Contacts of the helix formed by residues 109 - 120 (chain B) in PDB entry 1HE1
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 ALA 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B VAL 3.1 6.6 + - - +
106B LEU 3.6 10.8 - - - +
107B GLN 3.1 0.8 - - - -
108B GLN* 1.3 77.2 - - - +
110B LEU* 1.3 64.1 + - - +
111B PRO 3.4 0.9 - - - -
112B MET* 2.9 20.5 + - - +
113B THR* 3.2 15.0 + - + +
154B GLY* 5.9 1.8 - - - -
36D VAL* 3.8 28.9 - - + -
64D TYR* 4.7 6.3 - - + -
67D LEU* 3.8 20.1 - - + +
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Residues in contact with LEU 110 (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 LEU 3.9 2.8 + - - -
107B GLN 3.3 13.1 + - - +
108B GLN 3.3 0.6 - - - -
109B ALA* 1.3 74.9 - - - +
111B PRO* 1.3 70.0 - - + +
113B THR* 2.5 32.1 + - - +
114B LEU* 3.6 5.7 + - - +
154B GLY 4.6 2.2 - - - +
155B ILE* 4.1 16.4 - - + +
158B GLY* 4.2 5.6 - - - +
159B SER* 4.0 26.5 - - - +
224B VAL* 3.7 19.1 - - + -
227B GLU* 3.3 43.3 - - + +
228B VAL* 4.1 11.4 - - + -
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Residues in contact with PRO 111 (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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107B GLN 4.4 1.8 - - - +
108B GLN* 3.4 17.7 - - - +
110B LEU* 1.3 93.2 - - + +
112B MET* 1.3 62.0 + - + +
114B LEU* 3.3 24.3 + - + +
115B LYS* 3.7 12.8 + - - +
228B VAL* 4.0 31.1 - - + -
66D ARG* 4.5 20.1 + - - +
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Residues in contact with MET 112 (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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108B GLN* 3.5 28.0 - - + +
109B ALA* 2.9 10.8 + - - +
111B PRO* 1.3 75.4 - - + +
113B THR* 1.3 65.8 + - - +
114B LEU 3.1 1.8 - - - -
115B LYS* 3.1 17.4 + - - +
116B GLY* 3.1 9.2 + - - -
63D ASP* 3.4 24.5 - - - +
64D TYR* 3.6 21.0 - - + -
66D ARG* 3.2 46.2 - - + +
67D LEU* 3.6 49.1 - - + +
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Residues in contact with THR 113 (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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109B ALA* 3.2 16.5 + - + +
110B LEU* 2.5 22.8 + - - +
112B MET* 1.3 77.1 - - - +
114B LEU* 1.3 57.7 + - - +
116B GLY* 3.1 1.6 + - - -
117B LEU* 2.8 33.0 + - - +
151B ALA* 3.5 28.6 - - - +
154B GLY* 3.9 19.7 - - - -
155B ILE* 3.4 21.1 - - + +
224B VAL* 4.5 2.9 - - - +
64D TYR* 3.7 21.8 - - + +
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Residues in contact with LEU 114 (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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110B LEU 4.0 6.7 - - - +
111B PRO* 3.4 15.9 - - + +
112B MET 3.1 0.4 - - - -
113B THR* 1.3 80.1 + - - +
115B LYS* 1.3 68.8 + - - +
117B LEU* 3.2 12.7 + - + +
118B ASP 3.1 16.6 + - - -
221B ARG* 3.3 51.3 + - + +
224B VAL* 3.6 28.5 - - + -
225B GLU* 4.1 24.5 - - + -
228B VAL* 4.2 20.0 - - + -
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Residues in contact with LYS 115 (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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111B PRO 4.0 13.7 - - - +
112B MET* 3.1 11.6 + - - +
114B LEU* 1.3 84.7 - - - +
116B GLY* 1.3 62.8 + - - +
118B ASP* 3.1 24.0 + - - +
119B LYS* 3.1 16.1 + - - +
221B ARG* 4.4 13.7 - - - +
63D ASP* 3.6 22.4 - - + +
66D ARG* 4.9 10.5 - - - +
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Residues in contact with GLY 116 (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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112B MET 3.1 9.8 + - - -
113B THR 3.1 7.4 + - - -
115B LYS* 1.3 75.4 - - - +
117B LEU* 1.3 64.1 + - - +
119B LYS* 3.0 17.9 + - - +
120B ALA* 3.3 8.8 + - - +
147B SER* 3.6 14.5 - - - +
151B ALA* 4.1 13.2 - - - -
63D ASP* 4.2 13.6 + - - -
64D TYR* 4.6 5.4 - - - -
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Residues in contact with LEU 117 (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 THR 2.8 16.8 + - - +
114B LEU* 3.2 13.2 + - + +
116B GLY* 1.3 75.2 - - - +
118B ASP* 1.3 63.3 + - - +
120B ALA* 3.0 18.5 + - - +
121B SER* 3.6 4.7 + - - -
148B LEU* 3.9 17.5 - - + -
151B ALA* 3.7 19.1 - - + -
152B LEU* 4.5 8.7 - - + -
155B ILE* 4.0 21.5 - - + -
214B MET* 4.8 4.7 - - - +
217B VAL* 3.9 27.5 - - + +
220B LEU* 5.3 1.8 - - + -
221B ARG* 4.0 40.8 - - + +
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Residues in contact with ASP 118 (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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114B LEU 3.1 5.2 + - - +
115B LYS* 3.1 23.9 + - - +
117B LEU* 1.3 78.3 - - - +
119B LYS* 1.3 57.5 + - + +
120B ALA 3.0 0.6 + - - -
121B SER* 3.0 28.8 + - - +
221B ARG* 2.6 47.1 + - - -
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Residues in contact with LYS 119 (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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115B LYS 3.1 16.0 + - - +
116B GLY* 3.0 11.5 + - - +
118B ASP* 1.3 75.4 - - - +
120B ALA* 1.3 56.9 + - - +
121B SER* 3.4 1.0 + - - -
122B GLU* 4.6 3.5 + - - +
142B ASP* 2.8 33.9 + - - +
144B ALA* 3.5 19.3 + - - +
147B SER* 3.4 16.6 - - - +
62D GLU* 2.9 23.8 + - - +
63D ASP* 3.0 38.7 + - - +
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Residues in contact with ALA 120 (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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116B GLY 3.3 7.5 + - - +
117B LEU* 3.0 14.1 + - - +
119B LYS* 1.3 78.9 - - - +
121B SER* 1.3 62.4 + - - +
122B GLU 3.1 3.8 - - - -
123B LEU* 3.1 18.7 + - + +
144B ALA* 3.7 24.7 - - - +
148B LEU* 3.8 22.2 - - + -
214B MET* 3.3 20.7 - - + +
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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