Contacts of the helix formed by residues 137 - 150 (chain G) in PDB entry 3MGO
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 ASP 137 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85G TYR* 2.8 36.5 + - - -
121G LYS* 5.1 7.7 + - - -
123G TYR* 4.6 1.1 - - - -
135G ALA* 4.2 0.4 - - - +
136G ALA* 1.3 82.9 - - + +
138G MET* 1.3 63.6 + - - +
139G ALA 4.0 3.4 - - - -
140G ALA* 3.2 22.0 + - - +
141G GLN* 3.0 30.1 + - - +
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Residues in contact with MET 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G ASP* 1.3 76.1 - - - +
139G ALA* 1.3 64.8 + - - +
141G GLN* 3.0 34.4 + - + +
142G THR* 3.5 7.8 + - - -
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Residues in contact with ALA 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G TYR* 3.9 29.0 - - + +
85G TYR* 3.6 36.3 - - + +
123G TYR* 3.1 13.2 + - - +
137G ASP* 3.4 1.6 + - - -
138G MET* 1.3 77.1 - - - +
140G ALA* 1.3 63.5 + - - +
142G THR* 3.1 24.2 + - - -
143G THR* 3.5 1.7 + - - -
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Residues in contact with ALA 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G TYR* 3.2 47.5 + - + +
124G ILE* 4.3 3.8 - - + +
135G ALA* 3.7 7.1 - - + +
136G ALA 3.7 9.4 - - - +
137G ASP* 3.2 21.2 + - - +
139G ALA* 1.3 79.0 - - - +
141G GLN* 1.3 57.4 + - - +
143G THR* 3.4 3.5 + - - -
144G LYS* 2.8 28.8 + - - +
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Residues in contact with GLN 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G ALA* 3.2 24.5 + - - +
137G ASP 3.0 17.3 + - - +
138G MET* 3.1 28.3 - - + +
140G ALA* 1.3 74.6 - - - +
142G THR* 1.3 66.7 + - - +
144G LYS* 3.0 15.8 + - - +
145G HIS* 2.8 46.4 + - + +
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Residues in contact with THR 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G TYR* 3.9 29.9 - - + +
138G MET 3.5 6.8 + - - -
139G ALA* 3.1 14.1 + - - -
141G GLN* 1.3 78.8 - - - +
143G THR* 1.3 62.1 + - - +
145G HIS* 3.3 10.3 + - - +
146G LYS* 3.0 27.8 + - - +
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Residues in contact with THR 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G TYR* 3.8 2.1 - - - -
123G TYR* 2.8 28.7 + - + -
124G ILE* 4.1 7.9 - - + -
139G ALA 3.5 0.7 + - - -
140G ALA 3.4 7.7 + - - -
141G GLN 3.2 0.2 - - - -
142G THR* 1.3 76.6 - - - +
144G LYS* 1.3 59.1 + - - +
146G LYS* 3.1 4.7 + - - +
147G TRP* 2.8 68.6 + - + +
9I ILE* 3.0 36.4 + - + +
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Residues in contact with LYS 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G ILE* 3.9 13.9 - - + +
132G SER* 6.2 0.4 - - - -
133G TRP* 3.4 41.8 - - + +
135G ALA* 3.8 12.3 - - + +
140G ALA 2.8 15.4 + - - +
141G GLN* 3.2 28.7 - - - +
143G THR* 1.3 76.6 - - - +
145G HIS* 1.3 65.4 + - + +
147G TRP* 3.5 2.9 + - - +
148G GLU* 2.7 65.4 + - - +
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Residues in contact with HIS 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G GLN* 2.8 48.6 + - + +
142G THR* 3.7 9.2 - - - +
144G LYS* 1.3 79.0 - - + +
146G LYS* 1.3 67.0 + - - +
148G GLU* 3.3 19.9 + - - +
149G ALA* 3.0 25.3 + - - +
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Residues in contact with LYS 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G THR* 4.9 2.8 - - - +
84G TYR* 3.3 14.4 + - - -
142G THR* 3.0 19.1 + - - +
143G THR 3.3 7.9 - - - +
145G HIS* 1.3 77.2 - - - +
147G TRP* 1.3 66.6 + - + +
149G ALA* 3.5 6.4 + - - +
150G ALA* 3.3 22.1 + - + +
7I THR* 5.2 7.2 - - + -
8I TYR* 3.5 25.0 + - + +
9I ILE 3.2 26.6 + - - +
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Residues in contact with TRP 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G HIS* 4.2 9.2 - - - -
116G TYR* 3.5 28.7 - + - -
124G ILE* 3.7 21.1 - - + -
133G TRP* 3.5 47.8 - + - +
143G THR* 2.8 28.5 + - + +
144G LYS* 4.0 3.6 - - - +
146G LYS* 1.3 81.1 - - + +
148G GLU* 1.3 64.9 + - - +
150G ALA 3.4 0.5 + - - -
151G HIS 3.1 3.1 + - - -
152G VAL* 2.9 55.0 + - + +
153G ALA 4.6 0.7 + - - -
7I THR* 4.0 25.5 - - + -
8I TYR 2.9 22.9 + - - -
9I ILE* 3.6 28.5 - - + -
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Residues in contact with GLU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G ARG 6.1 0.7 - - - +
132G SER* 6.0 0.7 - - - -
133G TRP* 4.2 18.6 + - + +
144G LYS* 2.7 56.2 + - - +
145G HIS* 3.5 23.8 + - - +
147G TRP* 1.3 76.8 - - - +
149G ALA* 1.3 57.9 + - - +
151G HIS* 3.0 28.6 + - - +
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Residues in contact with ALA 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G HIS 3.0 16.9 + - - +
146G LYS* 3.8 6.5 - - - +
148G GLU* 1.3 76.2 - - - +
150G ALA* 1.3 57.8 + - - +
151G HIS* 3.2 16.8 + - - -
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Residues in contact with ALA 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G LYS* 3.3 15.0 + - + +
147G TRP 3.4 0.2 + - - -
148G GLU 3.2 0.8 - - - -
149G ALA* 1.3 77.8 - - - +
151G HIS* 1.3 71.8 + - - +
152G VAL* 3.2 16.5 + - + +
155G GLN* 3.4 12.5 - - - +
7I THR* 4.8 11.4 - - + +
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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