Contacts of the helix formed by residues 137 - 148 (chain A) in PDB entry 6H2U
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLU* 5.4 0.2 + - - -
110A CSO 4.2 11.2 + - - +
128A PRO* 3.7 35.7 - - + -
129A PHE 4.0 1.2 + - - -
130A GLY* 2.7 30.9 + - - -
131A THR 4.8 0.2 + - - -
132A LYS* 3.7 18.8 - - - +
135A LYS 3.4 1.5 + - - -
136A GLY* 1.3 71.0 - - - -
138A ASP* 1.3 56.5 + - - +
140A ALA* 3.1 8.3 + - - +
141A PHE* 2.9 42.7 + - + -
301A SAM 5.2 3.6 - - - +
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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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125A MET* 4.6 0.9 - - - +
127A PRO* 3.7 24.5 - - + -
128A PRO 3.1 18.6 + - - +
129A PHE* 3.6 25.6 - - + +
136A GLY* 3.5 15.6 - - - -
137A THR* 1.3 73.1 + - - +
139A MET* 1.3 69.7 + - - +
141A PHE* 3.6 2.4 - - - +
142A LEU* 2.9 26.9 + - - +
157A HIS* 2.8 31.2 + - - +
158A LYS 5.0 0.3 + - - -
161A THR* 4.8 7.1 + - - +
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Residues in contact with MET 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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135A LYS* 5.3 8.3 - - + -
136A GLY* 3.0 18.6 + - - +
138A ASP* 1.3 89.7 - - - +
140A ALA* 1.3 60.4 + - - +
142A LEU* 3.6 24.4 - - + +
143A LYS* 3.1 26.9 + - - +
157A HIS* 4.5 2.0 - - - -
164A HIS* 4.0 21.8 - - + +
165A VAL* 4.0 27.1 - - - -
168A LYS* 3.7 36.6 - - + -
172A TRP* 4.1 13.4 - - + -
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Residues in contact with ALA 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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110A CSO 4.0 26.6 - - + +
132A LYS* 6.5 0.7 - - + -
135A LYS* 5.6 6.8 - - + +
136A GLY 3.4 5.2 + - - +
137A THR* 3.1 13.9 + - - +
139A MET* 1.3 75.7 - - - +
141A PHE* 1.3 66.2 + - - +
143A LYS* 3.4 6.7 + - - +
144A THR* 3.2 25.4 + - - -
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Residues in contact with PHE 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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58A LEU* 3.9 23.1 - - + +
59A GLY* 3.8 23.6 - - - -
109A VAL* 3.9 21.5 - - + -
110A CSO 4.2 6.7 - - - -
125A MET* 3.8 13.2 - - - -
127A PRO* 3.7 19.5 - - + -
128A PRO* 3.8 14.6 - - + -
137A THR* 2.9 38.6 + - + +
138A ASP 3.6 7.4 - - - +
140A ALA* 1.3 75.6 - - - +
142A LEU* 1.3 58.2 + - - +
144A THR* 3.3 2.6 + - - -
145A ALA* 2.8 31.2 + - - +
301A SAM 3.7 45.3 - + - -
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Residues in contact with LEU 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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125A MET* 3.6 11.2 - - + +
138A ASP 2.9 18.5 + - - +
139A MET* 3.6 22.7 - - + +
140A ALA 3.2 0.4 - - - -
141A PHE* 1.3 77.4 - - - +
143A LYS* 1.3 63.6 + - - +
145A ALA* 3.2 0.3 + - - +
146A LEU* 2.9 47.3 + - + +
153A VAL* 4.2 11.2 - - + -
157A HIS* 4.3 9.0 - - + +
165A VAL* 4.3 4.7 - - + +
168A LYS* 6.0 0.2 - - + -
172A TRP* 4.0 16.6 - - + -
207A PHE* 3.6 52.9 - - + -
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Residues in contact with LYS 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 MET 3.1 15.6 + - - +
140A ALA* 3.8 6.1 - - - +
141A PHE 3.4 0.2 - - - -
142A LEU* 1.3 76.9 - - - +
144A THR* 1.3 62.2 + - - +
146A LEU* 3.4 5.7 + - - +
147A GLU* 3.1 21.7 + - - +
172A TRP* 4.2 40.9 - - + +
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Residues in contact with THR 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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58A LEU* 4.3 1.1 - - + -
109A VAL* 3.3 41.4 + - + +
110A CSO 4.4 5.2 + - - -
112A LEU* 4.0 2.0 - - + -
140A ALA 3.2 14.9 + - - -
141A PHE 3.5 7.2 - - - -
143A LYS* 1.3 77.1 - - - +
145A ALA* 1.3 61.7 + - - +
147A GLU* 3.1 5.2 + - - +
148A MET* 3.0 42.7 + - - +
303A EDO 3.9 23.7 + - - -
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Residues in contact with ALA 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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58A LEU* 3.9 11.2 - - + +
123A VAL* 3.7 25.4 - - + +
125A MET* 3.9 6.7 - - + -
141A PHE 2.8 20.0 + - - +
142A LEU 3.6 4.3 - - - +
144A THR* 1.3 74.8 - - - +
146A LEU* 1.3 57.3 + - - +
148A MET* 3.1 4.8 + - - +
149A ALA* 2.9 32.7 + - - +
153A VAL* 3.7 21.1 - - + -
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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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118A LYS* 2.9 24.8 + - - -
142A LEU* 2.9 32.2 + - + +
143A LYS* 3.8 5.4 - - - +
145A ALA* 1.3 76.1 - - - +
147A GLU* 1.3 58.9 + - - +
149A ALA 3.5 5.0 - - - +
153A VAL* 3.9 13.5 - - + -
172A TRP* 3.6 35.2 - - + -
174A ILE* 4.0 25.1 - - + -
207A PHE* 3.8 30.5 - - + -
209A PHE* 3.5 19.7 - - + -
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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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117A SER* 2.5 28.8 + - - +
118A LYS* 2.8 35.7 + - - +
143A LYS 3.1 12.4 + - - +
144A THR* 3.1 10.3 + - - +
146A LEU* 1.3 78.1 - - - +
148A MET* 1.3 58.7 + - - +
303A EDO 3.5 32.3 - - - +
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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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56A ALA* 4.0 13.0 - - + -
58A LEU* 4.0 20.4 - - + -
80A PHE* 4.1 4.5 - - + -
112A LEU* 4.0 13.2 - - + -
116A MET* 3.5 40.2 - - + +
118A LYS* 3.2 2.5 - - - -
119A SER* 3.0 24.6 + - - +
120A PHE* 3.1 42.0 + - + -
123A VAL* 4.2 7.9 - - + -
144A THR* 3.0 36.6 + - - +
145A ALA 3.1 4.0 + - - +
147A GLU* 1.3 78.4 - - - +
149A ALA* 1.3 57.7 + - - +
303A EDO 3.9 5.4 - - - -
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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