Contacts of the helix formed by residues 138 - 149 (chain A) in PDB entry 3D8U
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 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ILE* 3.8 18.1 - - - +
113A GLU* 6.1 0.4 - - - -
116A GLU* 2.9 38.9 + - - +
137A HIS* 1.3 73.8 - - - +
139A GLN* 1.3 64.0 + - - +
140A ARG* 3.6 14.2 + - - +
141A THR* 3.5 5.7 - - - -
142A HIS* 2.9 21.4 + - - -
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Residues in contact with GLN 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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137A HIS 3.6 2.2 + - - -
138A SER* 1.3 72.3 - - - +
140A ARG* 1.3 52.6 + - - +
141A THR 2.8 12.4 + - - -
142A HIS* 3.3 16.4 + - + +
143A GLN* 3.3 25.5 + - - +
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Residues in contact with ARG 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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116A GLU* 4.6 4.1 - - + +
138A SER* 3.1 11.7 + - - +
139A GLN* 1.3 75.3 - - - +
141A THR* 1.3 59.7 + - - +
144A LEU* 5.4 1.1 - - - +
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Residues in contact with THR 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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116A GLU* 3.1 42.2 - - - -
119A LEU* 4.4 15.2 - - - +
137A HIS* 5.9 1.1 - - - -
138A SER* 3.5 4.0 - - - -
139A GLN 2.8 4.0 + - - -
140A ARG* 1.3 74.9 - - - +
142A HIS* 1.3 69.1 + - - +
143A GLN 3.3 2.6 - - - +
144A LEU* 3.2 22.1 + - - +
145A LEU* 3.3 13.2 + - - +
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Residues in contact with HIS 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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135A SER 4.9 1.1 - - - -
137A HIS* 3.1 50.3 - + + +
138A SER 2.9 14.9 + - - -
139A GLN* 3.4 10.7 - - + +
141A THR* 1.3 79.9 - - - +
143A GLN* 1.3 75.3 + - - +
144A LEU 3.2 1.2 + - - -
145A LEU* 3.3 4.6 + - - +
146A GLU* 2.7 35.7 + - + +
160A SER* 3.7 19.7 + - - -
161A LYS* 5.5 3.1 - - + -
164A TYR* 3.4 25.6 - + - -
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Residues in contact with GLN 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 GLN* 3.3 24.2 + - - +
141A THR 3.3 0.6 - - - -
142A HIS* 1.3 93.1 - - - +
144A LEU* 1.3 53.4 + - - +
146A GLU* 4.2 18.7 - - + +
147A ALA* 2.5 30.9 - - - +
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Residues in contact with LEU 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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119A LEU* 4.6 4.9 - - + -
120A SER* 6.5 0.4 - - - -
123A LEU* 4.1 17.0 - - + +
140A ARG 5.4 0.9 - - - +
141A THR* 3.2 20.4 + - - +
142A HIS 3.1 0.4 - - - -
143A GLN* 1.3 77.3 - - - +
145A LEU* 1.3 57.0 + - - +
147A ALA* 3.3 2.4 - - - +
148A SER* 2.7 39.6 + - - -
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Residues in contact with LEU 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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119A LEU* 5.3 11.7 - - + -
123A LEU* 4.5 5.6 - - + +
130A VAL* 5.3 4.0 - - + -
141A THR 3.3 6.8 + - - +
142A HIS* 3.3 7.5 + - - +
144A LEU* 1.3 74.9 - - - +
146A GLU* 1.3 53.6 + - - +
147A ALA 2.8 14.2 + - - -
148A SER* 4.0 5.6 - - - -
149A ASN* 3.0 23.6 + - - -
150A THR* 3.8 12.3 + - - +
152A VAL* 4.2 25.1 - - + -
164A TYR* 5.3 5.2 - - + -
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Residues in contact with GLU 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 HIS* 2.7 21.6 + - + +
143A GLN* 4.0 21.4 - - + +
145A LEU* 1.3 68.6 - - - +
147A ALA* 1.3 58.2 + - - +
149A ASN* 4.5 5.8 - - - +
161A LYS* 5.7 5.4 - - + -
163A SER* 5.9 2.7 - - - +
164A TYR* 5.2 14.0 - - + -
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Residues in contact with ALA 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 GLN 2.5 27.1 - - - +
144A LEU* 3.3 5.4 - - - +
145A LEU 2.8 3.0 + - - -
146A GLU* 1.3 78.2 - - - +
148A SER* 1.3 55.7 + - - +
149A ASN* 2.6 21.9 + - - +
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Residues in contact with SER 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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123A LEU* 3.8 21.3 - - - +
127A PRO* 6.3 0.4 - - - -
144A LEU 2.7 24.7 + - - -
145A LEU* 3.9 4.0 + - - -
147A ALA* 1.3 70.6 - - - +
149A ASN* 1.3 65.9 + - - +
150A THR* 3.0 21.5 + - - +
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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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145A LEU 3.0 11.9 + - - -
146A GLU* 5.0 3.6 - - - +
147A ALA 2.6 16.9 + - - +
148A SER* 1.3 73.9 - - - +
150A THR* 1.3 61.8 + - - +
151A PRO* 4.2 3.6 - - - +
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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