Contacts of the helix formed by residues 132 - 147 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASP* 3.4 35.2 + - - +
40A PHE* 3.3 30.9 - - + -
45A LEU* 3.5 8.2 - - - +
130A LEU* 4.2 0.2 - - - +
131A ARG* 1.3 79.1 - - + +
133A LEU* 1.3 61.6 + - - +
134A GLU* 3.1 14.9 + - - +
135A ASP* 2.9 32.6 + - - +
136A THR* 2.9 23.7 + - - -
439A FAD 5.8 0.6 + - - +
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Residues in contact with LEU 133 (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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36A ARG* 4.0 1.1 - - - -
37A ASP* 3.5 17.9 + - - +
40A PHE* 4.0 17.8 - - + -
45A LEU* 4.0 13.7 - - + -
48A VAL* 5.3 2.9 - - + -
56A ARG* 3.6 36.3 - - + +
59A ALA* 3.9 30.5 - - + +
60A LEU* 4.1 26.0 - - + -
132A ASN* 1.3 73.8 - - - +
134A GLU* 1.3 66.6 + - - +
136A THR* 3.2 12.4 + - + -
137A ASP* 2.9 30.7 + - - +
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Residues in contact with GLU 134 (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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35A ASP* 3.5 14.8 - - + +
36A ARG* 3.0 64.5 + - + +
37A ASP* 4.1 3.9 + - - +
78A TYR* 4.2 11.6 + - - -
96A ARG* 5.5 0.5 + - - -
132A ASN* 3.1 15.3 + - - +
133A LEU* 1.3 76.9 - - - +
135A ASP* 1.3 59.7 + - - +
137A ASP* 3.3 4.7 + - - +
138A ALA* 3.0 27.9 + - - +
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Residues in contact with ASP 135 (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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128A PHE* 5.2 0.8 - - - -
129A THR* 3.4 27.1 + - - +
130A LEU* 4.2 3.1 - - - -
131A ARG* 2.8 32.8 + - - +
132A ASN* 2.9 28.9 + - - +
133A LEU 3.2 0.2 - - - -
134A GLU* 1.3 78.3 - - - +
136A THR* 1.3 58.9 + - - +
138A ALA* 3.2 7.4 + - - +
139A ILE* 2.9 35.4 + - - +
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Residues in contact with THR 136 (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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45A LEU* 3.3 18.6 - - + +
48A VAL* 3.5 37.9 - - + -
49A ILE* 4.0 16.7 - - + +
130A LEU* 3.4 15.9 - - - +
132A ASN 2.9 14.5 + - - -
133A LEU* 3.2 15.5 + - + -
135A ASP* 1.3 76.3 - - - +
137A ASP* 1.3 65.6 + - - +
139A ILE* 3.3 6.4 + - - +
140A ASP* 3.0 25.4 + - + +
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Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 2.9 22.4 + - - +
48A VAL* 6.2 0.2 - - - +
56A ARG* 2.8 44.9 + - - -
133A LEU* 2.9 19.7 + - - +
134A GLU* 3.6 5.4 - - - +
136A THR* 1.3 77.6 - - - +
138A ALA* 1.3 57.2 + - - +
140A ASP* 3.5 6.0 + - - +
141A GLN* 2.9 31.8 + - - +
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Residues in contact with ALA 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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128A PHE* 4.1 19.7 - - + -
134A GLU 3.0 14.1 + - - +
135A ASP* 3.2 11.4 + - - +
137A ASP* 1.3 75.8 - - - +
139A ILE* 1.3 56.7 + - - +
141A GLN* 3.4 5.9 + - - +
142A PHE* 2.9 30.8 + - - +
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Residues in contact with ILE 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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49A ILE* 4.0 34.5 - - + -
128A PHE* 3.7 29.2 - - + -
129A THR 4.0 17.5 - - - +
130A LEU* 4.3 11.0 - - + -
135A ASP 2.9 23.5 + - - +
136A THR* 3.3 4.2 + - - +
