Contacts of the helix formed by residues 140 - 151 (chain A) in PDB entry 4PK7
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 GLN 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A HIS 4.1 3.6 + - - -
139A MET* 1.3 78.3 + - - +
141A ASN* 1.3 67.3 + - - +
142A SER* 3.8 17.0 - - - +
143A GLU* 3.1 21.4 + - - +
144A ILE* 3.0 20.6 + - - +
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Residues in contact with ASN 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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118A ILE* 5.9 1.2 - - - +
139A MET 5.3 0.2 - - - +
140A GLN* 1.3 74.5 + - - +
142A SER* 1.3 55.3 + - - +
144A ILE* 2.9 17.4 + - - +
145A ILE* 2.6 50.5 + - + +
199A THR 5.1 0.6 + - - -
202A SER* 3.4 45.2 + - - +
203A LEU* 3.5 20.0 - - + +
206A GLY* 5.6 2.0 - - - -
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 3.8 9.9 - - - +
141A ASN* 1.3 77.9 - - - +
143A GLU* 1.3 69.9 + - - +
145A ILE* 3.9 10.1 - - - +
146A ARG* 3.1 48.8 + - - +
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Residues in contact with GLU 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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138A HIS 5.0 0.7 - - - +
139A MET* 3.3 32.9 - - + +
140A GLN* 3.1 34.7 + - + +
141A ASN 3.0 0.6 - - - -
142A SER* 1.3 83.6 - - - +
144A ILE* 1.3 65.9 + - - +
146A ARG* 3.5 17.8 + - - +
147A LYS* 3.1 18.5 + - - +
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Residues in contact with ILE 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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118A ILE* 5.5 6.7 - - + -
122A ILE* 5.6 2.9 - - + -
131A VAL* 3.8 26.5 - - + -
135A MET* 3.7 37.2 - - + +
136A PHE* 4.6 7.0 - - + +
139A MET* 3.7 24.2 - - + +
140A GLN 3.0 17.7 + - - +
141A ASN* 2.9 21.2 + - - +
143A GLU* 1.3 73.9 - - - +
145A ILE* 1.3 68.3 + - + +
147A LYS* 3.2 2.3 + - - +
148A MET* 2.9 37.8 + - + +
203A LEU* 5.5 6.1 - - + -
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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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122A ILE* 5.9 1.6 - - + -
141A ASN* 2.6 35.3 + - + +
142A SER* 3.9 8.5 - - - +
144A ILE* 1.3 75.7 - - + +
146A ARG* 1.3 55.5 + - - +
148A MET* 3.3 6.4 + - - +
149A THR* 2.9 34.1 + - - +
203A LEU* 4.7 8.5 - - + +
206A GLY* 3.5 37.0 - - - +
207A LEU* 3.5 19.7 - - + +
210A SER* 4.3 14.4 - - - +
215A PHE* 4.1 23.4 - - + -
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Residues in contact with ARG 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 SER* 3.1 39.4 + - - +
143A GLU* 3.7 14.6 - - - +
144A ILE 3.2 0.2 - - - -
145A ILE* 1.3 77.1 - - + +
147A LYS* 1.3 56.6 + - - +
149A THR* 3.2 10.3 + - - -
150A GLU* 3.0 25.3 + - - +
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Residues in contact with LYS 147 (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 MET* 4.1 26.2 - - + -
139A MET* 4.6 7.4 - - + -
143A GLU 3.1 15.2 + - - +
144A ILE 3.6 4.3 - - - +
146A ARG* 1.3 79.5 - - - +
148A MET* 1.3 62.0 + - - +
150A GLU* 3.3 25.9 + - - +
151A GLU* 2.9 67.9 + - + +
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Residues in contact with MET 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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122A ILE* 3.3 30.7 - - + -
127A CYS* 3.3 21.1 - - - -
129A GLY* 3.2 35.7 - - - +
130A VAL* 3.5 28.3 - - - +
131A VAL* 4.2 9.2 - - + -
135A MET* 4.7 6.5 - - + -
144A ILE* 2.9 35.6 + - + +
145A ILE* 3.8 6.1 - - - +
147A LYS* 1.3 80.3 - - - +
149A THR* 1.3 62.5 + - - +
151A GLU* 4.0 3.8 - - - +
152A PHE* 3.4 12.0 + - - +
215A PHE* 4.2 14.8 - - + -
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Residues in contact with THR 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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145A ILE* 2.9 19.4 + - - +
146A ARG* 3.2 11.0 + - - -
148A MET* 1.3 76.1 - - - +
150A GLU* 1.3 64.9 + - - +
152A PHE* 3.3 19.6 - - + +
154A GLU* 5.3 0.3 - - - +
212A VAL* 3.7 33.8 - - + +
215A PHE* 3.9 7.4 - - - -
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Residues in contact with GLU 150 (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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146A ARG 3.0 13.3 + - - +
147A LYS* 3.3 36.3 + - - +
149A THR* 1.3 79.7 - - - +
151A GLU* 1.3 63.0 + - + +
152A PHE 3.2 3.0 + - - -
153A ASP 4.7 2.4 + - - -
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Residues in contact with GLU 151 (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 LYS 3.9 2.3 - - - +
129A GLY* 3.5 26.6 + - - -
130A VAL 5.6 0.2 - - - +
147A LYS* 2.9 54.8 + - + +
148A MET* 3.9 6.0 + - - -
149A THR 3.3 0.2 - - - -
150A GLU* 1.3 83.6 - - + +
152A PHE* 1.3 63.1 + - - +
153A ASP* 3.4 9.7 + - - +
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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