Contacts of the helix formed by residues 134 - 143 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.4 8.8 - - - +
133A ARG* 1.3 113.3 + - - +
135A LYS* 1.3 65.0 + - - +
136A ASP* 3.3 10.9 + - - +
137A GLU* 3.2 16.5 + - - +
138A LEU* 3.0 19.3 + - - +
177A ASP* 3.5 20.6 - - - +
178A LEU* 5.1 3.8 - - - -
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP* 1.3 75.9 - - - +
136A ASP* 1.3 56.9 + - - +
138A LEU* 3.3 13.2 + - + +
139A ILE* 2.9 56.7 + - + +
177A ASP* 3.0 39.2 + - - +
179A GLU* 4.5 16.5 + - - +
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Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ARG* 4.4 10.9 + - - -
134A ASP* 3.2 11.1 + - - +
135A LYS* 1.3 80.8 - - - +
137A GLU* 1.3 62.2 + - - +
139A ILE* 3.5 8.5 + - - +
140A HIS* 2.7 63.8 + - - -
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 5.7 3.7 - - + +
102A ARG* 6.1 3.4 - - - +
104A LYS* 2.7 42.2 + - - +
130A LEU* 4.7 2.9 - - - +
131A LEU 3.2 8.2 - - - +
132A ILE* 3.6 6.6 - - + -
133A ARG* 2.9 39.5 + - + +
134A ASP* 3.2 19.2 + - - +
136A ASP* 1.3 74.8 - - - +
138A LEU* 1.3 62.3 + - - +
140A HIS* 3.9 5.0 - - - +
141A THR* 2.6 42.5 + - - +
501A NAG 5.0 0.2 + - - -
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.6 33.0 - - + +
134A ASP 3.0 13.3 + - - +
135A LYS* 3.4 16.8 - - + +
137A GLU* 1.3 76.5 - - - +
139A ILE* 1.3 59.8 + - + +
141A THR* 3.2 3.9 + - - -
142A GLN* 2.9 62.6 + - + +
177A ASP 4.6 4.9 - - - +
178A LEU* 4.2 21.5 - - + +
192A ILE* 4.1 8.1 - - + -
197A VAL* 3.8 28.9 - - + -
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 2.9 54.9 + - + +
136A ASP* 3.9 9.4 - - - +
137A GLU 3.3 0.2 - - - -
138A LEU* 1.3 79.0 - - + +
140A HIS* 1.3 72.0 + - + +
142A GLN* 3.4 14.8 + - - +
143A ASN* 3.0 27.1 + - + +
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Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.7 27.6 - - + +
102A ARG* 4.1 36.9 + - - -
136A ASP* 2.7 55.6 + - - +
137A GLU* 4.0 5.4 - - + +
139A ILE* 1.3 87.0 - - + +
141A THR* 1.3 64.0 + - - +
143A ASN* 3.5 21.9 + - + +
144A LEU* 3.8 6.8 + - - +
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.6 16.9 - - - +
106A LEU* 4.2 18.1 - - + +
108A PHE* 4.4 9.8 - - + -
130A LEU* 3.9 28.9 - - + +
132A ILE* 5.4 1.2 - - - +
137A GLU* 2.6 32.3 + - - +
138A LEU* 3.6 5.6 - - - -
140A HIS* 1.3 74.8 - - - +
142A GLN* 1.3 60.2 + - - +
144A LEU* 2.9 27.3 + - - +
145A ILE* 3.8 6.1 + - - +
192A ILE* 4.2 14.4 - - + -
209A ILE* 4.6 0.9 - - + -
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Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 2.9 51.1 + - + +
139A ILE* 3.7 16.2 - - - +
141A THR* 1.3 73.0 - - - +
143A ASN* 1.3 58.4 + - - +
145A ILE* 2.9 36.6 + - - +
192A ILE* 4.7 6.3 - - + +
193A SER 3.0 25.0 + - - +
194A GLN* 3.3 23.5 - - - +
195A THR 3.5 5.1 + - - +
196A SER* 3.4 28.9 + - - +
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Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 6.2 1.0 - - - +
139A ILE* 3.0 14.4 + - + +
140A HIS* 3.6 19.3 + - + +
141A THR 3.2 0.6 - - - -
142A GLN* 1.3 77.7 - - - +
144A LEU* 1.3 66.3 + - - +
145A ILE 3.4 1.1 + - - +
146A ARG* 3.0 47.7 + - - +
194A GLN* 5.8 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