138A ALA* 1.3 76.2 - - - +
140A ASP* 1.3 63.1 + - - +
142A PHE* 3.2 6.0 + - - +
143A ILE* 3.0 41.9 + - + +
167A LEU* 5.6 0.4 - - + -
232A MET* 4.4 12.3 - - + +
234A ILE* 4.3 13.2 - - + -
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Residues in contact with ASP 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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48A VAL* 5.6 4.0 - - + +
49A ILE* 6.0 3.8 - - - -
51A GLU* 4.4 1.6 - - - +
136A THR* 3.0 19.3 + - + +
137A ASP* 3.8 6.0 - - - +
139A ILE* 1.3 77.7 - - - +
141A GLN* 1.3 64.4 + - - +
143A ILE* 3.3 4.9 + - - +
144A LYS* 2.5 59.2 + - - +
170A ARG* 2.9 32.5 + - - +
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Residues in contact with GLN 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 ASP 2.9 17.5 + - - +
138A ALA* 3.6 7.4 - - - +
140A ASP* 1.3 79.7 + - - +
142A PHE* 1.3 57.1 + - - +
144A LYS* 3.3 11.4 + - - +
145A ALA* 2.8 40.4 + - + +
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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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125A ASP* 3.6 18.4 - - + -
126A ILE* 3.9 20.4 - - + -
128A PHE* 3.4 23.1 - + + -
138A ALA 2.9 18.1 + - - +
139A ILE* 3.6 3.8 - - - +
141A GLN* 1.3 75.0 - - - +
143A ILE* 1.3 66.1 + - - +
145A ALA* 4.5 2.5 - - - -
146A ASN* 3.0 55.0 + - - +
148A VAL* 3.7 11.0 - - + -
231A ASP 3.3 26.5 - - - -
232A MET* 3.7 26.0 - - + -
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Residues in contact with ILE 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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49A ILE* 4.7 1.1 - - + -
139A ILE* 3.0 35.3 + - + +
140A ASP 3.3 6.3 + - - +
142A PHE* 1.3 74.8 - - - +
144A LYS* 1.3 61.2 + - + +
147A GLN* 2.9 25.7 + - - -
148A VAL* 3.1 30.3 + - + +
167A LEU* 4.3 8.5 - - + -
170A ARG* 3.5 40.6 - - - +
172A LEU* 4.0 22.2 - - + -
232A MET* 3.8 25.8 - - + -
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Residues in contact with LYS 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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51A GLU* 4.4 7.0 + - - -
140A ASP* 2.5 52.1 + - - +
141A GLN* 3.8 12.6 - - - +
143A ILE* 1.3 78.9 - - - +
145A ALA* 1.3 63.1 + - - +
146A ASN 3.2 0.5 + - - -
147A GLN* 3.3 17.1 + - - +
170A ARG* 3.6 12.9 - - - +
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Residues in contact with ALA 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 GLN* 2.8 32.2 + - + +
142A PHE* 4.5 1.1 - - - -
144A LYS* 1.3 73.2 - - - +
146A ASN* 1.3 72.9 + - - +
147A GLN* 3.6 1.6 + - - +
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Residues in contact with ASN 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* 3.0 56.5 + - + +
145A ALA* 1.3 87.8 + - - +
147A GLN* 1.3 72.8 + - - +
148A VAL* 3.1 12.6 + - + -
231A ASP* 5.4 5.6 - - + +
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Residues in contact with GLN 147 (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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143A ILE* 2.9 10.0 + - - -
144A LYS* 3.3 10.6 + - - +
145A ALA 5.3 1.8 - - - +
146A ASN* 1.3 80.6 - - - +
148A VAL* 1.3 66.4 + - - +
149A ASP* 3.4 6.1 + - - +
231A ASP* 4.5 2.4 - - - +
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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