Contacts of the helix formed by residues 147 - 163 (chain B) in PDB entry 1YDY
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 THR 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ASN* 4.9 5.2 - - + +
74B LEU 3.2 14.8 - - - +
75B VAL* 4.1 1.1 - - + +
76B VAL* 4.0 2.0 - - - -
109B LEU* 3.7 40.2 - - + -
113B LYS* 4.6 0.9 - - - -
146B HIS* 1.3 80.7 + - - +
148B PHE* 1.3 64.8 + - - +
149B GLU* 3.6 13.8 + - - +
150B GLU* 2.9 46.9 + - - +
151B GLU* 3.0 17.8 + - - +
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 4.0 17.5 - - + -
66B LEU* 3.7 31.6 - - + -
74B LEU* 2.9 34.0 + - + -
76B VAL* 4.0 9.0 - - - +
147B THR* 1.3 71.0 - - - +
149B GLU* 1.3 60.6 + - - +
151B GLU* 3.1 2.5 + - - -
152B ILE* 2.8 51.0 + - + +
170B PRO* 3.8 31.2 - - + -
189B THR* 4.2 6.1 - - + -
192B VAL* 3.5 34.3 - - + -
193B LEU* 3.8 29.8 - - + -
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 5.5 4.9 - - - +
74B LEU* 4.1 9.0 + - - +
147B THR* 3.7 17.5 - - - +
148B PHE* 1.3 83.2 + - - +
150B GLU* 1.3 57.7 + - + +
152B ILE* 3.3 4.3 + - - +
153B GLU* 2.9 36.8 + - - +
188B LYS* 4.6 10.4 + - - -
192B VAL* 3.7 37.4 - - + +
195B LYS* 5.1 8.6 + - + +
196B TYR* 3.7 27.1 - - + +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 6.2 0.2 - - - -
141A SER* 2.7 41.2 + - - +
142A ASP* 3.5 22.5 - - + +
48B LEU* 5.3 2.0 - - + -
113B LYS* 2.5 34.9 + - - -
146B HIS* 3.2 16.5 - - + +
147B THR* 2.9 45.4 + - - +
149B GLU* 1.3 77.1 - - + +
151B GLU* 1.3 59.2 + - - +
153B GLU* 4.6 1.8 - - - +
154B PHE* 3.1 13.7 + - - +
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Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.4 7.0 - - + -
51B LYS* 2.8 43.8 + - + +
62B LEU* 4.5 1.4 - - - +
64B GLN* 2.9 36.3 + - + +
76B VAL* 3.5 11.5 - - + +
146B HIS* 2.7 35.5 + - + +
147B THR 3.0 8.1 + - - +
148B PHE 3.7 6.5 - - - +
150B GLU* 1.3 76.8 - - - +
152B ILE* 1.3 65.6 + - + +
154B PHE* 3.1 6.4 + - + +
155B VAL* 3.0 28.4 + - + +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 5.2 1.8 - - - +
148B PHE* 2.8 52.9 + - + +
149B GLU* 3.8 5.8 - - - +
151B GLU* 1.3 76.7 - - - +
153B GLU* 1.3 58.4 + - - +
155B VAL* 3.2 5.1 + - - +
156B GLN* 2.9 43.0 + - + +
168B ILE* 3.5 34.5 - - + -
192B VAL* 5.0 3.4 - - + -
193B LEU* 5.1 1.6 - - + -
196B TYR* 3.6 41.1 - - + -
198B TYR* 3.9 9.4 - - + +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.7 4.5 - - - -
139A GLY 4.8 0.5 - - - +
140A LYS* 3.7 31.9 + - + +
141A SER* 2.8 34.0 + - - +
149B GLU* 2.9 22.0 + - - +
150B GLU* 3.9 3.5 - - - +
151B GLU 3.2 0.2 - - - -
152B ILE* 1.3 77.2 - - - +
154B PHE* 1.3 57.5 + - - +
156B GLN* 4.3 5.3 - - - +
157B GLY* 2.9 26.9 + - - -
196B TYR* 2.6 38.3 + - + -
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.7 18.6 - - + -
49A PRO* 3.9 15.7 - - + -
136A PHE* 3.5 10.2 - - - -
141A SER* 3.5 6.7 + - - +
143A PHE* 3.9 19.1 - + - -
48B LEU* 3.5 40.4 - - + -
51B LYS* 3.8 23.3 - - + -
52B ALA* 3.7 19.1 - - + -
62B LEU* 4.9 2.5 - - + -
150B GLU 3.1 15.5 + - - +
151B GLU* 3.1 12.3 + - + +
153B GLU* 1.3 76.3 - - - +
