Contacts of the helix formed by residues 140 - 153 (chain E) in PDB entry 2TEC
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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E TRP* 3.9 36.6 - - + +
116E ALA* 5.3 0.3 - - - +
139E GLY* 1.3 76.5 + - - +
141E SER* 1.3 61.3 + - - +
142E GLY* 3.3 8.6 + - - +
143E LEU* 2.8 37.5 + - + +
144E GLN* 2.9 24.1 + - - +
175E TYR* 3.1 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ASN* 1.3 73.4 - - - +
142E GLY* 1.3 57.0 + - - +
144E GLN* 3.6 11.5 - - - +
145E GLN* 2.8 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E ALA* 4.0 12.0 - - - +
140E ASN* 3.3 10.8 + - - +
141E SER* 1.3 77.1 + - - +
143E LEU* 1.3 57.7 + - - +
145E GLN* 3.6 11.1 - - - +
146E ALA* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E TRP* 3.6 47.8 - - + -
115E VAL* 4.0 8.1 - - + -
116E ALA* 4.5 6.5 - - + +
119E ILE* 3.9 25.1 - - + -
140E ASN* 2.8 27.5 + - + +
142E GLY* 1.3 76.9 - - - +
144E GLN* 1.3 62.1 + - - +
146E ALA* 3.1 5.8 + - - +
147E VAL* 3.0 23.4 + - - +
171E TYR* 4.1 13.2 - - + -
172E PRO* 4.1 14.6 - - + -
175E TYR* 3.8 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ASN 2.9 13.8 + - - +
141E SER* 3.6 14.6 - - - +
143E LEU* 1.3 72.4 - - - +
145E GLN* 1.3 64.2 + - - +
147E VAL* 3.2 5.9 + - - +
148E ASN* 2.9 40.5 + - - +
175E TYR* 3.6 46.2 + - + +
176E SER* 5.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E SER* 2.8 47.8 + - - +
142E GLY* 3.6 12.3 - - - +
144E GLN* 1.3 73.6 - - - +
146E ALA* 1.3 57.8 + - - +
148E ASN* 3.2 6.9 + - - +
149E TYR* 2.8 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E ALA* 3.7 35.2 - - + +
119E ILE* 3.7 14.1 - - + +
120E THR* 3.7 17.9 - - + +
142E GLY 2.8 21.2 + - - +
143E LEU 3.1 4.5 + - - +
145E GLN* 1.3 71.7 - - - +
147E VAL* 1.3 64.3 + - - +
149E TYR* 3.1 3.9 + - - +
150E ALA* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ILE* 4.3 19.1 - - + -
143E LEU* 3.0 15.9 + - + +
144E GLN 3.5 8.3 - - - +
146E ALA* 1.3 76.6 - - - +
148E ASN* 1.3 60.3 + - - +
150E ALA* 3.4 3.9 + - - +
151E TRP* 3.0 27.5 + - - +
157E VAL* 4.3 18.8 - - + +
172E PRO* 3.8 28.3 - - + -
175E TYR* 4.2 20.2 - - + -
177E ASN* 4.2 30.1 - - + +
178E ALA* 4.4 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 148 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLN* 2.9 38.9 + - - +
145E GLN* 3.7 6.4 - - - +
147E VAL* 1.3 75.8 - - - +
149E TYR* 1.3 62.3 + - - +
151E TRP* 3.1 5.3 + - - +
152E ASN* 3.0 37.6 + - - +
175E TYR* 6.1 1.2 - - - +
176E SER* 5.6 1.4 + - - -
177E ASN* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E THR* 3.7 37.7 - - + -
123E ALA* 4.0 9.2 - - + -
124E ASP* 2.5 35.7 + - - -
145E GLN* 2.8 18.3 + - + +
146E ALA* 3.3 6.5 - - - +
148E ASN* 1.3 74.2 - - - +
150E ALA* 1.3 67.0 + - - +
152E ASN* 3.7 5.3 + - - +
153E LYS* 3.0 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ILE* 3.9 9.0 - - + +
123E ALA* 3.7 14.6 - - + -
130E ILE* 3.7 29.8 - - + -
146E ALA 2.9 12.1 + - - +
147E VAL 3.7 7.0 - - - +
149E TYR* 1.3 76.7 - - - +
151E TRP* 1.3 64.8 + - - +
153E LYS* 3.1 9.0 + - - +
154E GLY 3.2 0.5 + - - -
155E SER* 3.0 22.9 + - - -
157E VAL* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E VAL 3.0 14.5 + - - +
148E ASN* 3.1 6.9 + - - +
150E ALA* 1.3 77.0 - - - +
152E ASN* 1.3 75.8 + - - +
154E GLY* 2.9 23.4 + - - -
155E SER 3.5 22.1 + - - -
156E VAL* 4.2 18.4 - - + -
157E VAL* 4.6 1.5 - - + +
177E ASN* 3.7 54.6 - - + +
179E ILE* 5.9 0.2 - - + -
245E ALA* 3.6 36.9 - - + +
246E SER* 3.9 21.1 - - - -
249E ARG* 4.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E ASN* 3.0 27.3 + - - +
149E TYR* 4.2 5.7 - - - +
151E TRP* 1.3 88.2 - - - +
153E LYS* 1.3 61.1 + - + +
154E GLY* 3.1 6.5 + - - -
177E ASN* 5.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E ALA* 4.4 20.0 - - + +
124E ASP* 4.2 18.6 + - - +
149E TYR* 3.0 48.4 + - + +
150E ALA 3.1 5.3 + - - +
152E ASN* 1.3 76.6 - - + +
154E GLY* 1.3 57.5 + - - +
155E SER* 3.7 2.4 + - - +
----------------------------------------------------------
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