Contacts of the helix formed by residues 136 - 144 (chain A) in PDB entry 6Q6Q
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 THR 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLU 5.4 1.3 - - - +
135A PRO* 1.3 81.1 - - - +
137A LEU* 1.3 65.3 + - - +
138A ASP* 3.9 13.9 + - - +
139A GLN* 2.9 40.5 + - - +
140A LEU* 3.4 7.3 + - - +
165A CYS* 3.5 6.6 - - - -
166A LYS* 6.3 4.5 - - + -
167A THR* 6.4 0.4 - - - -
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Residues in contact with LEU 137 (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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136A THR* 1.3 72.8 - - - +
138A ASP* 1.3 75.4 + - - +
140A LEU* 3.2 7.2 + - + +
141A THR* 3.0 39.8 + - + +
158A ILE* 3.9 16.2 - - + +
161A CYS* 5.7 2.7 - - + -
162A LYS* 3.6 44.6 - - + +
165A CYS* 3.2 19.7 - - + -
167A THR* 5.6 7.2 - - + +
560A HIS* 4.6 22.2 - - - +
561A HIS* 4.9 7.2 - - + +
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Residues in contact with ASP 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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136A THR* 3.1 13.7 + - - +
137A LEU* 1.3 91.5 + - - +
139A GLN* 1.3 59.5 + - + +
141A THR* 3.0 18.3 + - - -
142A ASP* 3.0 27.0 - - - +
560A HIS* 5.0 13.8 + - - -
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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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128A LEU* 3.4 29.0 - - + +
132A HIS* 3.8 36.1 + - - +
134A GLU 4.7 0.7 - - - +
135A PRO* 3.4 12.2 - - - +
136A THR* 2.9 41.5 + - - +
138A ASP* 1.3 77.0 - - + +
140A LEU* 1.3 62.1 + - - +
142A ASP* 3.5 7.7 + - - +
143A ALA 3.2 16.3 + - - -
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Residues in contact with LEU 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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125A ILE* 3.8 36.1 - - + +
128A LEU* 3.6 22.2 - - + -
129A LEU* 5.0 5.6 - - + -
135A PRO* 4.3 11.9 - - + -
136A THR 3.4 3.9 + - - +
137A LEU* 3.2 8.3 + - - +
139A GLN* 1.3 75.8 - - - +
141A THR* 1.3 65.6 + - + +
143A ALA* 3.2 5.0 + - + +
144A LEU* 3.1 29.0 + - - +
161A CYS* 3.2 50.5 - - + +
164A PHE* 4.6 5.4 - - + -
165A CYS* 4.0 17.5 - - - -
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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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137A LEU* 3.0 32.0 + - + +
138A ASP* 3.0 15.8 + - - -
140A LEU* 1.3 76.4 - - + +
142A ASP* 1.3 63.7 + - - +
144A LEU* 3.4 8.3 + - - +
145A GLY* 3.2 19.4 + - - -
158A ILE* 3.8 28.0 - - + -
161A CYS* 6.3 0.7 - - + -
435A GLU* 4.9 3.3 - - - +
561A HIS* 4.1 22.0 - - + +
1241A ILE* 4.6 13.1 - - + +
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Residues in contact with ASP 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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138A ASP* 3.0 23.6 + - - +
139A GLN* 3.9 7.3 - - - +
140A LEU 3.2 0.8 - - - -
141A THR* 1.3 78.4 + - - +
143A ALA* 1.3 64.6 + - - +
145A GLY* 3.4 11.3 + - - +
347A SER* 3.9 11.4 + - - -
350A ARG* 3.9 15.8 + - - +
435A GLU* 5.2 8.4 - - - +
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Residues in contact with ALA 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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70A PRO* 6.5 0.7 - - + -
124A SER* 4.1 22.8 - - - +
128A LEU* 4.0 20.8 - - + +
139A GLN 3.2 14.1 + - - +
140A LEU* 3.2 9.8 + - + +
142A ASP* 1.3 77.8 - - - +
144A LEU* 1.3 59.7 + - + +
145A GLY 3.1 3.7 + - - -
146A GLY 4.0 0.3 + - - -
147A ASN* 4.0 1.9 + - - -
347A SER* 3.9 17.3 - - - +
348A GLN* 3.5 22.3 + - - -
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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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121A MET* 4.0 18.3 - - - +
124A SER* 4.2 4.5 - - - -
125A ILE* 3.8 25.4 - - + -
140A LEU 3.1 16.2 + - - +
141A THR 3.6 2.5 - - - +
142A ASP 3.3 0.2 - - - -
143A ALA* 1.3 73.4 - - + +
145A GLY* 1.3 62.6 + - - +
146A GLY 3.2 3.1 - - - -
147A ASN* 3.2 42.7 + - + +
157A ILE* 3.8 15.9 - - + -
158A ILE* 4.3 7.0 - - + -
161A CYS* 3.7 27.8 - - - -
1241A ILE* 3.6 33.0 + - + +
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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