Contacts of the helix formed by residues 153 - 170 (chain A) in PDB entry 4M0A
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 ASN 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A HIS* 3.0 6.6 + - - +
152A HIS* 1.3 84.2 - - - +
154A THR* 1.3 67.2 + - - +
155A GLY 3.3 2.2 - - - -
156A LEU* 3.2 24.6 + - + +
157A SER* 3.0 21.3 + - - -
186A LEU* 3.4 37.8 + - + +
189A LEU* 3.9 10.5 - - - +
191A SER 3.1 24.4 + - - -
192A PRO* 3.5 0.9 - - - +
193A VAL* 2.8 30.4 + - - +
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Residues in contact with THR 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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151A HIS* 3.5 35.7 + - - +
152A HIS 3.7 1.0 - - - -
153A ASN* 1.3 73.9 - - - +
155A GLY* 1.3 57.9 + - - +
157A SER* 2.9 3.5 + - - +
158A GLU* 2.9 57.0 + - + +
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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
----------------------------------------------------------
153A ASN 3.3 0.6 - - - -
154A THR* 1.3 78.9 - - - +
156A LEU* 1.3 63.8 + - - +
158A GLU* 3.4 10.6 + - - +
159A ALA* 3.1 22.7 + - - +
216A LEU* 4.7 4.7 - - - +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN* 3.2 29.2 + - + +
155A GLY* 1.3 75.6 - - - +
157A SER* 1.3 63.4 + - - +
159A ALA* 3.3 4.3 + - - +
160A LEU* 3.2 26.3 + - - +
186A LEU* 3.6 23.3 - - + -
193A VAL* 3.9 25.4 - - + +
213A VAL* 4.2 24.6 - - + +
216A LEU* 3.8 38.4 - - + +
217A LEU* 4.6 7.9 - - + -
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A HIS* 3.2 21.6 + - - -
153A ASN 3.0 12.9 + - - -
154A THR* 2.9 18.5 + - - +
156A LEU* 1.3 77.1 - - - +
158A GLU* 1.3 65.1 + - - +
160A LEU 3.3 1.0 + - - -
161A GLU* 3.0 30.0 + - - +
183A ALA* 3.7 35.5 - - - +
186A LEU* 4.2 4.6 - - - +
187A LYS* 4.2 10.1 - - - -
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A THR* 2.9 41.7 + - + +
155A GLY* 3.8 9.1 - - - +
156A LEU 3.3 0.2 - - - -
157A SER* 1.3 79.4 + - - +
159A ALA* 1.3 61.8 + - - +
161A GLU* 3.3 13.8 + - - +
162A ILE* 3.1 26.9 + - + +
229A ARG* 5.5 3.8 - - - +
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Residues in contact with ALA 159 (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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155A GLY 3.1 10.3 + - - +
156A LEU 3.7 3.8 - - - +
157A SER 3.2 0.2 - - - -
158A GLU* 1.3 78.3 - - - +
160A LEU* 1.3 62.8 + - - +
162A ILE* 3.2 14.4 + - - +
163A LEU* 3.3 15.6 + - - +
212A VAL* 4.5 2.0 - - + -
216A LEU* 3.6 34.8 - - + -
225A VAL* 3.9 27.8 - - + +
229A ARG* 4.8 6.7 - - - +
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Residues in contact with LEU 160 (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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156A LEU 3.2 14.6 + - - +
157A SER 3.3 5.4 + - - +
159A ALA* 1.3 76.3 - - - +
161A GLU* 1.3 59.6 + - - +
163A LEU* 3.2 8.2 + - + +
164A ALA 2.9 22.7 + - - -
179A PHE* 3.6 37.0 - - + +
182A ALA* 4.3 1.6 - - + -
183A ALA* 3.9 20.4 - - + +
186A LEU* 3.8 23.6 - - + -
205A PHE* 3.9 18.4 - - + -
209A SER* 4.0 17.7 - - - +
212A VAL* 4.1 26.2 - - + -
213A VAL* 4.5 4.7 - - + -
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 3.0 23.6 + - - +
158A GLU* 3.8 12.0 - - - +
160A LEU* 1.3 74.2 - - - +
162A ILE* 1.3 59.7 + - - +
164A ALA* 3.5 10.4 - - + +
165A GLU* 2.9 30.4 + - - +
180A CYS* 5.0 9.8 - - - +
183A ALA* 3.6 15.5 - - + +
187A LYS* 2.7 37.8 + - - -
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Residues in contact with ILE 162 (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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158A GLU 3.1 16.9 + - - +
159A ALA* 3.2 8.9 + - - +
161A GLU* 1.3 76.2 - - - +
163A LEU* 1.3 60.1 + - + +
165A GLU* 3.2 8.0 + - - +
166A ALA* 2.9 28.1 + - - +
225A VAL* 4.2 18.2 - - + +
