Contacts of the helix formed by residues 138 - 153 (chain B) in PDB entry 1HTI
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 ILE 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B ASP* 5.2 1.3 - - - +
133B GLU* 2.8 33.7 + - + +
136B ALA* 3.4 26.9 - - + +
137B GLY* 1.3 74.3 - - - +
139B THR* 1.3 63.4 - - - +
140B GLU* 3.2 3.6 - - - +
141B LYS* 3.4 22.8 + - + +
142B VAL* 3.0 43.7 + - + +
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Residues in contact with THR 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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129B GLU* 3.8 14.1 - - - +
133B GLU 3.8 1.2 + - - -
134B ARG* 3.4 55.6 + - - +
137B GLY* 3.1 8.4 + - - -
138B ILE* 1.3 74.4 - - - +
140B GLU* 1.3 61.3 + - - +
142B VAL* 3.0 12.8 + - - +
143B VAL* 2.8 39.6 + - + +
164B TYR* 4.7 0.2 - - - +
183B GLU* 5.1 3.8 - - - +
184B VAL* 4.0 18.2 - - + -
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Residues in contact with GLU 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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137B GLY 4.3 4.4 + - - +
138B ILE* 4.9 1.6 - - - -
139B THR* 1.3 80.0 - - - +
141B LYS* 1.3 69.7 + - - +
143B VAL* 3.7 2.8 + - - +
144B PHE* 2.8 56.0 + - + +
183B GLU* 5.0 2.6 - - - +
184B VAL* 5.7 0.9 - - - +
187B LYS* 3.0 49.2 + - - +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ILE* 3.4 24.9 + - + +
140B GLU* 1.3 83.7 - - - +
142B VAL* 1.3 72.1 + - + +
144B PHE* 2.7 17.2 + - - -
145B GLU* 2.8 56.1 + - + +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLY 5.4 0.4 - - - -
129B GLU* 3.5 31.6 - - + -
133B GLU* 3.4 27.8 - - + +
138B ILE* 3.0 27.0 + - + +
139B THR* 3.0 16.2 + - - +
141B LYS* 1.3 85.6 - - + +
143B VAL* 1.3 56.8 + - - +
145B GLU* 4.2 8.1 - - + +
146B GLN* 3.0 36.7 - - + +
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Residues in contact with VAL 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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127B ILE* 4.7 5.5 - - + +
128B GLY* 4.3 15.5 - - - +
129B GLU* 4.4 7.4 - - - +
139B THR* 2.8 24.9 + - + +
140B GLU* 4.3 1.6 - - - +
142B VAL* 1.3 74.2 - - + +
144B PHE* 1.3 68.2 + - + +
146B GLN* 3.3 6.8 + - - +
147B THR* 2.7 30.8 + - - +
164B TYR* 3.8 29.8 - - + -
184B VAL* 5.4 6.1 - - + +
188B LEU* 3.7 35.4 - - + -
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Residues in contact with PHE 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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140B GLU* 2.8 43.9 + - + +
141B LYS* 2.7 10.9 + - - +
143B VAL* 1.3 82.4 - - + +
145B GLU* 1.4 59.4 + - - +
147B THR* 3.3 4.2 + - - -
148B LYS* 2.9 22.7 + - - +
187B LYS* 2.9 42.0 - - + -
188B LEU* 3.9 10.8 - - + -
191B TRP* 3.5 46.1 + + + +
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Residues in contact with GLU 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 ASP* 6.4 0.2 - - - -
141B LYS* 2.8 66.0 + - + +
142B VAL* 4.6 5.0 - - - +
144B PHE* 1.4 66.7 - - - +
146B GLN* 1.3 69.0 + - + +
148B LYS* 2.9 19.2 + - - +
149B VAL* 3.3 16.4 + - + +
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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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99B ARG* 3.7 35.1 + - - +
100B HIS* 5.2 5.5 - - - -
106B ASP* 4.1 13.5 + - - +
127B ILE* 3.0 18.0 - - + +
128B GLY 2.7 42.7 + - - +
133B GLU* 5.8 1.0 + - - -
142B VAL* 3.0 28.6 + - + +
