Contacts of the helix formed by residues 139 - 147 (chain E) in PDB entry 1MDU
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 GLN 139 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E ASP* 3.9 9.9 + - - +
14E ASN 3.3 20.6 + - - -
15E GLY* 5.3 1.4 - - - -
76E GLY* 5.2 4.8 + - - -
108E THR* 3.2 31.6 + - - +
109E GLU* 3.0 26.8 + - - +
110E ALA* 3.4 21.1 - - - +
111E PRO* 4.4 4.6 - - + +
137E ALA 3.6 1.2 + - - -
138E ILE* 1.3 69.8 - - - +
140E ALA* 1.3 64.0 + - - +
142E LEU* 3.0 16.7 + - - +
143E SER 3.1 9.5 + - - -
156E ASP* 4.4 7.5 - - - +
341E VAL* 3.6 27.8 - - + +
400E ATP 5.4 3.3 + - - -
401E CA 4.6 5.8 - - - -
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Residues in contact with ALA 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E PRO* 4.5 5.3 - - + +
138E ILE* 3.4 7.1 - - + +
139E GLN* 1.3 77.6 - - - +
141E VAL* 1.3 62.8 + - - +
143E SER* 3.3 9.3 + - - -
144E LEU 3.1 16.8 + - - -
154E VAL* 3.5 25.5 - - + +
156E ASP* 4.4 10.6 + - + +
165E VAL* 3.7 41.5 - - + -
167E ILE* 4.2 2.0 - - - -
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Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ALA* 6.5 0.2 - - + -
138E ILE* 3.1 32.9 + - + +
140E ALA* 1.3 74.1 - - + +
142E LEU* 1.3 67.8 + - + +
144E LEU* 3.2 3.5 + - + +
145E TYR* 3.1 57.4 + - + +
165E VAL* 5.3 0.2 - - + -
167E ILE* 3.9 26.9 - - + -
170E GLY 4.0 9.4 - - - +
172E ALA* 4.2 16.8 - - + +
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.6 2.0 - - + -
108E THR* 3.9 24.5 - - + -
137E ALA* 3.9 21.8 - - + -
138E ILE 3.2 12.1 + - - +
139E GLN 3.0 7.8 + - - +
141E VAL* 1.3 76.8 - - + +
143E SER* 1.3 58.2 + - - +
145E TYR* 3.2 17.0 + - + +
146E ALA 2.9 23.6 + - - -
340E SER 4.5 0.4 - - - -
341E VAL* 3.6 27.1 - - + +
344E GLY* 3.4 26.9 - - - +
345E GLY* 3.9 13.2 - - - +
348E LEU* 3.9 25.4 - - + -
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Residues in contact with SER 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E GLN 3.1 7.0 + - - -
140E ALA* 3.5 12.1 - - - -
141E VAL 3.2 0.2 - - - -
142E LEU* 1.3 75.3 - - - +
144E LEU* 1.3 64.7 + - - +
146E ALA* 3.1 12.6 + - - +
147E SER* 3.2 13.5 + - - -
154E VAL* 4.6 6.7 - - - -
300E VAL* 4.8 5.4 - - - +
302E SER* 3.1 33.0 + - - -
340E SER* 3.5 13.7 + - - -
341E VAL* 3.2 26.4 + - - +
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Residues in contact with LEU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E ALA 3.1 10.3 + - - +
141E VAL 3.2 7.4 + - - +
143E SER* 1.3 78.1 - - - +
145E TYR* 1.3 64.6 + - + +
147E SER* 2.6 26.1 + - - +
149E ARG* 3.3 38.4 + - + +
150E THR* 3.6 22.4 - - - -
151E THR 3.7 11.2 - - - +
152E GLY* 4.0 9.0 - - - +
154E VAL* 4.0 14.5 - - + +
167E ILE* 3.5 40.2 - - + -
300E VAL* 4.1 17.9 - - + -
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Residues in contact with TYR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D GLY* 3.2 21.9 - - - +
78D ALA* 4.8 4.7 - - + +
79D ILE* 3.9 44.0 - - + -
82D VAL* 4.2 20.7 - - + +
141E VAL* 3.1 36.8 + - + +
142E LEU* 3.2 24.0 + - + +
144E LEU* 1.3 79.9 - - + +
146E ALA* 1.3 61.9 + - - +
148E GLY* 3.1 10.9 + - - -
149E ARG 3.7 17.5 - - - +
150E THR* 4.8 1.3 - - - -
170E GLY* 2.9 37.5 + - - -
171E TYR* 5.4 1.6 - - - -
344E GLY* 5.1 4.5 - - - -
347E ILE* 5.6 0.4 - - - -
348E LEU* 5.5 6.3 - - + -
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLN* 3.0 41.7 + - - +
74D SER* 5.1 2.1 + - - -
75D GLY* 5.2 0.2 - - - -
142E LEU 2.9 12.1 + - - +
143E SER* 3.1 10.3 + - - +
145E TYR* 1.3 76.7 - - - +
147E SER* 1.3 57.9 + - - +
148E GLY 3.2 1.9 + - - -
340E SER* 3.7 27.1 - - - +
343E ILE* 4.4 3.8 - - + -
344E GLY* 4.0 11.8 - - - +
347E ILE* 4.7 8.5 - - - -
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Residues in contact with SER 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLN* 5.3 0.2 - - - +
74D SER* 5.2 1.8 - - - -
96D ARG* 4.0 4.2 + - - -
143E SER 3.2 8.2 + - - -
144E LEU* 2.6 24.7 + - - -
146E ALA* 1.3 76.1 - - - +
148E GLY* 1.3 58.8 + - - +
149E ARG* 2.9 43.1 + - - +
300E VAL* 3.8 20.3 - - - +
332E ILE* 5.1 0.2 - - - -
334E PRO* 4.6 14.6 - - - -
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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