Contacts of the helix formed by residues 134 - 143 (chain G) in PDB entry 6CM9
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 MET 134 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100G HIS* 3.6 39.0 - - + +
101G LEU* 4.9 6.3 - - + -
103G MET* 3.8 16.8 - - + -
104G THR* 3.9 26.9 - - - +
107G ILE* 3.8 22.0 - - + -
126G LEU* 3.8 27.6 - - + -
129G MET* 4.6 1.1 - - - +
130G GLY* 3.9 6.7 - - - -
131G SER* 3.4 21.6 + - - +
133G GLU* 1.3 77.9 - - - +
135G CYS* 1.3 62.8 + - - +
137G ASP* 3.2 4.8 + - - -
138G LEU* 3.1 31.3 + - + +
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Residues in contact with CYS 135 (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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126G LEU* 5.0 4.5 - - - -
130G GLY* 4.7 2.7 - - - -
131G SER 3.2 22.6 + - - +
133G GLU 3.2 1.2 - - - -
134G MET* 1.3 80.8 - - - +
136G ARG* 1.3 57.0 - - - +
138G LEU* 4.3 5.6 - - - +
139G ALA* 2.9 34.1 + - - +
163G HIS* 4.3 15.3 - - - -
164G VAL* 3.6 40.2 - - + -
167G LYS* 4.6 5.2 - - - -
168G VAL* 4.0 16.4 - - + -
171G LEU* 4.2 2.9 - - + +
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Residues in contact with ARG 136 (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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132G SER 4.2 12.4 + - - +
133G GLU* 3.8 25.7 + - - +
134G MET 3.3 0.6 - - - -
135G CYS* 1.3 76.9 - - - +
137G ASP* 1.3 66.6 + - - +
139G ALA* 4.7 2.7 + - - +
168G VAL* 3.5 33.3 - - + +
170G GLU* 2.4 36.9 + - - +
171G LEU* 5.1 13.1 - - + +
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Residues in contact with ASP 137 (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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101G LEU* 5.9 0.7 - - - +
104G THR* 4.1 16.6 - - + +
108G LYS* 3.5 21.0 + - - +
133G GLU 3.9 8.2 + - - +
134G MET 3.2 8.5 + - - +
135G CYS 3.1 0.2 - - - -
136G ARG* 1.3 85.2 - - - +
138G LEU* 1.3 59.1 + - - +
139G ALA 3.8 0.7 - - - -
140G GLY 5.2 0.7 - - - -
141G GLU* 3.3 14.6 - - - +
49H ILE* 3.8 27.7 - - + +
73H LYS* 3.6 22.3 + - - -
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Residues in contact with LEU 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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104G THR* 3.7 33.7 - - + +
107G ILE* 4.1 10.5 - - + -
108G LYS* 4.5 13.9 - - + -
111G LEU* 3.7 30.3 - - + -
126G LEU* 3.7 30.5 - - + -
134G MET* 3.1 28.3 + - + +
135G CYS* 3.2 4.4 + - - +
137G ASP* 1.3 85.9 - - - +
139G ALA* 1.3 59.0 + - - +
140G GLY 3.2 2.5 - - - -
141G GLU* 3.1 9.6 + - + +
142G VAL* 2.9 29.4 + - - +
164G VAL* 5.7 0.7 - - + -
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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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135G CYS* 2.9 17.6 + - - +
136G ARG* 4.7 1.7 - - - -
137G ASP 3.8 0.4 - - - -
138G LEU* 1.3 78.5 - - - +
140G GLY* 1.3 61.6 + - - +
142G VAL* 4.1 7.3 - - - +
143G GLU* 3.3 27.2 + - - +
164G VAL* 4.5 6.5 - - + -
171G LEU* 3.7 32.1 - - + -
174G MET* 4.2 8.2 - - - +
175G PHE* 4.2 13.6 - - + -
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Residues in contact with GLY 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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136G ARG 5.8 0.6 + - - -
137G ASP 5.2 1.0 - - - -
138G LEU 3.2 1.4 - - - +
139G ALA* 1.3 79.3 - - - +
141G GLU* 1.3 65.9 + - - +
143G GLU* 3.7 18.2 - - - +
144G LYS* 3.9 12.0 + - - +
174G MET* 4.3 15.3 - - - +
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Residues in contact with GLU 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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108G LYS* 4.0 30.6 + - + +
111G LEU* 4.1 19.5 - - + +
112G ASN* 4.6 14.8 - - - +
137G ASP 3.3 21.0 - - - +
138G LEU* 3.1 10.2 + - + +
140G GLY* 1.3 81.5 + - - +
142G VAL* 1.3 65.0 + - - +
143G GLU 3.4 0.2 - - - -
144G LYS* 3.9 16.9 + - + +
145G LEU* 3.3 26.7 + - - +
46H ILE* 5.2 6.2 - - - +
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Residues in contact with VAL 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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111G LEU* 4.5 4.3 - - + -
123G LEU* 4.5 7.9 - - + -
126G LEU* 3.7 26.7 - - + -
138G LEU 2.9 21.7 + - - +
139G ALA* 3.5 7.2 + - - +
141G GLU* 1.3 78.1 - - - +
143G GLU* 1.3 58.4 + - - +
144G LYS 3.2 0.2 - - - -
145G LEU* 2.9 23.5 + - - +
146G LEU* 3.0 10.2 + - - +
157G ALA* 3.8 26.0 - - - +
160G CYS* 3.8 14.8 - - + -
161G ALA* 4.1 19.3 - - + +
164G VAL* 4.9 4.7 - - + -
175G PHE* 4.7 4.3 - - + -
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Residues in contact with GLU 143 (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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139G ALA 3.3 15.7 + - - +
140G GLY* 3.7 12.8 - - - +
142G VAL* 1.3 78.1 - - - +
144G LYS* 1.3 63.6 + - - +
145G LEU 3.3 0.2 - - - -
146G LEU* 3.1 23.8 + - + +
147G LYS* 3.1 31.7 + - - +
174G MET* 4.2 27.7 - - + +
175G PHE* 3.6 26.7 - - + -
178G ALA* 4.5 4.8 - - + +
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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