Contacts of the helix formed by residues 134 - 149 (chain B) in PDB entry 3HMX
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ALA 5.6 2.0 - - - +
29B MET* 3.6 20.7 - - + -
32B LYS* 3.4 26.1 + - + +
132B PHE 3.3 6.5 + - - +
133B LEU* 1.3 84.9 - - - +
135B GLN* 1.3 70.2 + - - +
136B ASN* 3.1 22.6 + - - +
137B MET* 3.0 16.6 + - + +
138B LEU 3.5 0.7 + - - -
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU 3.0 8.1 + - - +
134B ASP* 1.3 75.4 + - - +
136B ASN* 1.3 70.3 + - - +
138B LEU* 2.9 30.2 + - + +
139B ALA* 2.9 23.5 + - - +
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Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA* 5.0 6.2 - - + +
134B ASP* 3.1 21.0 + - - +
135B GLN* 1.3 87.6 - - - +
137B MET* 1.3 56.8 + - - +
139B ALA* 3.3 6.8 + - - +
140B VAL* 3.1 38.7 + - - +
143B GLU* 5.4 2.2 + - - -
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Residues in contact with MET 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA* 4.1 18.8 - - + +
26B VAL* 3.8 18.8 - - + +
29B MET* 4.0 26.5 - - + -
116B PHE* 3.5 42.8 - - + -
133B LEU* 4.1 13.0 - - + -
134B ASP* 3.0 18.2 + - + +
136B ASN* 1.3 76.3 - - - +
138B LEU* 1.3 61.0 + - + +
139B ALA 3.2 0.4 - - - -
140B VAL* 3.3 12.3 - - + +
141B ILE* 3.0 31.5 - - + +
177B LEU* 4.0 7.6 - - + -
180B PHE* 3.6 23.8 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLN* 5.4 2.3 - - - +
116B PHE* 3.6 37.7 - - + +
117B LYS* 4.5 6.5 - - + +
120B ASN* 3.5 33.4 - - + +
133B LEU* 3.7 20.2 - - + +
134B ASP 3.5 1.3 + - - +
135B GLN* 2.9 22.3 + - + +
137B MET* 1.3 79.4 - - - +
139B ALA* 1.3 61.4 + - - +
141B ILE* 3.6 16.7 + - + +
142B ASP* 3.6 10.4 + - - +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLN* 2.9 26.5 + - - +
136B ASN* 3.6 13.0 - - - +
138B LEU* 1.3 74.0 - - - +
140B VAL* 1.3 51.1 + - - +
141B ILE 3.1 4.7 - - - -
142B ASP* 2.9 10.4 + - - +
143B GLU* 2.8 51.0 + - + +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS* 5.0 3.8 - - - +
21B ASN* 4.3 22.9 - - + +
22B LEU* 3.7 33.3 - - + +
25B ALA* 3.8 12.3 - - + -
136B ASN* 3.1 25.9 + - - +
137B MET* 3.3 22.9 - - - +
139B ALA* 1.3 74.6 - - - +
141B ILE* 1.3 60.1 + - - +
142B ASP 3.3 0.2 - - - -
143B GLU* 3.9 23.2 - - + +
144B LEU* 3.3 21.8 + - - +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.9 15.7 - - + -
109B LEU* 3.6 39.0 - - + +
112B TYR 5.1 2.0 - - - +
113B GLN* 4.6 13.9 - - + +
116B PHE* 4.1 14.6 - - + -
137B MET* 3.0 31.2 - - + +
138B LEU* 3.7 13.5 - - + +
139B ALA 3.1 0.4 - - - -
140B VAL* 1.3 77.5 - - - +
142B ASP* 1.3 59.7 + - - +
144B LEU* 3.8 4.5 + - - +
145B MET* 3.0 33.2 + - - +
180B PHE* 3.7 25.4 - - + -
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLN* 3.5 19.7 - - - +
138B LEU 3.6 7.1 + - - +
