Contacts of the helix formed by residues 134 - 143 (chain G) in PDB entry 5MGS
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 134 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132G ILE* 3.4 8.8 - - - +
133G ARG* 1.3 98.2 + - - +
135G LYS* 1.3 59.7 + - - +
136G ASP* 3.3 12.5 + - - +
137G GLU 3.0 20.1 + - - -
138G LEU* 2.9 23.8 + - - -
177G ASP* 3.6 20.9 - - - +
178G LEU* 5.5 2.5 - - - -
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Residues in contact with LYS 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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134G ASP* 1.3 73.9 - - - +
136G ASP* 1.3 58.0 + - - +
138G LEU* 3.3 10.4 + - + +
139G ILE* 2.8 45.8 + - + +
176G ASN 5.1 0.9 - - - -
177G ASP* 3.3 51.6 + - + +
178G LEU* 6.0 0.2 - - - -
179G GLU* 4.6 18.6 + - - -
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Residues in contact with ASP 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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102G ARG* 4.2 12.0 + - - -
133G ARG* 5.7 1.6 + - - -
134G ASP* 3.2 12.6 + - - +
135G LYS* 1.3 80.5 - - - +
137G GLU* 1.3 63.3 + - - +
139G ILE* 4.0 6.4 - - - +
140G HIS* 2.8 56.9 + - - -
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Residues in contact with GLU 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* 5.8 3.7 - - + +
102G ARG* 6.2 2.0 - - - +
104G LYS* 2.6 37.3 + - - +
130G LEU* 4.7 2.5 - - - +
131G LEU 3.4 9.3 - - - +
132G ILE* 3.3 8.0 - - + -
133G ARG* 2.8 62.8 + - + +
134G ASP* 3.0 20.2 + - - +
136G ASP* 1.3 75.3 + - - +
138G LEU* 1.3 65.6 + - - +
140G HIS* 3.3 4.8 + - - +
141G THR* 2.8 37.0 + - - +
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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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132G ILE* 3.5 32.0 - - + +
134G ASP 2.9 12.0 + - - +
135G LYS* 3.3 13.0 + - + +
137G GLU* 1.3 76.3 - - - +
139G ILE* 1.3 55.8 + - + +
141G THR* 3.2 4.7 + - - -
142G GLN* 2.7 66.6 + - + +
177G ASP 4.4 11.2 - - - +
178G LEU* 4.1 15.9 - - + +
192G ILE* 4.0 18.2 - - + -
197G VAL* 3.9 21.8 - - + -
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Residues in contact with ILE 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 LYS* 2.8 34.6 + - + +
136G ASP* 4.0 7.0 - - - +
138G LEU* 1.3 75.7 - - + +
140G HIS* 1.3 67.2 + - + +
142G GLN* 3.2 16.8 + - - +
143G ASN* 2.9 42.4 + - - +
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Residues in contact with HIS 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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101G LEU* 3.7 19.8 - - + +
102G ARG* 3.1 48.5 + - - +
136G ASP* 2.8 49.6 + - - +
137G GLU* 4.0 4.5 - - + +
139G ILE* 1.3 84.7 - - + +
141G THR* 1.3 60.4 + - - +
143G ASN* 3.4 34.4 + - - +
144G LEU* 3.9 5.7 + - - +
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Residues in contact with THR 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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101G LEU* 3.7 15.7 - - - +
106G LEU* 4.1 19.9 - - + +
108G PHE* 4.2 10.9 - - + -
130G LEU* 3.8 30.2 - - + +
132G ILE* 5.3 2.1 - - - +
137G GLU* 2.8 29.3 + - - +
138G LEU* 3.7 5.1 - - - -
140G HIS* 1.3 74.6 - - - +
142G GLN* 1.3 68.4 + - - +
144G LEU* 3.0 20.9 + - - +
145G ILE* 3.8 5.9 + - - +
192G ILE* 4.2 12.3 - - + -
209G ILE* 4.6 0.4 - - + -
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Residues in contact with GLN 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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138G LEU* 2.7 54.8 + - + +
139G ILE* 3.4 18.4 - - - +
141G THR* 1.3 74.7 - - - +
143G ASN* 1.4 56.6 + - - +
145G ILE* 2.9 36.8 + - + +
192G ILE* 4.9 2.9 - - + -
193G SER 3.0 27.3 + - - +
194G GLN* 3.3 23.0 - - - +
195G THR 3.5 22.4 + - - -
196G SER* 3.5 8.3 + - - +
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Residues in contact with ASN 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 ILE* 2.9 28.3 + - - +
140G HIS* 3.5 36.7 - - - +
141G THR 3.1 0.4 - - - -
142G GLN* 1.4 75.9 - - - +
144G LEU* 1.3 64.6 + - + +
145G ILE 3.5 4.2 + - - +
146G ARG* 5.6 1.4 - - - +
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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