Contacts of the helix formed by residues 141 - 155 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A MET 3.4 2.2 + - - -
140A PRO* 1.3 69.9 - - - +
142A GLY* 1.3 58.8 + - - +
144A PHE* 3.1 4.7 + - - +
145A ALA* 2.9 29.3 + - - +
219A THR* 3.6 20.5 + - - +
222A SER 2.6 29.2 + - - -
223A SER* 2.9 12.8 + - - -
224A THR* 3.7 11.2 - - - +
225A VAL* 3.9 12.7 - - - +
239A TYR* 4.1 16.2 + - - -
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PRO* 3.2 2.9 - - - +
141A SER* 1.3 80.2 + - - +
143A GLU* 1.3 64.2 + - - +
145A ALA* 3.4 5.8 + - - +
146A ARG* 3.0 24.3 + - - +
219A THR* 3.9 11.9 - - - +
223A SER 4.7 0.2 + - - -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 4.7 3.4 - - - -
140A PRO* 3.1 41.1 + - + +
142A GLY* 1.3 74.3 - - - +
144A PHE* 1.3 63.9 + - - +
146A ARG* 3.2 6.5 + - - +
147A ILE* 3.0 40.6 + - + +
182A LEU* 3.4 20.8 - - - +
193A GLU* 5.5 1.9 - - - +
195A VAL* 4.0 9.7 - - - +
110C LYS* 3.3 37.3 + - - +
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 3.7 26.2 - - + -
140A PRO 3.1 5.8 + - - +
141A SER 3.1 6.5 + - - +
143A GLU* 1.3 73.8 - - - +
145A ALA* 1.3 65.4 + - - +
147A ILE* 3.4 6.0 + - + +
148A CYS* 3.2 41.8 + - - -
160A ILE* 5.7 2.5 - - + -
169A PHE* 4.2 15.3 - + - -
212A LEU* 4.6 20.2 - - + -
215A PHE* 5.8 0.4 - - + -
216A THR* 3.8 24.9 - - + -
225A VAL* 3.6 28.7 - - + -
227A LEU* 3.7 32.1 - - + -
235A LEU* 6.0 0.7 - - + -
237A VAL* 4.1 14.4 - - + -
239A TYR* 4.1 4.9 - - - -
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A SER 2.9 15.7 + - - +
142A GLY* 3.7 7.9 - - - +
144A PHE* 1.3 79.9 - - - +
146A ARG* 1.3 61.2 + - - +
148A CYS* 3.4 2.5 + - - +
149A ARG* 3.1 24.1 + - - +
213A ASN* 5.1 0.3 - - - +
216A THR* 3.9 23.3 + - - +
219A THR* 3.8 18.8 - - + +
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 3.0 16.3 + - - +
143A GLU* 3.2 7.1 + - - +
145A ALA* 1.3 77.6 - - - +
147A ILE* 1.3 54.5 + - - +
149A ARG* 3.0 38.6 + - - +
150A ASP* 2.8 55.4 + - - +
13C LYS* 4.7 1.8 - - - +
80C LYS 2.9 25.9 + - - -
81C CYS 3.7 10.5 + - - -
82C ALA 3.0 22.8 + - - -
83C GLY* 4.2 8.8 - - - +
110C LYS* 4.2 18.7 - - - +
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Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 4.6 4.9 - - - -
143A GLU* 3.0 29.7 + - + +
144A PHE* 3.6 6.7 - - + +
145A ALA 3.3 0.2 - - - -
146A ARG* 1.3 77.1 - - - +
148A CYS* 1.3 61.4 + - - +
150A ASP* 3.7 1.9 - - - +
151A LEU* 3.0 33.9 + - + +
169A PHE* 3.8 47.6 - - + -
180A ILE* 4.0 32.8 - - + -
182A LEU* 4.0 27.4 - - + -
110C LYS* 4.8 7.4 - - - +
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Residues in contact with CYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.2 52.7 + - - +
145A ALA* 4.1 4.0 - - - +
146A ARG 3.3 0.2 - - - -
147A ILE* 1.3 77.6 - - - +
149A ARG* 1.3 64.0 + - - +
151A LEU* 3.6 0.4 + - - -