155B VAL* 1.3 68.6 + - + +
157B GLY 3.4 0.2 + - - -
158B LEU* 2.9 47.8 + - + +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 4.3 3.8 - - + -
62B LEU* 3.7 28.7 - - + -
151B GLU* 3.0 26.4 + - + +
152B ILE 3.7 3.1 - - - +
154B PHE* 1.3 84.7 - - + +
156B GLN* 1.3 58.1 + - + +
158B LEU* 3.3 5.9 + - - +
159B ASN* 2.9 38.0 + - - +
166B ILE* 3.5 33.0 - - + +
167B GLY 4.5 1.8 - - - +
168B ILE* 4.2 27.4 - - + -
198B TYR* 5.1 4.0 - - - +
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Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ILE* 2.9 28.9 + - - +
153B GLU* 4.3 3.8 - - - +
155B VAL* 1.3 72.9 - - + +
157B GLY* 1.3 62.3 + - - +
159B ASN* 3.3 13.0 + - - +
160B HIS* 3.0 22.3 + - - +
196B TYR* 3.1 41.2 + - - +
198B TYR* 3.0 33.5 + - - +
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Residues in contact with GLY 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.5 16.3 - - - -
137A PRO* 3.5 26.3 - - - +
153B GLU 2.9 20.9 + - - -
156B GLN* 1.3 77.8 - - - +
158B LEU* 1.3 55.7 + - - +
160B HIS* 3.3 5.7 + - - +
161B SER* 2.9 24.8 + - - -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.6 22.2 - - + +
43A LEU* 3.7 20.6 - - + -
53A MET* 3.9 15.0 - - + -
136A PHE* 3.7 0.2 - - - -
52B ALA* 4.9 0.4 - - - -
55B TYR* 3.3 41.7 - - + -
154B PHE* 2.9 50.3 + - + +
155B VAL 3.7 0.2 - - - +
157B GLY* 1.3 72.3 - - - +
159B ASN* 1.3 60.5 + - - +
160B HIS 3.1 1.8 - - - -
161B SER* 3.6 6.3 - - - +
162B THR* 2.7 53.1 + - + +
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Residues in contact with ASN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 2.6 27.7 + - - -
155B VAL* 2.9 22.3 + - - +
156B GLN* 3.3 16.8 + - - +
158B LEU* 1.3 75.5 - - - +
160B HIS* 1.3 58.3 + - - +
163B GLY* 2.9 28.4 + - - -
164B LYS 3.2 20.4 - - - +
165B ASN* 3.7 12.2 + - - +
166B ILE* 2.9 38.6 + - - +
198B TYR* 5.5 1.4 + - - -
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO 3.0 26.7 + - - -
134A GLY* 3.6 11.4 + - - +
135A ARG 3.1 22.4 + - - -
137A PRO* 4.2 13.9 - - + +
156B GLN 3.0 13.5 + - - +
157B GLY* 3.4 8.5 - - - +
158B LEU 3.1 0.2 - - - -
159B ASN* 1.3 80.5 - - - +
161B SER* 1.3 63.5 + - - +
162B THR 3.4 0.2 + - - -
163B GLY* 3.6 5.7 + - - -
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLY 4.2 1.6 - - - +
42A TYR* 2.8 51.7 + - - +
134A GLY 3.3 17.8 - - - +
135A ARG* 3.7 1.8 - - - -
136A PHE 3.6 20.6 - - - -
347A PHE* 5.7 0.7 - - - -
157B GLY 2.9 16.6 + - - -
158B LEU* 3.4 9.7 + - - +
160B HIS* 1.3 76.1 - - - +
162B THR* 1.3 62.1 + - - +
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.6 30.2 - - + -
53A MET* 5.0 2.9 - - + -
57A GLN* 6.1 0.4 - - - +
55B TYR* 3.0 27.2 + - + -
158B LEU* 2.7 43.4 + - + +
161B SER* 1.3 78.5 - - - +
163B GLY* 1.3 57.7 + - - +
164B LYS* 3.2 19.2 + - + +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ASN 2.9 13.3 + - - -
160B HIS 3.6 4.8 + - - -
161B SER 3.6 2.0 - - - -
162B THR* 1.3 78.5 - - - +
164B LYS* 1.3 64.5 + - - +
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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