Contacts of the helix formed by residues 143 - 158 (chain A) in PDB entry 3HPD
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 GLY 143 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 5.0 3.8 - - - -
144A GLU* 1.3 60.1 + - - +
145A GLU 3.7 1.5 - - - +
146A GLU* 3.3 16.4 + - - +
147A ALA* 2.5 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY* 1.3 76.6 + - - +
145A GLU* 1.3 58.5 + - - +
147A ALA* 5.9 0.2 - - - +
148A LYS* 2.9 31.4 + - - +
167A ALA* 5.1 2.9 - - - +
168A VAL* 3.2 37.7 + - + +
170A TYR* 2.9 34.6 - - + +
181A TYR* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY 3.7 0.6 - - - +
144A GLU* 1.3 77.8 - - - +
146A GLU* 1.3 58.3 + - - +
148A LYS* 2.8 40.8 + - - +
149A LYS* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.7 28.3 - - + -
143A GLY* 3.3 16.7 + - - +
144A GLU 3.2 0.4 - - - -
145A GLU* 1.3 77.1 - - - +
147A ALA* 1.3 58.1 + - - +
149A LYS* 3.4 8.3 + - + +
150A LEU* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.9 22.6 - - + -
143A GLY 2.5 25.7 + - - +
144A GLU* 3.7 3.4 - - - +
146A GLU* 1.3 71.3 - - - +
148A LYS* 1.3 60.2 + - - +
150A LEU* 3.3 2.3 + - - +
151A THR* 2.8 33.8 + - - -
164A VAL* 4.3 9.4 - - + +
168A VAL 5.5 1.8 - - - +
170A TYR* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU 2.9 16.8 + - - +
145A GLU* 2.8 34.9 + - - +
147A ALA* 1.3 77.6 - - - +
149A LYS* 1.3 62.5 + - - +
151A THR* 3.4 4.8 + - - -
152A MET* 3.2 22.6 + - + +
170A TYR* 4.0 29.1 - - + -
177A THR* 4.4 10.2 - - + +
263A VAL* 3.3 37.7 - - + +
264A GLU* 3.9 20.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
145A GLU* 3.0 21.2 + - - +
146A GLU* 3.8 8.1 - - + +
147A ALA 3.3 0.2 - - - -
148A LYS* 1.3 77.1 - - - +
150A LEU* 1.3 62.8 + - - +
152A MET* 3.4 8.5 + - - +
153A ASN* 3.0 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.6 48.7 - - + +
124A ILE* 4.1 17.5 - - + -
125A SER* 3.8 26.5 - - - +
128A LEU* 3.6 24.7 - - + -
146A GLU 3.0 17.5 + - - +
147A ALA 3.5 4.5 - - - +
149A LYS* 1.3 78.3 - - - +
151A THR* 1.3 64.5 + - - +
153A ASN* 4.8 3.6 - - - +
154A ALA* 2.9 27.4 + - - +
164A VAL* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA 2.8 21.1 + - - -
148A LYS 3.6 5.6 - - - -
149A LYS 3.3 0.2 - - - -
150A LEU* 1.3 76.8 - - - +
152A MET* 1.3 55.8 + - - +
154A ALA* 3.8 2.1 - - - +
155A ALA* 3.0 27.7 + - - +
162A VAL* 3.1 35.6 - - + +
164A VAL* 3.1 19.6 - - - +
170A TYR* 3.4 28.1 - - + +
172A SER* 3.5 20.6 - - - +
177A THR* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS* 3.2 11.5 + - + +
149A LYS* 3.7 9.9 - - - +
151A THR* 1.3 76.4 - - - +
153A ASN* 1.3 92.0 + - - +
155A ALA* 3.2 2.8 + - - +
156A ARG* 3.0 69.2 + - - +
172A SER* 4.1 16.5 - - - +
174A GLY* 4.2 10.1 - - - +
177A THR* 5.1 4.0 - - - +
264A GLU* 5.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.8 22.0 - - + +
149A LYS* 3.0 59.1 + - - +
150A LEU* 4.0 1.4 - - - +
152A MET* 1.3 99.7 - - - +
154A ALA* 1.3 57.0 + - - +
156A ARG* 3.4 3.5 + - - +
157A GLU* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.7 26.5 - - + -
128A LEU* 4.1 11.1 - - + +
150A LEU 2.9 19.0 + - - +
151A THR 3.8 3.4 - - - +
153A ASN* 1.3 74.2 - - - +
155A ALA* 1.3 61.0 + - - +
157A GLU* 4.1 5.8 - - - -
158A PHE* 2.9 46.8 + - + +
162A VAL* 3.8 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A THR 3.0 18.8 + - - +
152A MET 3.2 6.3 + - - +
154A ALA* 1.3 77.9 - - - +
156A ARG* 1.3 57.0 + - - +
159A ASN* 2.9 22.7 + - - -
160A THR 3.1 30.4 + - - +
162A VAL* 3.6 8.0 - - + +
172A SER 3.4 18.6 - - - +
173A ASP 4.9 1.8 - - - +
174A GLY* 3.6 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 3.0 48.2 + - + +
153A ASN* 3.9 4.5 - - - +
155A ALA* 1.3 74.0 - - - +
157A GLU* 1.3 66.5 + - - +
159A ASN* 3.4 12.0 + - - +
174A GLY* 2.9 35.1 + - - -
175A ARG* 4.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.6 26.2 - - + +
131A GLU* 3.5 36.1 - - + +
132A GLY* 5.5 5.0 + - - -
153A ASN 2.8 20.0 + - - +
154A ALA* 3.6 3.8 - - - +
156A ARG* 1.3 79.8 - - - +
158A PHE* 1.3 68.1 + - + +
159A ASN* 3.7 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.9 17.5 - - + -
110A LEU* 3.9 44.1 - - + +
113A GLY* 5.9 1.6 - - - -
114A VAL 5.2 2.3 + - - +
117A LEU* 4.0 18.2 - - + -
124A ILE* 5.4 0.7 - - + -
127A LEU* 3.6 33.4 - - + -
128A LEU* 4.3 8.5 - - - -
131A GLU* 3.8 28.7 - - + -
154A ALA* 2.9 33.5 + - + +
157A GLU* 1.3 84.1 - - + +
159A ASN* 1.3 72.5 + - - +
160A THR* 3.2 18.9 + - + -
----------------------------------------------------------
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