152A SER* 2.9 28.4 + - - -
158A VAL* 6.0 0.2 - - - -
169A PHE* 6.1 0.9 - - - -
209A LEU* 3.8 17.8 - - + +
212A LEU* 3.9 24.9 - - + -
213A ASN* 3.3 17.4 - - - +
216A THR* 4.7 4.0 - - + -
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA 3.1 17.8 + - - +
146A ARG* 3.0 49.9 - - - +
148A CYS* 1.3 74.2 - - - +
150A ASP* 1.3 83.4 + - - +
152A SER* 3.2 19.2 - - - -
153A HIS* 3.7 24.8 + - + +
213A ASN* 3.6 10.0 + - - +
80C LYS* 4.2 6.1 + - - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG* 2.8 40.7 + - - +
147A ILE* 3.7 6.6 - - - +
149A ARG* 1.3 98.3 + - - +
151A LEU* 1.3 62.7 + - - +
153A HIS* 3.0 26.9 + - - +
154A ILE* 4.0 3.5 - - - +
180A ILE* 4.7 5.3 - - + +
80C LYS 4.2 1.0 - - - +
81C CYS* 3.5 53.9 + - + +
110C LYS* 5.2 3.5 + - - -
114C TYR* 4.1 7.0 + - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.0 24.6 + - + +
148A CYS 4.3 1.8 - - - +
149A ARG 3.3 0.2 - - - -
150A ASP* 1.3 76.8 - - - +
152A SER* 1.3 56.8 + - - +
154A ILE* 3.0 22.0 + - + +
155A GLY 3.1 14.4 + - - +
158A VAL* 3.7 18.6 - - + -
169A PHE* 3.6 37.5 - - + +
170A SER 4.1 3.6 - - - +
171A ALA* 3.9 21.2 - - + +
178A GLY 4.2 14.4 - - - +
180A ILE* 3.9 19.7 - - + -
209A LEU* 4.0 12.6 - - + -
114C TYR* 4.3 17.3 - - + +
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Residues in contact with SER 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A CYS 2.9 12.2 + - - -
149A ARG* 3.2 15.3 - - - -
150A ASP 3.1 0.2 - - - -
151A LEU* 1.3 77.3 - - - +
153A HIS* 1.3 63.7 + - - +
154A ILE 4.5 0.2 - - - -
155A GLY 3.5 17.8 + - - +
209A LEU* 3.9 9.9 - - - +
213A ASN* 2.8 31.4 + - - -
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Residues in contact with HIS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG* 3.7 30.6 + - + +
150A ASP* 3.0 21.7 + - - +
152A SER* 1.3 81.4 - - - +
154A ILE* 1.3 65.3 + - + +
175A LEU* 3.8 18.1 - - - +
77C LYS* 4.1 52.4 + - + +
80C LYS* 4.9 13.8 - - + +
81C CYS* 4.5 3.1 - - - -
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ASP 4.0 10.5 - - - +
151A LEU* 3.0 14.1 + - + +
153A HIS* 1.3 85.1 - - + +
155A GLY* 1.3 57.5 + - - +
171A ALA* 3.8 18.8 - - + +
173A GLY* 3.2 21.3 - - - -
174A GLU 4.2 1.4 + - - -
175A LEU* 3.7 26.1 - - + +
176A GLY 3.6 21.1 - - - +
177A ASN* 3.7 14.8 - - - -
178A GLY 4.0 1.8 - - - +
78C ILE* 4.1 11.7 - - + +
81C CYS* 5.3 1.1 - - - -
114C TYR* 3.7 34.8 - - + -
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU 3.1 15.9 + - - +
152A SER* 3.5 13.0 + - - +
153A HIS 3.8 0.6 - - - -
154A ILE* 1.3 77.9 - - - +
156A ASP* 1.3 60.9 + - - -
157A ALA 3.5 3.1 - - - -
171A ALA* 4.4 1.1 - - - +
172A SER 3.7 21.3 - - - -
173A GLY* 4.5 1.8 - - - -
209A LEU* 3.4 9.2 - - - +
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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