Contacts of the helix formed by residues 132 - 147 (chain B) in PDB entry 1YQZ
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 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASP* 3.4 35.6 + - - +
40B PHE* 3.4 30.1 - - + -
45B LEU* 3.6 7.4 - - - +
130B LEU* 4.2 0.3 - - - +
131B ARG* 1.3 79.5 - - + +
133B LEU* 1.3 59.0 + - - +
134B GLU* 3.2 13.5 + - - +
135B ASP* 2.9 32.0 + - - +
136B THR* 2.9 28.4 + - - -
440B FAD 5.8 0.4 + - - +
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Residues in contact with LEU 133 (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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36B ARG* 3.9 1.1 - - - -
37B ASP* 3.5 19.3 + - - +
40B PHE* 3.8 19.1 - - + -
45B LEU* 4.0 16.4 - - + -
48B VAL* 5.3 2.7 - - + -
56B ARG* 3.6 43.1 - - - +
59B ALA* 3.9 31.4 - - + +
60B LEU* 4.1 20.0 - - + -
132B ASN* 1.3 73.8 - - - +
134B GLU* 1.3 66.1 + - - +
136B THR* 4.0 10.3 - - + -
137B ASP* 2.9 33.2 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 3.4 15.1 - - - +
36B ARG* 2.9 68.1 + - + +
37B ASP* 4.0 3.3 + - - +
78B TYR* 4.1 13.3 + - - -
96B ARG* 5.1 0.9 + - - -
132B ASN* 3.2 14.8 + - - +
133B LEU* 1.3 77.5 - - - +
135B ASP* 1.3 65.6 + - - +
137B ASP* 3.4 2.4 + - - +
138B ALA* 3.0 23.8 + - - +
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Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 5.1 1.1 - - + -
129B THR* 3.5 26.9 + - - +
130B LEU* 3.8 3.7 - - + -
131B ARG* 2.8 32.3 + - - +
132B ASN* 2.9 29.4 + - - +
134B GLU* 1.3 79.3 - - - +
136B THR* 1.3 56.8 + - - +
138B ALA* 3.3 6.2 + - - +
139B ILE* 3.0 36.0 + - - +
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Residues in contact with THR 136 (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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45B LEU* 3.3 17.0 - - + +
48B VAL* 3.7 36.8 - - + -
49B ILE* 4.0 16.2 - - + +
130B LEU* 3.3 19.2 - - - +
132B ASN 2.9 14.1 + - - -
133B LEU* 3.6 16.8 - - + -
135B ASP* 1.3 78.1 - - - +
137B ASP* 1.3 63.1 + - - +
139B ILE* 3.3 6.3 + - - +
140B ASP* 3.0 24.4 + - + +
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 2.8 32.7 + - - +
48B VAL* 5.8 1.6 - - - +
56B ARG* 2.8 34.9 + - - -
133B LEU* 2.9 20.7 + - - +
134B GLU* 3.7 4.3 - - - +
136B THR* 1.3 76.1 - - - +
138B ALA* 1.3 58.8 + - - +
140B ASP* 3.3 5.8 + - - +
141B GLN* 2.9 50.3 + - - +
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Residues in contact with ALA 138 (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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128B PHE* 4.1 19.7 - - + -
134B GLU 3.0 18.5 + - - +
135B ASP* 3.3 8.0 + - - +
137B ASP* 1.3 77.5 - - - +
139B ILE* 1.3 57.7 + - - +
141B GLN* 3.5 8.8 + - - +
142B PHE* 2.9 30.1 + - - +
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Residues in contact with ILE 139 (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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49B ILE* 4.0 36.6 - - + -
128B PHE* 3.7 28.5 - - + -
129B THR 4.0 17.9 - - - +
130B LEU* 4.3 9.2 - - + -
135B ASP 3.0 23.9 + - - +
136B THR* 3.7 4.5 - - - +
138B ALA* 1.3 73.9 - - - +
140B ASP* 1.3 65.0 + - - +
142B PHE* 3.2 5.9 + - - +
143B ILE* 3.0 41.7 + - + +
232B MET* 4.2 13.6 - - + +
234B ILE* 4.5 13.5 - - + -
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Residues in contact with ASP 140 (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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48B VAL* 5.5 5.6 - - + +
49B ILE* 5.9 4.3 - - - -
51B GLU* 4.4 3.1 - - - +
136B THR* 3.0 17.4 + - + +
137B ASP* 3.7 6.7 - - - +
139B ILE* 1.3 77.1 - - - +
141B GLN* 1.3 68.0 + - - +
143B ILE* 3.3 4.1 + - - +
144B LYS* 3.2 44.2 + - - +
170B ARG* 2.9 44.4 + - - +
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Residues in contact with GLN 141 (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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137B ASP* 2.9 38.2 + - - +
138B ALA* 3.8 7.4 - - - +
140B ASP* 1.3 83.0 + - - +
142B PHE* 1.3 56.5 + - - +
144B LYS* 3.3 7.8 + - + +
145B ALA* 2.9 32.3 + - - +
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Residues in contact with PHE 142 (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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125B ASP* 3.6 17.3 - - + -
126B ILE* 3.8 20.4 - - + -
128B PHE* 3.6 22.9 - + + -
138B ALA 2.9 18.3 + - - +
139B ILE 3.2 5.1 + - - +
141B GLN* 1.3 72.7 - - - +
143B ILE* 1.3 67.0 + - - +
145B ALA* 4.6 1.8 - - - -
146B ASN* 3.1 56.4 + - + +
148B VAL* 3.8 10.3 - - + -
231B ASP 3.2 26.7 - - - -
232B MET* 3.6 26.5 - - + -
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Residues in contact with ILE 143 (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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49B ILE* 4.7 1.3 - - + -
139B ILE* 3.0 35.6 + - + +
140B ASP 3.3 6.5 + - - +
142B PHE* 1.3 76.4 - - - +
144B LYS* 1.3 59.2 + - + +
147B GLN* 3.0 25.3 + - - -
148B VAL* 3.1 31.7 + - + +
167B LEU* 4.4 6.7 - - + -
170B ARG* 3.6 42.0 - - - +
172B LEU* 4.1 21.3 - - + -
232B MET* 3.7 24.7 - - + -
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Residues in contact with LYS 144 (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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51B GLU* 4.7 7.1 + - - -
140B ASP* 3.2 39.9 + - - +
141B GLN* 3.8 9.9 - - + +
143B ILE* 1.3 79.8 - - + +
145B ALA* 1.3 62.6 + - - +
146B ASN 3.4 0.3 + - - -
147B GLN* 3.6 12.9 + - - +
170B ARG* 4.1 11.9 - - - +
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Residues in contact with ALA 145 (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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141B GLN 2.9 19.2 + - - +
142B PHE* 4.6 1.1 - - - -
144B LYS* 1.3 77.9 - - - +
146B ASN* 1.3 71.9 + - - +
147B GLN* 3.6 3.3 + - - +
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Residues in contact with ASN 146 (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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142B PHE* 3.1 61.5 + - + +
145B ALA* 1.3 87.1 - - - +
147B GLN* 1.3 72.9 + - - +
148B VAL* 3.1 12.6 + - + +
231B ASP* 5.4 5.8 - - + +
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Residues in contact with GLN 147 (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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143B ILE 3.0 8.7 + - - -
144B LYS* 3.6 10.1 + - - +
145B ALA 5.3 2.5 + - - +
146B ASN* 1.3 78.4 - - - +
148B VAL* 1.3 66.3 + - - +
149B ASP* 3.4 6.2 + - - +
231B ASP* 4.7 2.1 - - - +
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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