Contacts of the helix formed by residues 135 - 149 (chain A) in PDB entry 1Y8Q
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 SER 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 5.3 0.2 + - - -
133A CYS 4.3 0.4 + - - -
134A CYS* 1.3 76.6 - - - +
136A ARG* 1.3 64.5 + - - +
137A ASP* 3.7 7.7 + - - +
138A VAL* 3.2 28.1 + - - +
139A ILE* 3.0 21.4 + - - +
247A LEU* 5.0 0.2 - - - -
250A ARG* 3.8 23.0 - - - +
251A THR* 4.8 8.7 - - - -
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 1.3 74.2 - - - +
137A ASP* 1.3 77.2 + - - +
139A ILE* 3.2 11.3 + - - +
140A VAL* 2.9 63.3 + - - +
217A LYS* 4.9 9.9 - - - +
220A LEU* 4.1 27.2 - - + +
221A GLU* 4.0 30.1 + - - +
244A GLN* 5.9 3.4 - - - +
247A LEU* 4.5 25.9 + - + +
251A THR* 4.4 15.4 + - - +
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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
----------------------------------------------------------
116A GLU* 5.8 3.8 - - - +
135A SER* 3.3 7.5 + - - +
136A ARG* 1.3 99.5 + - - +
138A VAL* 1.3 60.2 + - + +
140A VAL* 3.6 5.8 + - - +
141A LYS* 2.9 29.7 + - - +
251A THR* 5.4 9.1 + - - +
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 3.8 26.7 - - + -
116A GLU* 3.7 38.1 - - + +
131A LEU* 4.2 1.1 - - + -
134A CYS* 3.9 19.1 - - + -
135A SER* 3.2 24.0 + - - +
137A ASP* 1.3 76.3 - - + +
139A ILE* 1.3 61.0 + - - +
141A LYS* 3.6 7.1 - - + +
142A VAL* 2.9 42.5 + - + +
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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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131A LEU* 3.9 9.4 - - + -
134A CYS* 3.6 30.7 - - + +
135A SER 3.0 15.2 + - - +
136A ARG* 3.5 8.1 - - + +
138A VAL* 1.3 77.0 - - - +
140A VAL* 1.3 64.9 + - - +
143A ASP* 3.0 23.2 + - - +
153A PHE* 3.6 17.5 - - + -
155A THR* 3.8 26.2 - - + +
157A ASP* 4.9 3.4 - - - +
164A TYR* 4.1 11.9 - - - +
216A VAL* 4.0 23.6 - - + -
220A LEU* 4.7 6.5 - - + -
247A LEU* 4.3 16.8 - - + -
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 2.9 57.5 + - + +
137A ASP* 3.9 4.9 - - - +
139A ILE* 1.3 74.3 - - - +
141A LYS* 1.3 58.1 + - - +
143A ASP* 3.2 2.1 + - - +
144A GLN* 2.9 50.8 + - + +
216A VAL* 3.7 18.4 - - + -
217A LYS* 4.0 24.9 - - + +
220A LEU* 4.5 5.4 - - + -
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Residues in contact with LYS 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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115A ILE 5.4 0.6 + - - -
116A GLU* 3.6 39.2 + - + +
117A LYS 5.7 0.2 - - - -
118A LYS 4.6 10.0 + - - -
137A ASP 2.9 20.3 + - - +
138A VAL* 3.6 7.2 - - + +
140A VAL* 1.3 77.8 - - - +
142A VAL* 1.3 65.7 + - + +
144A GLN* 3.3 12.1 + - - +
145A ILE* 3.0 49.7 + - + +
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Residues in contact with VAL 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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115A ILE* 4.3 7.9 - - + +
123A PHE* 3.8 32.5 - - + -
129A VAL* 3.9 9.0 - - + -
131A LEU* 3.6 31.0 - - + -
138A VAL* 2.9 35.7 + - + +
141A LYS* 1.3 77.7 - - + +
143A ASP* 1.3 57.1 + - - +
145A ILE* 3.7 7.2 - - + +
146A CYS* 2.9 31.0 + - - -
153A PHE* 3.8 14.4 - - + -
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Residues in contact with ASP 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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139A ILE 3.0 18.3 + - - +
140A VAL 3.5 4.7 - - - +
142A VAL* 1.3 77.1 - - - +
144A GLN* 1.3 66.8 + - - +
146A CYS* 3.1 2.6 + - - +
147A HIS* 2.9 22.9 + - - +
153A PHE* 3.2 33.8 - - + +
168A ASN* 2.9 28.4 + - - +
215A PRO* 3.5 6.8 - - - +
216A VAL* 2.8 40.2 + - + +
217A LYS* 4.4 0.3 + - - +
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Residues in contact with GLN 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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140A VAL* 2.9 38.9 + - + +
141A LYS* 3.7 10.7 - - - +
143A ASP* 1.3 80.1 - - + +
145A ILE* 1.3 63.6 + - + +
147A HIS* 3.2 15.4 + - - +
148A LYS* 3.2 31.1 + - - +
215A PRO* 6.2 3.6 - - + -
217A LYS* 4.1 19.7 - - + +
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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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118A LYS 5.1 2.7 - - - +
120A GLU* 3.6 44.4 - - + +
123A PHE* 4.1 40.4 - - + -
141A LYS* 3.0 50.0 + - + +
142A VAL* 3.7 7.6 - - + +
144A GLN* 1.3 78.0 - - + +
146A CYS* 1.3 61.1 + - - +
148A LYS* 3.4 8.3 + - - +
149A ASN* 2.7 33.7 + - - +
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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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123A PHE* 4.8 4.7 - - - -
129A VAL* 3.8 23.6 - - - -
142A VAL* 2.9 32.0 + - - +
143A ASP 3.6 4.0 - - - +
145A ILE* 1.3 75.8 - - - +
147A HIS* 1.3 62.4 + - - +
149A ASN 3.2 1.0 + - - -
150A SER 3.0 4.7 + - - -
151A ILE* 2.7 74.6 + - + +
153A PHE* 4.1 13.7 - - + -
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Residues in contact with HIS 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 ASP* 2.9 13.2 + - - +
144A GLN* 3.2 12.5 + - - +
146A CYS* 1.3 77.6 - - - +
148A LYS* 1.3 65.5 + - + +
149A ASN 3.2 0.7 + - - -
150A SER* 3.3 12.7 + - - +
151A ILE 4.9 1.8 - - - +
168A ASN* 4.8 22.7 - - - +
170A GLY* 4.8 13.7 - - - -
215A PRO* 5.2 15.4 - - + +
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Residues in contact with LYS 148 (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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120A GLU* 4.1 24.3 + - - +
144A GLN* 3.2 25.9 + - - +
145A ILE* 3.7 6.8 - - - +
146A CYS 3.3 0.2 - - - -
147A HIS* 1.3 79.5 - - + +
149A ASN* 1.3 66.2 + - - +
150A SER* 3.8 2.3 + - - -
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Residues in contact with ASN 149 (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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120A GLU* 4.3 13.4 + - - +
124A THR* 3.5 27.1 - - + +
145A ILE* 2.7 36.5 + - - +
146A CYS 3.2 1.4 + - - -
147A HIS 3.1 0.8 - - - -
148A LYS* 1.3 87.7 - - - +
150A SER* 1.3 72.1 + - - +
151A ILE* 3.3 25.4 + - + +
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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