Contacts of the helix formed by residues 143 - 159 (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 GLY 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG* 3.4 15.9 - - - -
138B LEU* 3.1 16.4 - - - -
140B SER 2.8 15.4 + - - -
141B GLY 3.3 0.8 + - - -
142B ASP* 1.3 79.2 + - - +
144B ALA* 1.3 61.9 + - - -
146B ARG 3.1 4.0 + - - -
147B SER 2.8 24.9 + - - -
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Residues in contact with ALA 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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119B LYS 3.5 24.7 + - - +
120B ALA* 3.7 8.2 - - - +
122B GLU* 4.1 16.1 + - + +
123B LEU* 3.7 28.0 - - + -
137B ARG* 5.6 0.2 - - - +
138B LEU* 3.5 17.8 + - + +
142B ASP 3.6 1.0 + - - -
143B GLY* 1.3 69.4 - - - -
145B LEU* 1.3 57.4 + - - +
147B SER* 4.4 0.4 - - - -
148B LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 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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123B LEU* 3.7 33.4 - - + -
131B LEU* 4.6 5.8 - - + -
135B HIS* 3.6 23.1 - - + -
138B LEU* 3.0 32.8 + - + +
144B ALA* 1.3 73.9 - - - +
146B ARG* 1.3 57.5 + - - +
148B LEU* 3.4 4.2 + - + +
149B SER* 3.0 31.4 + - - -
181B LEU* 5.0 5.4 - - + -
184B TRP* 3.4 43.1 - - + +
185B GLY* 3.7 3.3 - - - -
210B LEU* 4.3 21.1 - - + -
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU 3.1 3.8 + - - +
139B ALA 3.7 20.7 + - - -
140B SER* 3.9 1.3 - - - +
141B GLY 3.6 23.6 - - - +
143B GLY 3.1 6.7 + - - +
145B LEU* 1.3 73.8 - - - +
147B SER* 1.3 59.0 + - - +
149B SER* 3.9 1.9 - - - +
150B THR* 2.7 37.3 + - - +
185B GLY* 3.0 33.5 + - - +
186B THR* 3.0 29.1 + - - +
13D ALA* 3.4 20.2 - - - +
32D TYR* 3.3 21.4 - - - +
61D GLN* 3.9 6.1 - - - +
200D GDP 2.9 49.3 + - - -
201D AF3 2.7 17.7 - - - -
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Residues in contact with SER 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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116B GLY* 3.6 24.4 - - - +
119B LYS* 3.4 16.3 - - - +
142B ASP* 2.8 34.4 + - - +
143B GLY 2.8 14.0 + - - -
144B ALA 3.8 4.3 - - - -
146B ARG* 1.3 77.1 - - - +
148B LEU* 1.3 57.7 + - - +
150B THR* 3.9 4.1 - - - -
151B ALA* 2.9 31.7 + - - +
61D GLN* 4.6 5.4 - - - +
63D ASP* 4.5 2.4 + - - -
64D TYR* 4.9 0.7 + - - -
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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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117B LEU* 3.9 17.0 - - + -
120B ALA* 3.8 15.7 - - + +
123B LEU* 3.7 20.0 - - + -
144B ALA 2.9 18.3 + - - +
145B LEU* 3.6 5.8 - - + +
146B ARG 3.2 0.2 - - - -
147B SER* 1.3 76.1 - - - +
149B SER* 1.3 66.7 + - - +
151B ALA* 3.3 3.0 + - - +
152B LEU* 2.9 52.4 + - + +
181B LEU* 3.9 33.0 - - + -
210B LEU* 5.7 0.4 - - + -
213B VAL* 4.2 12.6 - - + -
214B MET* 4.3 2.7 - - - -
217B VAL* 4.0 15.7 - - + -
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Residues in contact with SER 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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145B LEU 3.0 19.5 + - - -
146B ARG 3.4 4.0 + - - -
148B LEU* 1.3 77.5 - - - +
150B THR* 1.3 58.2 + - - +
152B LEU 3.6 0.2 + - - -
153B ALA* 3.0 30.0 + - - +
172B LEU* 3.7 13.3 - - - +
181B LEU* 3.7 6.3 + - - +
182B GLN* 3.0 35.2 + - - -
185B GLY* 3.7 5.2 - - - -
32D TYR* 3.9 14.8 - - - -
34D PRO* 3.6 9.5 - - - +
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Residues in contact with THR 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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146B ARG 2.7 22.9 + - - -
147B SER* 3.9 5.2 - - - -
149B SER* 1.3 78.3 - - - +
151B ALA* 1.3 55.6 + - - +
153B ALA* 3.3 2.9 + - - +
154B GLY 3.0 23.0 + - - -
32D TYR* 3.6 11.1 + - - -
34D PRO* 3.7 12.5 - - + +
35D THR 3.9 20.4 - - - +
36D VAL* 3.8 11.3 - - + +
61D GLN* 4.1 18.8 + - - +
64D TYR* 3.7 29.5 + - + +
201D AF3 4.4 2.6 - - - -
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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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113B THR* 3.5 30.6 - - - +