139B ALA* 2.9 11.2 + - - +
141B ILE* 1.3 76.9 - - - +
143B GLU* 1.3 55.1 + - + +
144B LEU 2.8 14.5 + - - -
145B MET* 2.9 17.3 + - - +
146B GLN* 3.0 37.8 + - - +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS* 3.6 34.4 + - + +
21B ASN* 5.1 4.9 + - - -
136B ASN* 5.4 2.1 + - - -
139B ALA* 2.8 38.6 + - + +
140B VAL* 4.1 19.6 - - - +
142B ASP* 1.3 71.6 - - + +
144B LEU* 1.3 55.8 + - - +
146B GLN* 3.7 20.7 + - - +
147B ALA* 3.6 17.7 + - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B CYS* 4.7 5.8 - - - +
18B HIS* 3.7 25.4 - - + +
19B SER* 4.3 8.1 - - - +
22B LEU* 3.5 31.6 - - + -
109B LEU* 3.8 16.4 - - + -
140B VAL 3.3 15.9 + - - +
141B ILE 3.9 5.2 - - - +
142B ASP 2.8 1.0 - - - -
143B GLU* 1.3 80.2 - - - +
145B MET* 1.3 59.6 + - + +
146B GLN 3.3 0.4 - - - -
147B ALA* 3.3 4.7 + - + +
148B LEU* 3.0 53.8 + - + +
187B ILE* 4.1 17.7 - - + -
191B MET* 5.1 7.4 - - + -
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B TYR* 3.2 45.7 + - + +
109B LEU* 3.7 29.6 - - + +
110B LYS* 3.8 33.2 - - + +
113B GLN* 3.7 24.7 - - - +
141B ILE* 3.0 21.1 - - - +
142B ASP* 2.9 7.5 + - - +
144B LEU* 1.3 73.8 - - - +
146B GLN* 1.3 57.2 + - - +
147B ALA 3.2 4.9 - - - -
148B LEU* 3.8 1.3 - - - +
149B ASN* 3.0 31.4 + - - +
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP* 3.0 37.4 + - - +
143B GLU* 3.7 26.1 + - - +
145B MET* 1.3 75.8 - - - +
147B ALA* 1.3 60.0 + - - +
149B ASN* 3.9 18.8 + - - +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO* 6.1 0.7 - - + -
15B CYS* 4.8 11.0 - - - -
18B HIS* 3.8 20.4 - - + +
86B GLY 4.4 0.3 - - - +
87B SER* 3.1 36.6 + - - +
88B CYS* 4.2 4.1 - - - -
143B GLU 3.6 14.6 - - - +
144B LEU* 3.3 10.9 + - + +
145B MET 3.2 0.6 - - - -
146B GLN* 1.3 79.6 - - - +
148B LEU* 1.3 60.4 + - - +
149B ASN* 3.2 2.4 + - - -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B CYS* 3.7 26.7 - - - -
84B THR* 4.8 2.6 + - - -
87B SER* 4.0 15.1 - - - +
102B LEU* 5.2 6.5 - - + +
105B ILE* 4.5 14.8 - - + -
106B TYR* 4.1 28.9 - - + -
109B LEU* 5.3 2.7 - - + -
144B LEU* 3.0 36.5 + - + +
145B MET* 3.6 4.7 + - - +
147B ALA* 1.3 76.7 - - - +
149B ASN* 1.3 66.9 + - - +
150B PHE* 3.0 37.5 + - + -
191B MET* 3.9 18.2 - - + -
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Residues in contact with ASN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B THR* 3.9 22.0 - - + +
85B ASN 5.0 0.6 + - - -
86B GLY 2.6 26.7 + - - +
87B SER* 5.1 0.2 - - - -
106B TYR* 3.3 8.8 + - - -
145B MET 3.0 20.3 + - - +
146B GLN* 3.9 17.6 + - - +
147B ALA 3.2 4.8 + - - +
148B LEU* 1.3 74.7 - - - +
150B PHE* 1.3 80.5 + - - +
151B ASN* 5.3 3.0 - - - +
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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