Contacts of the helix formed by residues 139 - 151 (chain Q) in PDB entry 2NX5
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 ALA 139 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Q TYR* 3.8 21.9 - - + +
85Q TYR* 3.6 42.6 - - + -
123Q TYR* 2.7 15.7 + - - +
137Q ASP* 3.2 2.1 + - - +
138Q THR* 1.3 76.4 + - - +
140Q ALA* 1.3 57.0 + - - +
141Q GLN 3.1 4.7 - - - -
142Q ILE* 3.2 26.1 + - - +
143Q THR* 3.6 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123Q TYR* 3.2 50.2 + - + +
124Q ILE* 3.4 9.0 - - + +
135Q ALA* 3.5 12.1 - - + +
136Q ALA 3.6 1.8 - - - +
137Q ASP* 3.1 22.4 + - - +
139Q ALA* 1.3 74.1 - - - +
141Q GLN* 1.3 57.4 + - - +
142Q ILE 3.3 0.4 - - - -
143Q THR* 3.9 1.3 - - - -
144Q GLN* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135Q ALA* 4.0 10.0 - - + +
137Q ASP 3.4 13.9 + - - +
138Q THR* 3.3 23.2 + - + +
139Q ALA 3.1 0.4 - - - -
140Q ALA* 1.3 77.5 - - - +
142Q ILE* 1.3 63.6 + - + +
144Q GLN* 2.9 37.3 + - - +
145Q ARG* 3.3 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Q TYR* 3.6 35.9 - - + +
138Q THR 3.6 14.4 - - - +
139Q ALA* 3.2 17.9 + - - +
141Q GLN* 1.3 77.8 - - + +
143Q THR* 1.3 63.9 + - - +
145Q ARG* 3.4 7.5 + - + +
146Q LYS* 3.1 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Q TYR* 3.5 3.3 - - - -
123Q TYR* 3.1 28.5 + - + -
124Q ILE* 4.1 10.3 - - + -
139Q ALA 3.6 1.2 + - - -
140Q ALA 3.8 7.6 - - - -
141Q GLN 3.5 0.2 - - - -
142Q ILE* 1.3 78.7 - - - +
144Q GLN* 1.3 56.8 + - - +
146Q LYS* 3.3 5.4 + - - +
147Q TRP* 2.9 60.2 + - + -
11S TYR* 2.6 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124Q ILE* 3.9 11.4 - - + +
133Q TRP* 3.2 38.5 - - + +
135Q ALA* 4.0 9.9 + - - +
140Q ALA 3.1 18.9 + - - +
141Q GLN* 2.9 32.2 + - - +
143Q THR* 1.3 76.9 - - - +
145Q ARG* 1.3 62.1 + - - +
147Q TRP* 3.2 5.4 + - - +
148Q GLU* 2.7 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141Q GLN* 3.3 44.7 + - - +
142Q ILE* 3.9 5.8 - - + +
143Q THR 3.4 0.2 - - - -
144Q GLN* 1.3 85.0 - - - +
146Q LYS* 1.3 64.4 + - - +
148Q GLU* 4.0 13.4 - - - +
149Q ALA* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q ASN* 3.9 21.6 + - - +
84Q TYR* 2.8 34.5 + - - +
142Q ILE* 3.1 20.6 + - + +
143Q THR 3.3 9.4 - - - +
145Q ARG* 1.3 77.3 - - - +
147Q TRP* 1.3 66.6 - - + +
149Q ALA* 3.8 4.6 + - - +
150Q ALA* 3.2 26.3 + - - +
8S LEU* 4.7 3.3 - - - +
10S ALA 4.7 4.0 - - - +
11S TYR* 3.9 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 147 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q ARG* 4.8 9.6 - - - -
114Q ASP* 4.9 2.7 - - - -
116Q SER* 5.7 0.2 - - - -
124Q ILE* 4.0 16.4 - - + -
133Q TRP* 3.6 52.7 + + - +
143Q THR* 2.9 27.1 + - + +
144Q GLN* 3.2 4.7 + - - +
146Q LYS* 1.3 81.0 - - + +
148Q GLU* 1.3 61.6 + - - +
149Q ALA 3.3 0.2 - - - -
151Q ARG* 2.8 24.8 + - - -
152Q VAL* 3.1 27.0 + - + -
153Q ALA 4.8 0.5 + - - -
8S LEU 4.0 12.8 - - - -
9S THR* 2.9 23.1 + - - -
10S ALA 2.7 24.9 + - - -
11S TYR* 3.4 52.8 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131Q SER 5.4 4.4 - - - +
132Q SER* 5.4 5.7 - - - -
133Q TRP* 4.1 20.2 + - + +
144Q GLN* 2.7 45.0 + - - +
145Q ARG* 4.0 12.8 - - - +
146Q LYS 3.5 0.2 - - - -
147Q TRP* 1.3 74.5 - - - +
149Q ALA* 1.3 60.0 + - - +
151Q ARG* 3.6 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145Q ARG 3.2 17.3 + - - +
146Q LYS* 4.1 4.7 - - - +
148Q GLU* 1.3 75.8 - - - +
150Q ALA* 1.3 59.7 + - - +
151Q ARG* 3.2 6.8 + - - +
101U GLN* 5.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146Q LYS 3.2 16.8 + - - +
149Q ALA* 1.3 76.5 - - - +
151Q ARG* 1.3 70.7 + - - +
152Q VAL* 3.5 9.0 + - + +
155Q GLN* 4.9 0.2 + - - -
8S LEU* 3.4 48.2 - - + +
98U ASP* 5.1 1.0 - - - +
100U ASN* 3.3 13.7 + - - +
101U GLN* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Q TRP 2.8 9.8 + - - -
148Q GLU* 3.6 12.1 + - - +
149Q ALA 3.2 6.3 - - - +
150Q ALA* 1.3 80.4 - - - +
152Q VAL* 1.3 61.7 + - - +
153Q ALA* 3.3 3.3 + - - +
154Q GLU* 3.1 52.1 + - - +
155Q GLN 3.6 2.8 + - - -
48T TYR* 4.1 33.9 + - - +
50T VAL* 4.7 6.1 - - - +
51T LEU* 5.8 1.0 - - - +
55T GLU* 4.4 20.2 + - - -
57T LYS* 5.8 1.4 - - - +
100U ASN* 2.8 26.1 + - - +
101U GLN* 5.3 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