Contacts of the helix formed by residues 151 - 161 (chain A) in PDB entry 2X5N
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 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A HIS* 6.0 3.4 - - - -
147A LEU 4.6 12.9 + - - -
152A ALA* 1.3 66.7 + - - +
153A LEU* 3.2 4.2 - - - +
154A GLN* 3.3 21.6 + - - +
155A HIS* 3.3 36.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 6.1 0.7 - - + -
122A GLU* 4.0 27.8 - - + +
125A LEU* 4.0 22.9 - - + +
126A ILE* 5.2 0.5 - - - +
151A SER* 1.3 76.3 + - - +
153A LEU* 1.3 60.0 + - + +
155A HIS* 3.3 7.0 + - - +
156A PHE* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 4.7 9.9 - - + -
114A VAL* 4.4 3.4 - - + -
118A ILE* 3.3 35.2 - - + -
125A LEU* 4.6 4.0 - - + -
141A ILE* 4.0 20.2 - - + -
143A HIS* 3.5 45.5 - - + +
151A SER* 3.2 2.1 - - - +
152A ALA* 1.3 76.4 - - + +
154A GLN* 1.3 59.1 + - - +
156A PHE* 3.4 22.0 + - + +
157A ILE* 3.0 33.5 + - + +
168A LEU* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 3.3 18.8 + - - +
152A ALA 3.2 0.4 - - - -
153A LEU* 1.3 79.5 - - - +
155A HIS* 1.3 63.3 + - + +
157A ILE* 3.4 8.5 + - - +
158A ASP* 3.0 64.8 + - - +
168A LEU* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 2.5 36.5 + - - +
126A ILE* 3.6 11.7 - - + +
151A SER* 3.4 33.6 + - - -
152A ALA 3.3 4.2 + - - +
153A LEU 3.3 0.2 - - - -
154A GLN* 1.3 85.2 - - + +
156A PHE* 1.3 61.9 + - - +
158A ASP* 3.7 11.2 - - - +
159A ALA* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 4.1 18.2 - + - -
91A ILE* 5.0 2.2 - - + -
125A LEU* 3.2 40.8 - - + +
126A ILE* 3.9 9.7 - - - +
128A LEU* 4.1 10.1 - - + -
129A ALA* 3.3 27.5 - - + +
132A MET* 4.4 12.3 - - - -
139A ILE* 4.0 39.9 - - + -
141A ILE* 4.3 5.6 - - + -
152A ALA 3.1 12.8 + - - +
153A LEU* 3.4 24.2 - - + +
155A HIS* 1.3 76.3 - - - +
157A ILE* 1.3 77.5 + - + +
159A ALA 3.1 1.7 + - - -
160A ALA* 3.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 3.7 24.2 - - + +
141A ILE* 3.9 20.2 - - + -
153A LEU 3.0 21.1 + - - +
154A GLN* 4.0 7.6 - - - +
156A PHE* 1.3 85.9 - - + +
158A ASP* 1.3 66.6 + - - +
160A ALA* 3.2 2.7 + - - +
161A ASN* 3.0 25.9 + - - +
166A CYS* 4.0 25.3 - - + +
167A HIS* 3.5 22.4 - - - +
168A LEU* 3.9 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 5.8 0.7 + - - -
154A GLN* 3.0 49.9 + - - +
155A HIS* 3.7 12.7 - - - +
157A ILE* 1.3 78.3 - - - +
159A ALA* 1.3 61.7 + - - +
160A ALA 3.6 0.2 + - - -
161A ASN* 3.6 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 4.2 15.0 - - + -
129A ALA* 3.7 16.5 - - + +
130A LYS* 4.2 26.8 - - + +
133A LYS* 3.5 21.3 + - - +
155A HIS 3.0 17.5 + - - +
156A PHE 3.1 4.7 + - - +
158A ASP* 1.3 78.5 - - - +
160A ALA* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 3.6 24.4 - - + +
132A MET* 4.9 5.6 - - + -
133A LYS* 3.5 18.0 - - - +
137A VAL 5.0 2.4 - - - +
139A ILE* 3.9 27.4 - - + -
156A PHE* 3.0 16.0 + - + +
157A ILE* 3.9 4.5 - - - +
159A ALA* 1.3 77.0 - - - +
161A ASN* 1.3 66.8 + - - +
162A SER* 3.6 2.8 + - - -
166A CYS* 3.8 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 3.4 19.9 + - - +
157A ILE* 3.0 19.5 + - - +
158A ASP* 3.9 14.7 + - - +
159A ALA 3.4 2.2 - - - -
160A ALA* 1.3 78.8 - - - +
162A SER* 1.3 60.7 + - - +
164A ASP* 4.0 19.4 + - - +
165A SER 3.0 12.2 + - - -
166A CYS* 2.9 44.8 + - - -
----------------------------------------------------------
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