Contacts of the helix formed by residues 136 - 146 (chain A) in PDB entry 1YQL
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 ASP 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA* 5.9 2.9 + - - -
61A ASP* 5.6 1.9 - - - +
135A GLN* 1.3 74.0 - - - +
137A PRO* 1.3 72.1 - - + +
138A ILE* 3.2 3.3 + - + +
139A GLU* 3.8 26.4 + - + +
140A CYS* 2.8 24.8 + - - +
229A ARG* 4.4 3.2 + - - +
258A ALA* 4.0 0.2 - - - -
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Residues in contact with PRO 137 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A GLN 3.5 0.2 - - - -
136A ASP* 1.3 86.0 - - + +
138A ILE* 1.3 54.4 + - + +
140A CYS* 3.6 0.9 - - - +
141A LEU* 2.7 38.1 + - - +
225A LEU* 3.6 33.6 - - + +
226A GLN* 4.7 21.1 - - + +
229A ARG* 3.5 32.1 - - - +
254A ILE* 4.9 3.2 - - + +
258A ALA* 3.9 14.8 - - + +
259A LEU* 4.5 8.3 - - + -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASP* 3.3 3.2 - - + +
137A PRO* 1.3 78.3 - - + +
139A GLU* 1.3 69.3 + - - +
141A LEU* 3.4 1.3 + - - -
142A PHE* 3.1 47.5 + - + +
181A PHE* 4.0 4.9 - - + -
182A PRO 3.9 21.1 - - - +
183A SER* 5.2 0.7 - - - -
184A LEU* 3.4 37.7 - - + +
215A ILE* 4.8 1.3 - - + -
222A LEU* 3.3 30.1 - - + -
225A LEU* 3.5 20.4 - - + -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER* 4.8 3.5 + - - -
46A ARG* 3.1 40.9 + - - +
58A VAL 5.7 1.0 - - - +
135A GLN* 4.7 14.7 + - - +
136A ASP* 3.3 27.9 + - + +
138A ILE* 1.3 79.8 - - - +
140A CYS* 1.3 58.3 + - - +
143A SER* 2.9 40.1 + - - +
181A PHE* 3.2 45.0 - - + +
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Residues in contact with CYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLN* 4.3 14.8 - - + +
136A ASP 2.8 18.3 + - - +
137A PRO 3.6 3.1 - - - +
139A GLU* 1.3 75.5 - - - +
141A LEU* 1.3 64.2 + - - +
143A SER* 4.6 1.8 - - - -
144A PHE* 3.0 56.9 + - - +
254A ILE* 3.9 20.1 - - + +
257A MET* 3.9 14.1 - - - -
258A ALA* 3.7 24.0 - - + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PRO 2.7 22.6 + - - +
138A ILE 3.7 2.5 - - - +
140A CYS* 1.3 73.8 - - - +
142A PHE* 1.3 79.8 + - + +
144A PHE* 4.1 0.7 - - - -
145A ILE* 3.0 37.0 + - + +
211A SER* 4.9 2.5 - - - -
215A ILE* 3.6 31.6 - - + -
225A LEU* 4.5 10.5 - - + -
240A LEU* 4.8 2.9 - - + -
243A LEU* 3.9 14.1 - - + -
246A VAL* 3.7 24.7 - - + -
254A ILE* 3.5 31.7 - - + +
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Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 3.1 33.7 + - + +
141A LEU* 1.3 98.6 - - + +
143A SER* 1.3 68.3 + - - +
145A ILE* 3.4 16.0 + - + +
146A CYS* 3.4 18.9 + - - -
162A LEU* 5.3 4.8 - - + +
181A PHE* 3.8 15.0 - - + -
184A LEU* 3.9 18.6 - - + -
187A LEU* 3.6 22.0 - - + -
208A VAL* 3.2 48.3 - - + +
211A SER* 4.0 10.3 - - - -
212A ALA* 3.7 29.2 - - + -
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLN 5.8 0.2 - - - -
45A PHE* 3.9 28.1 + - - +
46A ARG* 5.6 0.3 - - - +
135A GLN* 6.1 2.0 - - - -
139A GLU* 2.9 29.5 + - - +
140A CYS* 3.4 3.8 + - - -
142A PHE* 1.3 75.8 - - - +
144A PHE* 1.3 62.3 + - - +
146A CYS* 3.0 25.3 + - - +
147A SER* 3.5 3.6 + - - -
155A ILE* 4.3 5.9 - - - +
159A VAL* 3.8 24.2 - - - +
181A PHE* 3.9 11.9 - - - -
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY 3.2 27.1 - - - -
43A GLN 3.2 20.6 - - - -
45A PHE* 3.6 17.0 - + - -
135A GLN* 4.5 0.7 - - - -
140A CYS* 3.0 43.2 + - - +
141A LEU 4.1 0.2 - - - -
143A SER* 1.3 76.9 - - - +
145A ILE* 1.3 64.5 + - - +
146A CYS 2.9 1.6 - - - -
147A SER* 2.8 44.0 + - - +
250A VAL* 3.3 29.4 - - + +
253A CYS* 4.0 26.0 - - + -
254A ILE* 5.0 0.9 - - + -
257A MET* 3.4 22.7 - - - -
23C PPW 3.8 15.5 - + - -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 3.0 30.5 + - + +
142A PHE* 3.7 19.7 - - + +
143A SER 3.3 0.6 - - - -
144A PHE* 1.3 77.6 - - - +
146A CYS* 1.3 60.5 + - - +
147A SER 3.3 0.9 + - - -
148A SER* 3.8 15.9 + - - -
204A ARG* 4.5 7.5 - - + +
207A TYR* 3.7 31.9 - - + +
208A VAL* 4.3 14.1 - - + -
211A SER* 3.6 33.9 - - - +
244A PRO 4.1 1.6 - - - +
245A GLY* 4.3 14.2 - - - +
246A VAL* 3.7 24.0 - - + -
250A VAL* 4.5 2.8 - - + +
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Residues in contact with CYS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PHE 3.5 13.9 - - - -
143A SER* 3.0 13.9 + - - +
144A PHE 2.9 0.6 - - - -
145A ILE* 1.3 79.0 - - - +
147A SER* 1.3 58.8 + - - +
148A SER 3.3 1.3 + - - -
150A ASN* 3.1 24.1 - - - +
155A ILE* 4.0 9.5 - - + +
158A MET* 4.4 11.7 - - + -
159A VAL* 4.9 7.2 - - + -
162A LEU* 4.9 6.7 - - - -
201A LEU* 4.0 31.2 - - - -
204A ARG* 3.6 20.8 + - - +
208A VAL* 4.3 11.9 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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