Contacts of the helix formed by residues 141 - 155 (chain B) in PDB entry 5E0T
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 SER 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B MET 3.4 1.6 + - - -
140B PRO* 1.3 70.8 - - - +
142B GLY* 1.3 57.6 + - - +
144B PHE* 3.3 5.7 + - - +
145B ALA* 3.0 27.9 + - - +
219B THR* 3.5 21.6 + - - +
222B SER 2.6 28.8 + - - -
223B SER* 2.8 18.3 + - - -
224B THR 4.0 8.5 - - - -
225B VAL* 3.8 11.7 - - - -
239B TYR* 4.2 16.3 + - - -
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Residues in contact with GLY 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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140B PRO* 3.3 2.3 - - - +
141B SER* 1.3 81.3 + - - +
143B GLU* 1.3 55.9 + - - +
145B ALA* 3.2 5.9 + - - +
146B ARG* 2.9 30.0 + - - +
219B THR* 4.1 10.4 - - - +
223B SER 4.7 0.2 + - - -
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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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107A ASN* 4.9 9.8 + - - +
110A LYS* 3.6 31.1 - - - +
139B MET* 4.7 2.0 - - - -
140B PRO* 3.1 42.8 + - + +
142B GLY* 1.3 76.5 - - - +
144B PHE* 1.3 58.5 - - - +
146B ARG* 3.3 6.8 + - - +
147B ILE* 2.9 40.4 + - + +
182B LEU* 3.2 31.2 - - - +
193B GLU 5.3 0.5 - - - +
195B VAL* 4.0 10.1 - - - +
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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
----------------------------------------------------------
139B MET* 3.8 17.2 - - + -
140B PRO 3.2 5.3 + - - -
141B SER 3.7 2.5 - - - +
143B GLU* 1.3 77.8 - - - +
145B ALA* 1.3 61.2 + - - +
147B ILE* 3.3 6.8 + - + +
148B CYS* 3.1 42.8 + - - -
160B ILE* 5.7 1.6 - - + -
169B PHE* 4.5 14.1 - + - -
212B LEU* 4.4 22.0 - - + -
215B PHE* 5.6 0.9 - - + -
216B THR* 3.6 27.1 - - + -
225B VAL* 3.6 31.2 - - + -
227B LEU* 3.8 33.9 - - + -
235B LEU* 6.2 0.4 - - + -
237B VAL* 4.1 18.8 - - + -
239B TYR* 4.0 7.4 - - - -
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Residues in contact with ALA 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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141B SER 3.0 15.6 + - - +
142B GLY* 3.2 8.2 + - - +
144B PHE* 1.3 77.3 - - - +
146B ARG* 1.3 57.8 + - - +
148B CYS* 3.4 3.5 + - - +
149B ARG* 3.0 30.4 + - - +
213B ASN* 4.8 0.9 - - - +
216B THR* 3.9 24.0 + - - +
219B THR* 3.9 17.9 - - + +
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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
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13A LYS* 4.9 1.6 - - - +
80A LYS 3.0 25.1 + - - -
81A CYS 4.0 3.2 + - - -
82A ALA 3.3 24.0 + - - -
83A GLY* 4.3 9.3 - - - -
110A LYS* 4.4 13.7 - - - +
142B GLY 2.9 16.5 + - - +
143B GLU* 3.6 8.1 - - - +
144B PHE 3.2 0.2 - - - -
145B ALA* 1.3 75.3 - - - +
147B ILE* 1.3 58.9 + - - +
149B ARG* 3.3 39.8 - - - +
150B ASP* 2.8 62.8 + - - +
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Residues in contact with ILE 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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110A LYS* 4.5 9.0 - - - +
139B MET* 4.5 5.8 - - - -
143B GLU* 2.9 28.2 + - + +
144B PHE* 3.5 6.7 - - + +
146B ARG* 1.3 77.0 - - - +
148B CYS* 1.3 63.4 + - - +
150B ASP* 3.7 1.8 - - - +
151B LEU* 3.0 35.1 + - + +
158B VAL* 5.9 0.2 - - + -
169B PHE* 3.9 55.6 - - + -
180B ILE* 4.2 32.5 - - + -
182B LEU* 4.2 20.0 - - + -
209B LEU* 6.5 0.2 - - + -
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Residues in contact with CYS 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* 3.1 52.4 + - - +
145B ALA* 3.8 5.4 - - - +
