Contacts of the helix formed by residues 146 - 164 (chain A) in PDB entry 1M1U
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 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLY 5.1 2.7 - - - +
144A SER* 3.1 28.2 + - - +
145A ILE* 1.3 73.9 - - - +
147A PRO* 1.3 76.8 - - + +
148A HIS* 3.3 27.4 - - + +
149A ASP* 2.9 31.9 + - - +
150A PHE* 2.9 10.6 + - - +
204A GLN* 4.6 0.2 - - - -
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Residues in contact with PRO 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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145A ILE 3.6 2.9 - - - +
146A ILE* 1.3 91.9 - - + +
148A HIS* 1.3 61.1 + - - +
150A PHE* 3.2 3.1 + - + +
151A ARG* 3.1 23.7 + - - +
204A GLN* 4.2 13.7 - - - +
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Residues in contact with HIS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.2 15.3 - - + +
147A PRO* 1.3 78.1 - - - +
149A ASP* 1.3 65.0 + - - +
151A ARG* 3.5 7.8 + - - +
152A ARG* 3.2 36.1 + - + +
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Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 4.1 12.8 - - + -
146A ILE* 2.9 29.3 + - - +
148A HIS* 1.3 83.3 + - - +
150A PHE* 1.3 64.0 + - - +
151A ARG 3.2 1.3 - - - -
152A ARG* 3.2 13.3 + - - +
153A MET* 3.0 27.6 + - - +
271A VAL* 4.3 12.4 - - + +
272A GLY* 3.9 28.9 + - - -
299A VAL* 5.5 2.6 - - - +
300A ASN* 5.6 2.6 + - - -
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Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 4.1 15.9 - - + -
140A ASP 3.7 17.0 - - - -
141A GLY* 3.9 7.0 - - - -
145A ILE* 3.8 5.5 - - + +
146A ILE 2.9 8.0 + - - +
147A PRO* 3.2 7.8 + - + +
149A ASP* 1.3 76.3 - - - +
151A ARG* 1.3 62.3 + - - +
153A MET* 3.1 11.2 + - - +
154A LYS* 3.0 46.8 + - + +
175A GLN* 3.3 36.1 - - - -
202A ILE* 3.9 16.4 - - + -
203A THR 3.9 3.4 - - - -
204A GLN* 3.4 52.7 - - + +
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Residues in contact with ARG 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 PRO 3.1 13.2 + - - +
148A HIS* 3.5 12.1 - - - +
149A ASP 3.2 0.2 - - - -
150A PHE* 1.3 75.1 - - - +
152A ARG* 1.3 59.1 + - + +
154A LYS* 3.1 26.5 + - - +
155A GLU* 2.8 61.1 + - - +
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Residues in contact with ARG 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 HIS* 3.2 28.4 + - + +
149A ASP* 3.2 17.0 + - - +
151A ARG* 1.3 76.9 - - - +
153A MET* 1.3 53.5 + - - +
155A GLU* 3.1 43.1 + - - +
156A PHE* 2.7 48.3 + - - +
271A VAL* 5.6 0.4 - - + -
299A VAL* 2.9 45.4 + - + +
300A ASN* 2.7 30.4 + - - +
302A PHE* 3.6 29.0 - - - -
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Residues in contact with MET 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 4.3 12.3 - - + -
140A ASP* 3.3 44.4 - - + +
145A ILE* 3.7 18.2 - - + -
149A ASP 3.0 16.7 + - - +
150A PHE* 3.2 17.9 - - + +
152A ARG* 1.3 76.6 - - - +
154A LYS* 1.3 59.6 + - + +
156A PHE* 3.8 5.3 - - - +
157A VAL* 3.0 35.5 + - - +
240A ILE* 3.8 30.2 - - + +
271A VAL* 3.4 36.3 - - + -
299A VAL* 5.1 1.3 - - - -
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 5.1 5.8 - - + -
150A PHE* 3.0 33.2 + - + +
151A ARG* 3.1 27.1 + - + +
153A MET* 1.3 78.4 - - + +
155A GLU* 1.3 58.2 + - + +
157A VAL* 3.9 3.1 - - - +
158A SER* 2.9 33.5 + - - -
196A ARG* 5.3 0.4 - - - -
199A VAL* 3.4 29.6 + - + +
200A LYS* 3.5 20.9 + - - +
202A ILE* 2.5 41.1 + - + +
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Residues in contact with GLU 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 ARG* 2.8 53.2 + - + +
152A ARG* 3.1 33.7 + - - +
154A LYS* 1.3 76.2 - - + +
156A PHE* 1.3 60.5 + - - +
158A SER* 3.6 1.4 + - - -
159A THR* 2.6 34.9 + - - +
196A ARG* 4.3 16.2 + - - +
