Contacts of the helix formed by residues 145 - 157 (chain A) in PDB entry 6B3I
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 145 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.1 27.8 + - - +
144A THR* 1.3 80.3 - - - +
146A GLY* 1.3 69.6 + - - +
148A LEU* 3.4 14.8 + - - +
149A LYS* 3.2 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER* 1.3 78.1 - - - +
147A ASN* 1.3 63.1 + - - -
149A LYS* 3.4 15.5 + - - +
150A LYS* 3.7 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 1.3 71.0 - - - -
148A LEU* 1.3 64.5 + - - +
149A LYS 3.2 1.3 - - - -
150A LYS* 3.1 11.8 + - - +
151A ILE* 3.0 24.4 + - - +
190A GLU* 2.9 37.7 + - + +
191A LEU* 3.6 30.5 - - - +
194A ASN* 3.6 10.3 + - - +
232A LEU* 4.3 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 4.1 28.3 - - + +
110A ILE* 4.0 9.6 - - + -
144A THR* 4.8 3.1 - - + -
145A SER* 3.4 12.5 + - - +
146A GLY 3.3 0.8 - - - -
147A ASN* 1.3 79.1 - - - +
149A LYS* 1.3 59.9 + - - +
151A ILE* 3.2 5.2 - - + +
152A LEU* 3.2 51.8 + - + +
231A ASP* 3.7 28.7 - - + +
232A LEU* 4.2 15.9 - - + +
235A ALA* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 3.7 49.4 + - - +
144A THR* 3.2 32.7 - - - +
145A SER* 3.2 11.5 + - - +
146A GLY 3.5 12.1 - - - +
147A ASN 3.2 0.2 - - - -
148A LEU* 1.3 80.2 - - - +
150A LYS* 1.3 62.9 + - - +
152A LEU* 4.1 1.1 - - - +
153A VAL* 3.1 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY 3.7 2.6 + - - +
147A ASN* 3.1 19.9 + - - +
149A LYS* 1.3 80.6 - - - +
151A ILE* 1.3 57.6 + - - +
153A VAL* 4.2 4.4 - - - +
154A SER* 3.2 25.5 + - - -
191A LEU* 3.8 31.6 - - + +
194A ASN* 4.2 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN 3.0 11.8 + - - +
148A LEU* 3.2 27.6 - - + +
150A LYS* 1.3 76.6 - - - +
152A LEU* 1.3 63.6 + - + +
154A SER* 3.2 6.0 + - - -
155A LEU* 2.9 32.3 + - + +
194A ASN* 3.5 39.2 - - + +
198A ALA* 3.7 29.8 - - + -
232A LEU* 4.5 8.5 - - + -
235A ALA* 4.7 8.7 - - + -
236A TYR* 4.8 4.5 - - + -
239A LEU* 4.3 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 5.6 0.4 - - - -
109A LEU* 3.7 35.4 - - + +
110A ILE* 4.5 8.7 - - + -
113A LEU* 3.7 32.7 - - + +
114A CYS* 4.5 9.6 - - - -
140A VAL* 4.2 8.1 - - + -
144A THR* 3.7 12.8 - - + -
148A LEU* 3.2 41.2 + - + +
149A LYS 4.2 1.8 - - - +
151A ILE* 1.3 77.0 - - + +
153A VAL* 1.3 64.1 + - - +
155A LEU* 3.3 14.6 + - + +
156A LEU* 3.1 27.8 + - - +
235A ALA* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 3.7 27.4 - - + +
140A VAL* 4.2 13.7 - - + -
141A LYS* 3.8 33.7 - - + +
149A LYS* 3.1 24.1 + - + +
150A LYS* 4.2 4.5 - - - +
152A LEU* 1.3 76.3 - - - +
154A SER* 1.3 62.9 + - - +
156A LEU* 3.1 18.5 + - + +
157A GLN* 3.3 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LYS 3.2 20.2 + - - -
151A ILE* 3.2 15.6 + - - -
153A VAL* 1.3 78.7 - - - +
155A LEU* 1.3 61.4 + - - +
157A GLN* 3.3 16.6 + - - +
159A ASN* 3.8 0.5 - - - +
194A ASN* 4.7 4.8 + - - -
198A ALA* 4.1 6.5 - - - +
199A LYS* 2.8 46.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.3 37.2 - - + +
114A CYS* 3.6 26.0 - - - -
121A ILE* 3.3 21.5 - - + +
151A ILE* 2.9 24.9 + - + +
152A LEU* 3.7 12.1 - - + +
153A VAL 3.2 0.4 - - - -
154A SER* 1.3 72.7 - - - +
156A LEU* 1.3 65.7 + - - +
157A GLN 3.1 2.2 - - - -
158A ALA* 3.1 11.8 + - - -
160A ARG* 3.7 26.9 - - + +
198A ALA* 3.7 23.6 - - + +
239A LEU* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.7 27.1 - - + -
121A ILE* 3.9 8.3 - - + +
125A LYS* 2.9 45.0 + - + +
136A LEU* 3.8 22.0 - - + -
137A GLU* 3.7 37.9 - - + +
140A VAL* 3.8 24.7 - - + -
152A LEU 3.1 19.1 + - - +
153A VAL* 3.1 15.2 + - - +
155A LEU* 1.3 73.4 - - - +
157A GLN* 1.3 62.8 + - - +
158A ALA 3.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS* 4.4 6.3 + - - +
137A GLU* 4.2 13.3 + - - +
153A VAL* 3.3 31.7 + - - +
154A SER* 3.3 14.3 - - - +
155A LEU 3.1 0.6 - - - -
156A LEU* 1.3 77.7 - - - +
158A ALA* 1.3 67.3 + - - +
159A ASN* 3.2 29.1 + - - +
199A LYS* 4.4 2.0 - - - +
----------------------------------------------------------
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