Contacts of the helix formed by residues 137 - 149 (chain A) in PDB entry 1D0L
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 TYR 137 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 3.0 55.3 + + + +
134A TRP 3.4 3.1 - - - -
136A GLN* 1.3 114.6 + - + +
138A GLU* 1.3 64.0 + - - +
139A ASP* 3.3 3.1 - - - -
140A ALA* 3.2 6.8 + - + +
141A LEU* 3.0 25.8 + - + +
223A TYR* 4.8 3.2 + - - -
249A PRO* 3.3 32.5 - - + +
250A VAL* 4.1 21.5 - - + -
253A ILE* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 2.8 23.0 + - + +
135A ASN* 3.5 16.0 + - - +
136A GLN 3.6 0.8 + - - -
137A TYR* 1.3 77.2 - - - +
139A ASP* 1.3 61.9 + - - +
141A LEU* 3.3 5.6 + - - +
142A ASN* 2.9 49.5 + - - +
359A ARG* 3.1 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR 3.3 1.2 - - - -
138A GLU* 1.3 80.3 - - - +
140A ALA* 1.3 58.4 + - - +
142A ASN* 3.3 10.2 + - - +
143A ARG* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 3.2 12.3 + - + +
139A ASP* 1.3 78.8 - - - +
141A LEU* 1.3 57.2 + - - +
143A ARG* 3.4 13.1 + - - +
144A ALA* 2.9 25.3 + - - +
238A PHE* 3.4 10.8 - - + -
250A VAL* 4.1 30.5 - - + -
253A ILE* 4.1 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 4.8 3.1 - - + +
134A TRP* 3.7 33.7 - - + +
137A TYR* 3.0 24.0 + - + +
138A GLU* 3.6 3.8 - - - +
140A ALA* 1.3 74.7 - - - +
142A ASN* 1.3 65.7 + - - +
144A ALA* 3.3 3.9 + - - +
145A TRP* 3.0 21.8 + - - +
150A VAL 4.8 0.7 - - - +
152A PRO* 4.0 23.0 - - + +
155A ILE* 3.8 37.2 - - + +
156A VAL* 3.7 28.3 - - + -
253A ILE* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 5.3 2.1 + - - -
138A GLU* 2.9 45.5 + - - +
139A ASP* 3.8 8.6 + - - +
141A LEU* 1.3 76.1 - - - +
143A ARG* 1.3 58.1 + - - +
145A TRP* 3.3 21.2 - - + +
146A GLN* 3.0 42.7 + - - +
152A PRO* 4.1 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP 3.0 16.3 + - - +
140A ALA* 3.6 12.5 - - - +
142A ASN* 1.3 74.7 - - - +
144A ALA* 1.3 58.9 + - - +
146A GLN* 3.2 14.5 + - - +
147A VAL* 2.9 44.6 + - + +
238A PHE* 3.0 64.3 + - + -
239A SER* 4.8 1.4 - - - +
250A VAL* 3.7 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA 2.9 17.2 + - - +
141A LEU 3.5 5.6 - - - +
143A ARG* 1.3 76.2 - - - +
145A TRP* 1.3 55.7 + - - +
148A TYR* 2.8 40.4 + - - +
149A GLY 3.6 0.5 + - - -
150A VAL 4.1 2.7 - - - +
155A ILE* 3.7 24.5 - - + -
238A PHE* 3.6 14.3 - - + -
253A ILE* 3.9 11.0 - - + +
257A ALA* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU 3.0 11.8 + - - +
142A ASN* 3.3 24.5 - - + +
144A ALA* 1.3 78.0 - - - +
146A GLN* 1.3 58.6 + - + +
149A GLY* 2.8 37.7 + - - -
150A VAL 3.3 26.4 + - - +
151A PRO* 4.2 15.4 - - + +
152A PRO* 3.7 24.9 - - + -
153A GLU* 5.6 1.8 - - - -
267A LYS* 4.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 3.0 30.5 + - - +
143A ARG* 3.2 15.6 + - - +
145A TRP* 1.3 79.9 - - + +
147A VAL* 1.3 64.7 + - + +
149A GLY 4.5 0.9 + - - -
267A LYS* 5.0 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 2.9 37.6 + - + +
146A GLN* 1.3 77.6 - - + +
148A TYR* 1.3 92.4 + - + +
238A PHE* 4.6 7.0 - - + -
261A LYS* 4.0 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA* 2.8 21.6 + - - +
147A VAL* 1.3 96.6 - - + +
149A GLY* 1.3 61.4 + - - +
150A VAL* 3.4 7.1 + - + +
236A VAL* 3.7 24.9 - - - +
238A PHE* 3.8 22.5 - + - -
254A GLY 3.9 10.8 - - - -
257A ALA* 3.5 36.1 - - + +
258A ASN* 3.3 36.1 - - + -
261A LYS* 3.8 35.2 - - + +
265A TRP* 5.1 3.3 - - - +
267A LYS* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA 3.6 0.2 + - - -
145A TRP* 2.8 28.9 + - - -
146A GLN 4.5 1.0 + - - -
147A VAL 3.7 1.0 - - - -
148A TYR* 1.3 72.9 - - - +
150A VAL* 1.3 60.4 + - - +
151A PRO* 3.7 2.6 - - - +
265A TRP* 3.3 19.2 + - - -
267A LYS* 3.5 38.6 - - - +
268A GLY 4.8 0.3 + - - -
----------------------------------------------------------
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