Contacts of the helix formed by residues 106 - 120 (chain D) in PDB entry 3Q37
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 106 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ARG* 4.6 0.2 - - - -
104D GLY* 3.1 13.0 + - - +
105D GLU* 1.3 76.1 - - - +
107D ASN* 1.3 67.0 + - - +
108D GLU* 3.2 15.4 + - - +
109D ILE* 3.1 30.0 + - + +
110D VAL* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ARG* 3.0 26.5 + - - +
106D THR* 1.3 74.5 - - - +
108D GLU* 1.3 69.8 + - - +
110D VAL* 3.6 3.2 + - - +
111D ALA* 3.0 27.9 + - - +
143D VAL 5.3 0.2 + - - -
146D THR* 3.7 28.1 + - - +
147D GLN* 3.5 25.7 + - - +
150D ALA* 3.7 18.9 - - + +
151D VAL* 5.1 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D THR* 3.7 11.7 + - - +
107D ASN* 1.3 97.6 + - - +
109D ILE* 1.3 60.0 + - + +
111D ALA* 3.3 6.4 + - - +
112D ASP* 3.0 38.6 + - - +
150D ALA* 4.5 8.2 - - + +
154D LYS* 4.6 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLY 3.4 23.8 - - - +
105D GLU* 4.3 13.9 - - + -
106D THR* 3.1 23.7 + - + +
108D GLU* 1.3 74.5 - - + +
110D VAL* 1.3 66.2 + - - +
112D ASP* 3.3 8.6 + - - +
113D LYS* 3.1 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU* 4.4 3.6 - - + +
95D GLY* 3.7 32.1 - - - +
100D ARG* 3.7 31.2 - - - +
105D GLU* 4.0 21.1 - - + +
106D THR 3.0 19.6 + - - +
107D ASN 3.8 4.3 - - - +
109D ILE* 1.3 75.6 - - - +
111D ALA* 1.3 63.6 + - - +
113D LYS* 3.1 9.8 + - - +
114D VAL* 2.9 35.8 + - + +
126D VAL* 4.7 2.2 - - + -
151D VAL* 4.5 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASN 3.0 18.5 + - - +
108D GLU* 3.6 8.1 - - - +
109D ILE 3.3 0.2 - - - -
110D VAL* 1.3 76.4 - - - +
112D ASP* 1.3 59.5 + - - +
114D VAL* 3.3 2.8 + - - +
115D ALA* 3.0 30.7 + - - +
150D ALA* 3.2 33.7 - - + +
151D VAL* 3.7 14.1 - - - +
154D LYS* 3.9 14.3 - - + +
155D LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR* 3.8 9.6 - - + +
108D GLU* 3.0 22.3 + - - +
109D ILE* 3.7 8.0 - - - +
111D ALA* 1.3 76.3 - - - +
113D LYS* 1.3 64.2 + - - +
115D ALA* 3.4 5.7 + - - +
116D ALA* 3.0 23.9 + - - +
154D LYS* 2.5 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ASN* 3.0 19.4 + - - +
68D ALA 3.2 21.2 + - - +
69D ILE* 4.4 14.2 - - - +
70D THR* 3.8 18.8 - - + -
78D GLU* 5.3 0.2 + - - -
81D LEU* 4.4 3.4 - - + +
94D LEU* 3.8 23.9 - - + +
95D GLY 6.0 0.2 - - - +
99D ARG* 5.2 0.4 - - - +
105D GLU* 2.9 33.5 + - - +
109D ILE* 3.1 32.3 + - + +
110D VAL* 3.6 9.0 - - - +
112D ASP* 1.3 77.0 - - + +
114D VAL* 1.3 57.4 + - - +
116D ALA* 3.3 2.6 + - - +
117D ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU* 3.8 20.6 - - + -
110D VAL* 2.9 35.1 + - + +
111D ALA 3.8 4.3 - - - +
112D ASP 3.3 0.2 - - - -
113D LYS* 1.3 75.6 - - - +
115D ALA* 1.3 62.5 + - - +
117D ALA* 3.3 2.4 + - - +
118D VAL* 3.0 29.4 + - + +
124D VAL* 4.1 7.4 - - + -
126D VAL* 3.9 29.8 - - + -
151D VAL* 4.0 24.5 - - + -
155D LEU* 4.2 13.2 - - + -
163D VAL* 4.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ALA 3.0 17.2 + - - +
112D ASP* 3.8 6.3 - - - +
114D VAL* 1.3 76.9 - - - +
116D ALA* 1.3 64.0 + - - +
118D VAL* 3.4 2.6 + - - +
119D ALA* 3.1 23.6 + - - +
154D LYS* 3.8 31.0 - - + +
155D LEU* 3.8 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR* 3.7 23.8 - - + +
81D LEU* 3.5 17.7 - - + -
112D ASP 3.0 17.8 + - - +
113D LYS 3.7 0.7 - - - +
115D ALA* 1.3 75.8 - - - +
117D ALA* 1.3 64.7 + - - +
119D ALA* 3.2 8.3 + - - +
120D SER* 3.0 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 3.4 26.1 - - + +
92D VAL* 4.0 10.5 - - + -
94D LEU* 4.1 3.1 - - + -
113D LYS 2.9 17.4 + - - +
114D VAL 3.3 1.5 + - - +
116D ALA* 1.3 77.0 - - - +
118D VAL* 1.3 63.0 + - - +
120D SER 3.1 6.8 + - - -
121D GLY 3.3 0.2 + - - -
122D PHE* 3.0 28.0 + - + +
124D VAL* 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D VAL* 3.0 20.8 + - + +
115D ALA 3.9 3.8 - - - +
117D ALA* 1.3 75.7 - - - +
119D ALA* 1.3 63.5 + - - +
121D GLY 3.1 3.8 + - - -
122D PHE 4.1 3.4 - - - +
124D VAL* 4.2 11.2 - - + -
155D LEU* 4.2 10.5 - - + -
159D ALA* 3.4 31.2 - - + +
162D ARG* 2.7 49.8 + - + +
163D VAL* 4.1 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLU* 6.0 2.2 - - - +
115D ALA 3.1 18.4 + - - +
116D ALA* 3.5 9.0 - - - +
117D ALA 3.2 0.4 - - - -
118D VAL* 1.3 78.6 - - - +
120D SER* 1.3 59.6 + - - +
121D GLY 3.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 4.4 12.5 - - - +
82D GLN* 4.4 12.0 + - - +
85D LYS* 3.2 40.7 + - - +
116D ALA 3.0 15.1 + - - -
117D ALA* 3.1 6.0 + - - -
119D ALA* 1.3 76.6 - - - +
121D GLY* 1.3 60.3 + - - +
122D PHE* 3.4 22.7 + - - -
----------------------------------------------------------
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