147B ILE* 1.3 79.1 - - - +
149B ARG* 1.3 65.2 + - - +
151B LEU 3.6 0.2 + - - -
152B SER* 3.0 26.5 + - - -
169B PHE* 6.2 0.7 - - - -
209B LEU* 3.8 16.1 - - + +
212B LEU* 3.9 24.7 - - + -
213B ASN* 3.3 19.9 - - - +
216B THR* 4.8 4.0 - - + -
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Residues in contact with ARG 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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80A LYS* 4.6 4.6 + - - +
145B ALA 3.0 17.7 + - - +
146B ARG* 3.3 56.9 - - - +
148B CYS* 1.3 73.6 - - - +
150B ASP* 1.3 71.6 + - - +
152B SER* 3.2 21.1 + - - -
153B HIS* 3.7 27.4 + - - +
213B ASN* 3.8 8.6 + - - +
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Residues in contact with ASP 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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80A LYS 4.0 2.8 - - - +
81A CYS* 3.5 49.9 - - + +
110A LYS* 5.3 5.4 + - - -
112A SER* 5.8 0.2 + - - -
114A TYR* 4.1 7.2 - - - +
146B ARG* 2.8 56.5 + - - +
147B ILE* 3.7 6.7 - - - +
149B ARG* 1.3 76.0 + - - +
151B LEU* 1.3 58.1 + - - +
153B HIS* 3.0 32.2 + - - +
154B ILE* 3.9 2.3 + - - +
180B ILE* 4.6 7.4 - - + +
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Residues in contact with LEU 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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114A TYR* 3.9 26.5 - - + +
147B ILE* 3.0 24.0 + - + +
148B CYS 4.3 1.3 - - - +
150B ASP* 1.3 76.7 - - - +
152B SER* 1.3 59.8 + - - +
153B HIS 3.2 0.2 - - - -
154B ILE* 3.2 8.3 + - + +
155B GLY 3.1 23.4 + - - +
158B VAL* 3.8 17.7 - - + -
169B PHE* 3.7 37.5 - - + +
170B SER 4.1 4.7 - - - +
171B ALA* 3.9 17.3 - - + +
178B GLY 4.3 12.3 - - - +
180B ILE* 3.9 15.3 - - + -
209B LEU* 3.6 15.5 - - + +
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Residues in contact with SER 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 CYS 3.0 8.2 + - - -
149B ARG* 3.3 13.5 - - - -
150B ASP 3.1 0.8 - - - -
151B LEU* 1.3 75.6 - - - +
153B HIS* 1.3 69.4 + - - +
155B GLY* 3.4 17.6 + - - +
209B LEU* 3.9 9.8 - - - +
213B ASN* 2.8 30.5 + - - -
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Residues in contact with HIS 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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77A LYS* 3.9 41.4 + - + +
80A LYS* 3.9 23.5 - - + +
81A CYS* 4.0 4.2 - - - -
149B ARG* 3.8 29.5 + - - +
150B ASP* 3.0 20.5 + - - +
152B SER* 1.3 81.9 - - - +
154B ILE* 1.3 66.5 + - + +
175B LEU* 3.6 19.6 - - - +
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Residues in contact with ILE 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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78A ILE* 4.1 12.8 - - + +
81A CYS* 4.8 4.0 - - - -
114A TYR* 3.8 30.5 - - + -
150B ASP 4.0 10.8 - - - +
151B LEU* 3.6 9.9 - - + +
152B SER 3.2 0.8 - - - -
153B HIS* 1.3 89.4 - - + +
155B GLY* 1.3 56.0 + - - +
171B ALA* 3.7 30.5 - - + +
173B GLY* 3.2 22.3 - - - -
175B LEU* 3.9 27.9 - - + +
176B GLY 3.7 18.8 - - - +
177B ASN* 3.8 7.2 - - - -
178B GLY 3.9 2.2 - - - +
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Residues in contact with GLY 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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151B LEU 3.1 16.8 + - - +
152B SER* 3.4 13.7 + - - +
153B HIS 3.7 1.0 - - - -
154B ILE* 1.3 79.6 - - - +
156B ASP* 1.3 59.7 + - - -
157B ALA 3.5 3.6 - - - -
171B ALA* 4.6 4.0 - - - +
172B SER 3.7 15.3 - - - -
173B GLY* 4.6 1.8 - - - -
209B LEU* 3.5 8.1 - - - +
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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