110B LEU* 1.3 65.2 + - - +
112B LYS* 3.5 10.3 + - - +
113B VAL* 3.5 19.6 + - - +
248B VAL* 5.0 3.8 - - + +
251B ASP* 3.1 34.0 - - - +
252B ILE* 3.7 23.5 + - + -
255B HIS* 2.3 35.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
43B MSE 3.2 38.6 - - + +
46B VAL* 4.7 10.1 - - + -
47B GLN* 3.6 27.6 - - + +
105B LEU 2.6 16.8 + - - +
106B LEU* 3.5 29.5 + - + +
108B GLU 3.5 0.4 - - - -
109B ASP* 1.3 75.7 - - - +
111B GLU* 1.3 61.8 + - - +
113B VAL* 3.4 2.3 + - - +
114B LYS* 2.9 34.8 + - + -
125M ILE* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 3.6 4.6 + - - +
107B ASN* 3.3 35.0 - - - +
108B GLU* 3.8 4.3 - - - +
110B LEU* 1.3 82.3 - - - +
112B LYS* 1.3 59.3 + - - +
114B LYS* 3.6 5.5 - - + +
115B ASN* 2.9 46.5 + - - +
----------------------------------------------------------
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 23.5 + - - +
109B ASP* 3.9 7.9 - - - +
110B LEU 3.3 0.2 - - - -
111B GLU* 1.3 73.4 - - - +
113B VAL* 1.3 64.0 + - + +
115B ASN* 3.4 8.0 + - - +
116B TRP* 3.0 23.4 + - - +
244B PHE* 4.0 18.2 - - + -
247B GLU* 3.0 44.3 + - - +
248B VAL* 4.2 11.1 - - + +
251B ASP* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS* 4.0 36.6 - - + +
42B LEU* 3.9 19.1 - - + -
43B MSE 3.2 12.8 - - + -
46B VAL* 6.3 1.8 - - + -
109B ASP 3.5 14.8 + - - +
110B LEU* 3.4 5.8 + - - +
111B GLU 3.3 0.2 - - - -
112B LYS* 1.3 73.2 - - - +
114B LYS* 1.3 66.6 + - - +
116B TRP* 3.1 2.1 + - + +
117B GLN* 2.9 22.9 + - - +
244B PHE* 3.8 15.3 - - + -
248B VAL* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B MSE 2.3 39.7 - - + +
110B LEU* 2.9 22.1 + - + +
111B GLU* 3.6 7.6 - - + +
113B VAL* 1.3 71.6 - - - +
115B ASN* 1.3 64.5 + - - +
117B GLN* 3.6 10.0 + - - +
118B LYS* 3.1 24.3 + - + +
----------------------------------------------------------
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 GLU* 2.9 43.7 + - - +
112B LYS* 3.7 7.3 - - - +
114B LYS* 1.3 73.7 - - - +
116B TRP* 1.3 65.5 + - - +
118B LYS* 2.9 24.0 + - - +
119B ASP* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS* 4.1 16.6 - - - -
112B LYS 3.0 4.5 + - - +
113B VAL 3.6 2.2 - - - +
115B ASN* 1.3 78.2 - - - +
117B GLN* 1.3 71.8 + - - +
119B ASP* 3.0 15.7 + - + +
120B ALA* 3.1 38.7 + - + +
121B TYR* 3.8 20.6 - + - -
237B PHE* 5.5 7.2 - + - -
240B LYS* 4.1 11.5 + - + +
241B ARG* 3.7 42.4 - - + -
244B PHE* 3.2 63.4 - + + +
----------------------------------------------------------
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
----------------------------------------------------------
36B HIS* 3.4 42.2 - - + +
39B CYS* 3.7 21.5 - - + +
40B ASN* 2.8 27.1 + - - +
43B MSE 4.6 14.6 - - - +
113B VAL 2.9 16.6 + - - +
114B LYS* 3.6 10.2 + - - +
116B TRP* 1.3 86.8 - - + +
118B LYS* 1.3 62.4 + - - +
120B ALA 3.0 12.0 + - - -
121B TYR* 3.1 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 3.1 12.2 + - + +
115B ASN* 2.9 17.2 + - - +
117B GLN* 1.3 81.0 - - - +
119B ASP* 1.3 68.8 + - - +
120B ALA 3.4 0.9 + - - -
121B TYR 3.9 10.6 - - - +
122B HIS* 4.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 3.0 11.8 + - - +
116B TRP* 3.0 8.6 + - - +
118B LYS* 1.3 91.4 + - - +
120B ALA* 1.3 59.4 + - - +
122B HIS* 3.7 17.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 3.4 47.6 - - + +
117B GLN 3.0 1.4 + - - -
118B LYS 3.3 0.2 - - - -
119B ASP* 1.3 81.3 - - - +
121B TYR* 1.3 70.5 + - + +
122B HIS* 4.1 1.6 - - - -
131B GLU* 3.3 22.2 - - - +
237B PHE* 3.5 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 3.2 37.0 + - + -
33B ASP* 5.1 0.2 - - - -
35B GLY* 3.3 23.0 - - - -
36B HIS* 3.6 48.0 - - + +
39B CYS* 4.5 1.6 - - - -
116B TRP* 3.8 24.8 - + - -
117B GLN* 3.1 18.0 + - + +
118B LYS* 3.9 12.8 - - - +
120B ALA* 1.3 90.2 - - + +
122B HIS* 1.3 63.5 + - - +
123B LYS 4.0 1.6 + - - -
129B PHE* 3.8 24.2 - + + -
131B GLU* 3.6 4.0 - - + -
237B PHE* 4.0 16.4 - + - -
241B ARG* 4.2 10.0 - - - +
----------------------------------------------------------
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