Contacts of the helix formed by residues 140 - 155 (chain A) in PDB entry 2XWU
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 ASN 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 2.9 26.6 + - + +
139A GLN* 1.3 82.5 - - + +
141A ARG* 1.3 62.7 + - - +
142A VAL* 3.2 18.8 + - - +
143A GLU* 2.9 32.0 + - + +
144A TYR 3.2 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE 3.7 1.1 + - - -
137A TYR* 2.7 76.2 + - - +
138A CYS* 5.1 4.2 + - - +
139A GLN 4.1 0.4 - - - -
140A ASN* 1.3 74.3 + - - +
142A VAL* 1.3 64.2 + - + +
144A TYR* 3.3 11.6 + - - +
145A GLU* 3.0 26.0 + - + +
73B GLU* 4.8 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASN* 3.3 10.6 - - - +
141A ARG* 1.3 78.6 - - + +
143A GLU* 1.3 62.0 + - - +
145A GLU* 3.8 7.7 + - - +
146A LYS* 3.2 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 4.0 11.9 - - + -
140A ASN* 2.9 30.9 + - - +
142A VAL* 1.3 77.9 - - - +
144A TYR* 1.3 66.4 + - - +
146A LYS* 3.2 10.7 + - - +
147A ARG* 2.9 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TRP* 4.0 19.4 - - - -
82A PHE* 3.7 29.8 - + - -
83A HIS* 4.1 0.6 - - - -
84A PRO* 3.5 23.5 - - + +
120A LEU 4.3 0.9 + - - -
121A ASN 6.0 1.6 - - - -
123A PRO* 3.4 20.6 - - + +
133A ALA 4.1 4.9 - - - -
136A ILE* 3.7 13.1 - - + +
137A TYR* 3.5 45.1 - + + -
140A ASN 3.2 10.2 + - - +
141A ARG* 3.3 19.7 - - - +
143A GLU* 1.3 81.2 - - - +
145A GLU* 1.3 63.3 + - + +
147A ARG* 3.2 2.8 + - - +
148A VAL* 2.9 46.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
52A PRO* 3.8 19.8 - - + +
141A ARG* 3.0 15.1 + - + +
142A VAL* 4.0 7.9 - - - +
144A TYR* 1.3 86.5 - - + +
146A LYS* 1.3 68.1 + - - +
148A VAL* 3.8 5.6 - - - +
149A ARG* 2.4 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 3.2 16.5 + - + +
143A GLU* 3.2 21.8 + - - +
145A GLU* 1.3 83.7 + - - +
147A ARG* 1.3 61.5 + - - +
149A ARG* 3.5 5.7 + - - +
150A ALA* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.9 30.5 - - + -
132A GLU* 2.7 31.3 + - - -
136A ILE* 2.9 22.6 - - - +
143A GLU* 2.9 46.8 + - - +
144A TYR 3.7 6.3 - - - +
146A LYS* 1.3 74.1 - - + +
148A VAL* 1.3 61.0 + - - +
150A ALA* 3.0 10.1 + - - +
151A GLN* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 4.1 11.7 - - + +
53A TRP* 3.3 50.9 - - + +
82A PHE* 4.1 11.2 - - + +
144A TYR* 2.9 56.0 + - + +
145A GLU* 3.8 7.0 - - - +
147A ARG* 1.3 76.0 - - - +
149A ARG* 1.3 57.2 + - - +
151A GLN* 3.2 8.8 + - - +
152A ALA* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR 4.6 5.5 + - - -
52A PRO* 3.7 40.0 + - + +
54A GLU* 5.8 2.2 + - - +
145A GLU* 2.4 44.2 + - - +
146A LYS* 3.8 6.3 - - - +
147A ARG 3.2 0.2 - - - -
148A VAL* 1.3 74.7 - - - +
150A ALA* 1.3 64.4 + - - +
152A ALA* 3.5 2.8 + - - +
153A LYS* 3.2 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS 3.3 10.7 + - - +
147A ARG* 3.0 13.6 + - - +
149A ARG* 1.3 77.4 - - - +
151A GLN* 1.3 60.4 + - - +
153A LYS* 3.2 10.7 + - - +
154A LYS* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TRP* 3.5 26.1 - - - -
58A PHE* 4.6 1.3 - - + -
80A PRO 4.7 0.3 - - - +
81A LEU* 3.3 18.3 - - + +
82A PHE* 2.5 54.9 + - + +
147A ARG 2.9 12.1 + - - +
148A VAL* 3.2 12.6 + - - +
150A ALA* 1.3 77.7 - - - +
152A ALA* 1.3 64.3 + - - +
154A LYS* 2.9 16.0 + - + -
155A PHE* 2.9 47.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
52A PRO 3.3 26.2 - - - +
53A TRP* 3.7 20.2 - - - +
54A GLU 3.8 8.3 - - - +
55A GLY 4.2 1.1 - - - -
56A GLY* 3.4 13.4 + - - -
58A PHE* 4.1 13.2 - - + -
148A VAL 2.9 11.8 + - - +
149A ARG 3.7 4.5 - - - +
151A GLN* 1.3 76.5 - - - +
153A LYS* 1.3 62.1 + - - +
155A PHE 3.5 0.2 + - - -
156A ALA* 3.4 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 3.2 19.4 + - - +
150A ALA* 3.5 11.0 - - - +
151A GLN 3.1 0.6 - - - -
152A ALA* 1.3 74.1 - - - +
154A LYS* 1.3 66.1 + - - +
156A ALA* 3.2 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 5.4 5.9 - - - +
150A ALA 2.9 13.1 + - - +
151A GLN* 2.9 15.9 + - + +
153A LYS* 1.3 78.7 - - - +
155A PHE* 1.3 85.8 + - + +
156A ALA 3.3 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 2.9 41.5 + - - +
58A PHE* 3.7 23.8 - + + -
59A LYS* 5.9 1.1 - - + -
79A PRO* 3.9 31.2 - - + -
80A PRO 5.1 3.6 - - - -
81A LEU* 3.8 17.5 - - + -
151A GLN* 2.9 54.1 + - + +
152A ALA 3.5 4.2 + - - +
153A LYS 3.2 0.2 - - - -
154A LYS* 1.3 106.1 - - + +
156A ALA* 1.3 65.8 + - - +
157A PRO* 3.7 0.9 - - - +
----------------------------------------------------------
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