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Residues in contact with PHE 156 (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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137A PHE* 4.9 1.8 - + - -
152A ARG* 2.7 27.8 + - - +
153A MET* 3.8 4.9 - - - +
155A GLU* 1.3 71.7 - - - +
157A VAL* 1.3 62.3 + - + +
159A THR* 3.2 6.0 + - - -
160A VAL* 3.0 56.4 + - + +
238A VAL* 4.2 12.6 - - + -
240A ILE* 3.8 16.2 - - + -
269A ILE* 3.7 44.2 - - + -
299A VAL* 4.3 28.3 - - + -
301A ASN 5.6 1.3 - - - -
304A ALA* 4.8 14.8 - - + -
305A LEU* 5.2 7.4 - - + -
308A ILE* 4.6 11.7 - - + -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 3.8 32.5 - - + -
139A ILE* 4.1 11.9 - - + -
153A MET 3.0 18.5 + - - +
154A LYS* 3.9 6.1 - - - +
156A PHE* 1.3 79.6 - - - +
158A SER* 1.3 62.2 + - - +
160A VAL* 3.4 2.3 + - - +
161A MET* 3.1 45.1 + - + +
173A LEU* 3.6 24.2 - - + -
199A VAL* 4.0 3.4 - - + -
240A ILE* 3.6 22.7 - - + -
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS 2.9 20.7 + - - -
155A GLU 3.8 0.9 - - - -
157A VAL* 1.3 76.9 - - - +
159A THR* 1.3 63.2 + - - +
161A MET* 3.6 12.5 + - - +
162A GLU* 3.1 32.2 + - - +
195A PRO* 4.0 4.3 + - - +
196A ARG* 3.2 38.9 + - - -
199A VAL* 3.3 22.2 - - - +
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Residues in contact with THR 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 GLU* 2.6 23.2 + - - +
156A PHE* 3.7 5.1 - - - -
158A SER* 1.3 73.6 - - - +
160A VAL* 1.3 55.3 + - - +
162A GLU* 3.2 10.9 + - + +
163A GLN* 2.8 39.3 + - + +
196A ARG* 4.6 7.4 + - - -
305A LEU* 3.8 16.8 - - + -
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Residues in contact with VAL 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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135A ILE* 5.6 1.6 - - + -
137A PHE* 3.8 22.2 - - + -
156A PHE* 3.0 54.6 + - + +
157A VAL* 3.6 5.2 - - - +
159A THR* 1.3 75.1 - - - +
161A MET* 1.3 58.5 + - - +
163A GLN 3.1 0.3 + - - -
164A LEU* 2.8 58.8 + - + +
171A PHE* 4.3 3.6 - - + -
238A VAL* 5.7 2.7 - - + -
305A LEU* 3.6 24.0 - - + +
308A ILE* 6.1 0.7 - - + -
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Residues in contact with MET 161 (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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137A PHE* 3.8 10.8 - - + -
157A VAL* 3.1 21.2 + - + +
158A SER* 3.7 11.2 - - - +
160A VAL* 1.3 81.2 - - - +
162A GLU* 1.3 59.6 + - - +
165A LYS* 3.2 27.9 + - - +
171A PHE* 3.7 40.6 - - + -
184A PHE* 3.8 23.8 - - + -
189A PHE* 4.4 5.6 - - - -
195A PRO* 3.8 31.6 - - + +
198A LEU* 5.2 0.4 - - + -
199A VAL* 3.3 34.3 - - + -
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Residues in contact with GLU 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 SER 3.1 19.7 + - - +
159A THR* 3.2 9.6 + - + +
161A MET* 1.3 76.3 - - - +
163A GLN* 1.3 64.7 + - + +
165A LYS* 3.6 27.0 - - - +
195A PRO* 3.3 21.6 - - + +
196A ARG* 3.0 51.0 + - - +
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Residues in contact with GLN 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 THR* 2.8 20.7 + - + +
160A VAL 3.7 0.4 - - - +
162A GLU* 1.3 79.2 + - + +
164A LEU* 1.3 60.6 + - + +
165A LYS 3.0 11.2 + - - +
305A LEU* 3.6 31.5 - - + +
306A LYS* 5.6 1.4 - - - +
309A GLN* 3.3 35.8 + - - +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 4.1 13.7 - - + -
160A VAL* 2.8 41.9 + - + +
163A GLN* 1.3 69.2 - - + +
165A LYS* 1.3 58.9 + - - +
166A LYS* 2.8 37.7 + - - +
169A THR* 3.8 2.4 - - - +
171A PHE* 3.7 18.8 - - + -
305A LEU* 3.6 16.8 - - + -
308A ILE* 4.7 6.1 - - + -
309A GLN* 3.4 44.2 - - + -
312A LEU* 3.6 25.4 - - + -
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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
------------------------------------------------------------
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