Contacts of the helix formed by residues 147 - 159 (chain C) in PDB entry 5MLE
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 147 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C LYS* 1.3 73.3 - - - +
148C ILE* 1.3 62.4 + - - +
149C GLN* 3.0 7.3 + - - +
150C GLU* 3.0 21.8 + - - +
151C GLU* 3.9 6.5 + - - +
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Residues in contact with ILE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 3.7 41.7 - - + -
141C ILE* 4.4 16.4 - - + -
142C SER 5.8 0.2 - - - +
143C GLU 3.6 21.1 - - - +
144C TRP* 3.3 36.1 - - + -
146C LYS* 3.2 37.1 + - - +
147C GLY* 1.3 73.1 - - - +
149C GLN* 1.3 65.8 + - - +
150C GLU 3.2 0.2 - - - -
151C GLU* 2.9 24.7 + - - +
152C MET* 3.0 14.9 + - + +
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Residues in contact with GLN 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C TRP* 4.2 21.1 - - + -
147C GLY 3.0 3.0 + - - +
148C ILE* 1.3 83.3 - - + +
150C GLU* 1.3 60.3 + - + +
152C MET* 3.8 7.5 - - - +
153C GLU* 3.2 45.7 + - - +
187C VAL* 3.8 29.7 - - + +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C GLY 3.0 12.5 + - - +
149C GLN* 1.3 79.2 - - + +
151C GLU* 1.3 63.6 + - - +
153C GLU* 3.6 16.3 + - - +
154C ALA* 3.2 23.9 + - - +
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Residues in contact with GLU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C SER* 3.3 31.7 + - - +
116C LEU* 3.2 32.0 + - + +
117C LEU* 4.2 15.7 - - + +
146C LYS* 3.3 24.7 + - - -
147C GLY 3.9 3.0 + - - +
148C ILE* 2.9 18.2 + - - +
150C GLU* 1.3 75.0 - - - +
152C MET* 1.3 65.7 + - - +
154C ALA* 3.2 6.3 + - - +
155C LEU* 2.9 30.4 + - - +
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Residues in contact with MET 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 3.9 17.4 - - + +
141C ILE* 3.7 19.5 - - + -
144C TRP* 3.6 33.2 - - - -
148C ILE* 3.0 15.6 + - - +
149C GLN* 3.8 7.4 - - - +
151C GLU* 1.3 75.6 - - - +
153C GLU* 1.3 64.4 + - - +
154C ALA 3.1 0.9 + - - -
155C LEU* 3.2 4.1 + - - +
156C VAL* 3.2 27.2 + - - +
164C PHE* 4.0 28.7 - - + -
184C VAL* 4.7 2.2 - - + +
187C VAL* 4.2 16.6 - - + -
188C ILE* 3.5 32.8 - - + -
191C ILE* 4.3 7.2 - - + -
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLN* 3.2 47.5 + - + +
150C GLU* 3.8 15.0 - - - +
151C GLU 3.3 0.4 - - - -
152C MET* 1.3 78.3 - - - +
154C ALA* 1.3 56.7 - - - +
156C VAL* 3.6 3.6 + - - +
157C LYS* 3.2 29.5 + - - +
187C VAL* 5.0 2.0 - - + +
191C ILE* 3.7 31.4 - - + +
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 4.7 15.3 - - + -
150C GLU 3.2 16.8 + - - +
151C GLU* 3.7 5.2 - - - +
152C MET 3.1 0.8 - - - -
153C GLU* 1.3 75.6 - - - +
155C LEU* 1.3 57.8 + - - +
156C VAL 3.2 0.4 - - - -
157C LYS* 4.4 6.5 - - - -
158C ASP* 2.8 46.5 + - - +
159C HIS* 3.7 3.7 - - + -
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 3.9 28.9 - - + -
117C LEU* 4.5 13.0 - - + -
120C PHE* 4.0 37.7 - - + -
139C VAL* 4.2 10.3 - - + -
151C GLU 2.9 18.8 + - - +
152C MET 3.5 6.5 - - - +
154C ALA* 1.3 75.4 - - - +
156C VAL* 1.3 57.4 + - - +
159C HIS* 2.9 47.5 + - + +
160C GLY 3.5 5.0 + - - -
161C VAL* 3.7 15.9 + - + -
164C PHE* 4.0 22.9 - - + -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C MET 3.2 15.9 + - - +
153C GLU 3.9 4.5 - - - +
155C LEU* 1.3 77.5 - - - +
157C LYS* 1.3 61.8 + - + +
160C GLY* 4.7 5.7 + - - -
161C VAL 3.5 25.0 + - - +
162C ASN* 5.1 1.1 - - - -
164C PHE* 3.7 27.6 - - + -
191C ILE* 3.8 38.4 - - + +
193C ALA* 4.7 4.0 - - + -
471C ARG 5.3 0.5 - - - +
473C PRO* 3.9 29.7 - - + +
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Residues in contact with LYS 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLU 3.2 20.6 + - - +
154C ALA* 4.3 4.7 - - - +
156C VAL* 1.3 79.9 - - + +
158C ASP* 1.3 92.8 + - - +
160C GLY 5.5 0.2 - - - -
473C PRO* 6.2 0.4 - - - -
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Residues in contact with ASP 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ALA* 2.8 30.0 + - - +
157C LYS* 1.3 103.6 - - - +
159C HIS* 1.3 75.1 + - + +
160C GLY 3.8 2.0 - - - -
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Residues in contact with HIS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 3.8 35.9 - - + +
120C PHE* 3.4 43.7 - + + -
121C ASP* 4.9 5.3 + - - -
124C ARG* 5.1 1.7 + - - +
154C ALA* 3.7 12.0 - - + +
155C LEU* 2.9 28.6 + - + +
158C ASP* 1.3 92.4 + - + +
160C GLY* 1.3 63.3 + - - +
161C VAL* 3.5 2.4 + - - -
468C TYR* 3.5 9.0 + - - -
470C PRO* 5.5 0.4 - - - -
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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
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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