228A VAL* 3.8 26.5 - - + -
229A ARG* 3.9 34.3 - - + +
234A TYR* 3.3 28.0 - - + +
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Residues in contact with LEU 163 (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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159A ALA 3.3 10.5 + - - +
160A LEU* 3.2 9.0 + - + +
162A ILE* 1.3 77.6 - - + +
164A ALA* 1.3 57.9 + - - +
166A ALA* 3.5 4.5 + - + +
167A ALA* 2.9 29.1 + - - +
175A ARG* 5.0 1.4 + - - -
179A PHE* 3.8 34.7 - - + -
212A VAL* 3.6 33.2 - - + -
224A GLU* 4.1 23.8 - - - +
225A VAL* 3.9 22.4 - - + -
228A VAL* 4.0 26.2 - - + -
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Residues in contact with ALA 164 (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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160A LEU 2.9 13.1 + - - +
161A GLU* 3.5 13.2 - - + +
162A ILE 3.2 0.2 - - - -
163A LEU* 1.3 77.0 - - - +
165A GLU* 1.3 61.3 + - - +
167A ALA* 3.2 2.9 + - - +
168A GLY 3.1 17.3 + - - -
176A LEU* 3.4 28.0 - - - +
179A PHE* 3.7 12.5 - - + +
180A CYS* 3.6 31.6 - - - +
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Residues in contact with GLU 165 (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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161A GLU 2.9 16.5 + - - +
162A ILE* 3.6 9.5 - - - +
164A ALA* 1.3 75.5 - - - +
166A ALA* 1.3 63.3 + - - +
168A GLY* 3.1 3.6 + - - -
169A PHE* 3.0 50.2 + - + -
176A LEU* 4.9 4.5 - - - -
234A TYR* 2.5 32.7 + - + -
238A LYS* 2.6 30.9 + - - +
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Residues in contact with ALA 166 (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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162A ILE 2.9 17.2 + - - +
163A LEU* 3.8 6.7 - - - +
165A GLU* 1.3 76.7 - - - +
167A ALA* 1.3 62.8 + - - +
169A PHE* 3.1 22.1 + - - +
170A GLU* 3.2 19.7 + - + +
228A VAL* 3.7 30.1 - - + -
234A TYR* 4.3 4.4 - - + -
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Residues in contact with ALA 167 (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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163A LEU 2.9 17.7 + - - +
164A ALA 3.2 4.9 + - - +
166A ALA* 1.3 75.6 - - - +
168A GLY* 1.3 61.8 + - - +
170A GLU* 3.1 10.8 + - - +
172A SER* 2.8 35.1 + - - +
175A ARG* 3.7 28.9 - - + +
176A LEU* 3.7 23.1 - - - +
179A PHE* 5.0 0.4 - - + -
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Residues in contact with GLY 168 (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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164A ALA 3.1 6.9 + - - -
165A GLU 3.1 8.0 + - - -
167A ALA* 1.3 77.9 - - - +
169A PHE* 1.3 63.4 + - - +
171A GLY* 3.0 14.6 + - - -
172A SER 4.6 2.7 - - - -
173A GLU* 4.9 6.9 - - - +
176A LEU* 3.7 23.0 - - - +
248A VAL* 3.7 16.3 - - - +
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Residues in contact with PHE 169 (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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165A GLU* 3.0 45.4 + - + -
166A ALA* 3.1 8.7 + - - +
168A GLY* 1.3 77.9 - - - +
170A GLU* 1.3 67.7 + - - +
171A GLY 3.3 0.8 + - - -
233A ARG* 3.1 22.5 + - + -
234A TYR* 3.7 37.2 - + - -
237A MET* 3.6 33.1 - - + +
238A LYS* 3.6 28.9 - - + -
241A THR* 3.7 20.0 - - + -
248A VAL* 3.8 20.8 - - + +
252A ASP* 5.3 0.3 - - - +
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Residues in contact with GLU 170 (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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166A ALA* 3.2 12.3 + - + +
167A ALA* 3.1 10.1 + - - +
168A GLY 3.0 0.6 - - - -
169A PHE* 1.3 88.3 - - - +
171A GLY* 1.3 60.0 + - - +
172A SER* 3.2 6.9 + - - +
175A ARG* 6.4 0.2 - - - +
233A ARG* 2.8 47.2 + - - +
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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