143B VAL* 3.3 3.7 - - - +
145B GLU* 1.3 84.2 - - + +
147B THR* 1.3 62.5 + - - +
149B VAL* 3.3 5.6 + - - +
150B ILE* 3.2 25.1 + - - +
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Residues in contact with THR 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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127B ILE* 3.7 11.8 - - + +
143B VAL 2.7 20.3 + - - -
144B PHE* 3.3 4.7 + - - -
146B GLN* 1.3 70.3 - - - +
148B LYS* 1.4 66.8 + - - +
150B ILE* 4.6 3.1 - - + +
151B ALA* 2.9 27.0 + - + +
157B TRP* 5.5 0.7 - - + -
162B LEU* 4.1 25.4 - - + -
188B LEU* 3.3 30.5 - - + +
191B TRP* 3.9 22.9 - - + -
192B LEU* 4.3 9.0 - - + -
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Residues in contact with LYS 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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144B PHE 2.9 10.0 + - - +
145B GLU* 2.9 17.9 + - - +
147B THR* 1.4 71.4 - - - +
149B VAL* 1.3 57.7 + - + +
151B ALA* 3.2 2.3 - - - +
152B ASP* 2.7 70.4 + - - +
191B TRP* 3.4 28.5 - - + -
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Residues in contact with VAL 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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106B ASP* 3.3 48.0 - - + +
107B GLU* 4.6 2.5 - - - +
110B GLY* 4.6 4.8 - - - +
145B GLU* 3.5 14.4 - - + +
146B GLN* 3.5 9.0 - - - +
148B LYS* 1.3 75.0 - - + +
150B ILE* 1.3 72.6 + - + +
152B ASP* 3.5 13.2 + - - +
153B ASN* 2.9 25.4 + - - +
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Residues in contact with ILE 150 (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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99B ARG* 4.0 13.0 - - - +
106B ASP* 6.5 0.2 - - - -
109B ILE* 4.2 18.8 - - + -
110B GLY* 5.4 2.7 - - - -
113B VAL* 4.3 12.9 - - + +
125B ALA* 3.6 31.9 - - + -
126B CYS 3.9 11.0 - - - +
127B ILE* 3.7 23.6 - - + -
146B GLN 3.2 27.3 + - - +
147B THR* 4.2 4.7 - - - +
149B VAL* 1.3 80.7 - - + +
151B ALA* 1.3 58.6 + - - +
153B ASN* 2.9 19.6 + - - +
154B VAL* 3.2 22.7 + - + +
157B TRP* 5.0 0.9 - - + -
160B VAL* 5.1 2.2 - - + -
162B LEU* 4.4 15.5 - - + -
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Residues in contact with ALA 151 (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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147B THR* 2.9 21.4 + - + +
148B LYS 3.2 3.6 - - - +
150B ILE* 1.3 76.0 - - - +
152B ASP* 1.3 56.5 + - - +
154B VAL* 3.0 26.0 + - - +
157B TRP* 3.6 32.9 + - + -
191B TRP* 3.9 18.8 - - + -
196B VAL* 4.8 5.4 - - + -
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Residues in contact with ASP 152 (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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148B LYS* 2.7 66.0 + - - +
149B VAL* 3.7 14.0 + - - +
150B ILE 3.2 0.2 + - - -
151B ALA* 1.3 71.3 - - - +
153B ASN* 1.3 66.2 + - - +
154B VAL 3.4 3.0 - - - +
155B LYS* 4.7 9.5 - - - -
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Residues in contact with ASN 153 (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 GLY* 3.6 40.6 - - - +
111B GLN* 4.1 4.9 + - - +
113B VAL* 4.3 3.1 - - + -
114B ALA* 3.8 32.1 - - + +
117B LEU* 3.9 4.2 - - - +
149B VAL* 2.9 25.7 + - - +
150B ILE 2.9 9.0 + - - +
152B ASP* 1.3 83.8 - - - +
154B VAL* 1.3 61.7 + - - +
155B LYS* 3.6 12.6 + - - +
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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