Contacts of the helix formed by residues 138 - 149 (chain A) in PDB entry 2QJ3
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 ASP 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A GLY* 1.3 69.1 - - - +
139A GLU* 1.3 70.2 + - - +
140A THR* 3.6 16.6 + - - +
141A GLU* 2.9 46.8 + - - +
142A VAL* 2.9 26.2 + - - +
180A ALA 4.9 2.4 + - - -
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Residues in contact with GLU 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 GLY 3.5 5.1 + - - -
138A ASP* 1.3 74.5 + - - +
140A THR* 1.3 62.6 + - - +
142A VAL* 3.3 6.9 + - - +
143A LEU* 3.0 37.9 + - + +
156A ARG* 2.5 34.8 + - - +
159A ALA* 6.0 3.0 - - - -
160A GLY 6.1 4.7 - - - +
162A ILE* 5.3 11.1 - - + +
251A ASP* 5.6 0.2 - - - +
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Residues in contact with THR 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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138A ASP* 3.3 14.8 + - - +
139A GLU* 1.3 77.1 + - - +
141A GLU* 1.3 64.3 + - + +
143A LEU* 3.3 8.0 + - - +
144A SER* 2.9 36.3 + - - +
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Residues in contact with GLU 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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138A ASP* 2.9 38.3 + - - +
140A THR* 1.3 78.8 - - + +
142A VAL* 1.3 62.7 + - + +
144A SER* 3.6 7.6 + - - -
145A ARG* 3.2 25.2 + - - +
179A PRO* 4.2 12.0 - - + +
180A ALA* 4.3 23.7 + - - +
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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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134A VAL* 3.9 28.3 - - + -
136A GLY* 4.9 2.0 - - - -
137A GLY 4.2 17.7 - - - +
138A ASP 2.9 25.0 + - - +
139A GLU* 3.9 7.0 - - - +
140A THR 3.2 0.2 - - - -
141A GLU* 1.3 74.8 - - + +
143A LEU* 1.3 66.3 + - + +
145A ARG* 3.4 2.1 + - - +
146A LEU* 3.2 35.9 + - + +
162A ILE* 4.4 22.2 - - + -
179A PRO* 4.0 23.8 - - + +
182A ALA* 5.0 1.8 - - + -
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Residues in contact with LEU 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 GLU* 3.0 28.5 + - + +
140A THR* 3.8 6.1 - - - +
142A VAL* 1.3 76.1 - - + +
144A SER* 1.3 62.9 + - - +
145A ARG 3.3 0.3 + - - -
146A LEU* 3.6 5.4 + - + +
147A GLU* 3.3 27.0 + - + +
153A PRO* 3.8 31.9 - - + +
156A ARG* 4.1 37.7 - - - +
162A ILE* 5.1 11.9 - - + -
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Residues in contact with SER 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 THR* 2.9 27.2 + - - +
141A GLU* 3.7 7.9 - - - -
143A LEU* 1.3 76.7 - - - +
145A ARG* 1.3 60.2 + - - +
147A GLU* 3.4 10.5 - - - +
148A GLN* 3.3 32.6 + - - +
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Residues in contact with ARG 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 GLU* 3.2 17.4 + - - +
142A VAL 3.7 5.6 - - - +
143A LEU 3.2 0.6 - - - -
144A SER* 1.3 76.9 - - - +
146A LEU* 1.3 66.9 + - + +
147A GLU 3.2 1.8 - - - -
148A GLN* 3.3 31.2 + - - +
149A LEU* 3.3 42.5 + - + +
174A LEU* 5.1 7.2 - - + -
177A ASP* 2.9 34.4 + - - +
178A PRO 4.2 7.3 + - - -
179A PRO* 4.1 41.1 - - + +
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Residues in contact with LEU 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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134A VAL* 5.0 2.9 - - + -
142A VAL* 3.2 27.0 + - + +
143A LEU* 3.6 5.1 + - + +
145A ARG* 1.3 75.7 - - + +
147A GLU* 1.3 59.1 + - - +
149A LEU 3.5 0.7 + - - +
150A ASP 2.9 8.7 + - - -
151A LEU* 2.7 51.5 + - + +
152A VAL 4.3 0.7 - - - +
153A PRO* 4.1 31.0 - - + -
162A ILE* 4.2 16.8 - - + -
164A ALA* 3.9 20.2 - - + -
174A LEU* 3.7 36.8 - - + -
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Residues in contact with GLU 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 LEU* 3.3 17.1 + - + +
144A SER* 3.4 12.6 - - - +
146A LEU* 1.3 75.1 - - - +
148A GLN* 1.3 66.6 + - - +
150A ASP* 2.9 25.4 + - - +
151A LEU 4.9 1.8 - - - -
181B LYS* 4.6 26.6 + - + +
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Residues in contact with GLN 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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144A SER* 3.3 25.1 + - - +
145A ARG* 3.3 40.5 + - - +
147A GLU* 1.3 80.3 - - + +
149A LEU* 1.3 66.3 + - + +
150A ASP* 3.4 5.4 + - - -
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Residues in contact with LEU 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 ARG* 3.3 33.9 + - + +
146A LEU 3.5 0.4 + - - +
147A GLU 3.2 0.8 - - - -
148A GLN* 1.3 88.3 - - + +
150A ASP* 1.3 67.8 + - - +
151A LEU* 3.5 13.6 - - + +
170A ALA* 3.4 44.7 - - + +
173A LYS* 3.8 14.8 - - + +
174A LEU* 3.4 35.2 - - + +
177A ASP 5.7 1.6 - - - +
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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