116B GLY 4.1 0.9 - - - -
117B LEU* 3.7 23.8 - - + +
147B SER 2.9 20.7 + - - +
148B LEU 3.8 0.7 - - - +
150B THR* 1.3 75.6 - - - +
152B LEU* 1.3 64.5 + - - +
154B GLY 3.2 1.0 + - - -
155B ILE* 3.0 29.7 + - - +
64D TYR* 3.5 13.6 + - - +
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Residues in contact with LEU 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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117B LEU* 4.5 9.2 - - + -
148B LEU* 2.9 49.3 + - + +
151B ALA* 1.3 75.8 - - - +
153B ALA* 1.3 58.1 + - - +
155B ILE* 3.3 3.9 + - + -
156B ARG* 2.9 30.3 + - - +
168B ALA* 3.5 11.3 - - - +
171B LEU* 4.0 24.5 - - + -
172B LEU* 3.6 26.0 - - + -
181B LEU* 3.8 20.9 - - + -
217B VAL* 4.9 2.9 - - + -
220B LEU* 3.7 29.8 - - + -
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Residues in contact with ALA 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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149B SER 3.0 19.5 + - - +
150B THR 3.5 4.9 - - - +
151B ALA 3.2 0.2 - - - -
152B LEU* 1.3 76.9 - - - +
154B GLY* 1.3 62.7 + - - +
156B ARG* 3.4 12.4 + - - +
157B ALA* 3.1 24.9 + - - +
172B LEU* 3.8 13.6 - - + +
33D ILE* 6.4 0.2 - - + -
34D PRO* 3.8 29.2 - - + +
36D VAL* 4.8 4.0 - - + -
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Residues in contact with GLY 154 (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* 4.6 6.7 - - - +
109B ALA* 5.9 1.7 - - - -
110B LEU* 4.6 2.2 - - - +
113B THR* 3.9 14.6 - - - -
150B THR 3.0 11.4 + - - -
151B ALA 3.2 3.8 + - - -
153B ALA* 1.3 74.3 - - - +
155B ILE* 1.3 54.2 + - - +
157B ALA* 3.7 3.7 - - - +
158B GLY* 2.7 35.3 + - - -
36D VAL* 3.8 23.5 - - - +
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Residues in contact with ILE 155 (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* 4.1 12.1 - - + -
113B THR* 3.4 22.4 - - - +
117B LEU* 4.0 26.7 - - + -
151B ALA 3.0 24.3 + - - +
152B LEU* 3.3 7.2 + - + +
154B GLY* 1.3 74.8 - - - +
156B ARG* 1.3 61.0 + - - +
159B SER* 2.9 42.8 + - - -
164B SER* 4.0 12.1 - - - +
165B ARG* 3.9 0.9 - - - +
168B ALA* 3.9 14.4 - - + -
220B LEU* 4.2 13.9 - - + -
224B VAL* 4.0 28.0 - - + -
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Residues in contact with ARG 156 (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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152B LEU 2.9 17.4 + - - +
153B ALA* 3.7 14.0 + - - +
155B ILE* 1.3 77.7 - - - +
157B ALA* 1.3 58.2 + - + +
165B ARG* 3.2 38.1 - - + +
168B ALA* 3.9 12.5 - - + +
169B GLY* 3.9 24.1 + - - +
172B LEU* 3.5 24.9 - - + +
173B GLU* 4.5 11.9 + - - +
182B GLN* 3.2 28.1 + - - +
33D ILE* 6.1 1.8 - - - +
34D PRO* 5.6 1.0 - - - +
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Residues in contact with ALA 157 (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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103B GLN* 2.9 24.8 + - - +
106B LEU* 3.9 29.1 - - + +
153B ALA 3.1 16.6 + - - +
154B GLY* 4.1 2.0 - - - +
156B ARG* 1.3 80.3 - - + +
158B GLY* 1.3 57.7 + - - +
159B SER 3.8 2.3 - - - +
165B ARG* 5.1 1.6 - - - -
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Residues in contact with GLY 158 (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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103B GLN* 4.4 2.5 - - - -
106B LEU* 3.5 24.4 + - - +
107B GLN* 3.7 23.6 - - - +
110B LEU* 4.2 13.3 - - - +
154B GLY 2.7 20.7 + - - -
157B ALA* 1.3 73.8 - - - +
159B SER* 1.3 63.8 + - - +
160B GLN* 3.7 2.8 + - - +
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Residues in contact with SER 159 (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 7.1 - - - +
155B ILE* 2.9 30.1 + - - -
157B ALA 3.8 1.2 - - - +
158B GLY* 1.3 75.1 - - - +
160B GLN* 1.3 60.4 + - - +
161B VAL 3.1 10.3 + - - -
164B SER* 3.3 22.5 - - - -
165B ARG* 2.8 30.9 + - - -
224B VAL* 5.5 0.2 - - - -
227B GLU* 2.7 27.7 + - - -
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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