Contacts of the helix formed by residues 129 - 138 (chain N) in PDB entry 1MVW
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 THR 129 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122N THR* 4.1 8.1 - - - +
125N GLY 4.0 1.9 + - - -
126N GLY* 2.8 31.3 + - - +
127N ARG 3.4 1.6 - - - -
128N PHE* 1.4 82.2 - - - +
130N PRO* 1.4 88.0 - - - +
131N GLU* 3.7 5.2 + - - +
132N GLU* 3.0 24.9 + - - +
133N ILE* 3.0 6.6 + - - +
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Residues in contact with PRO 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122N THR* 3.9 16.5 - - + +
129N THR* 1.4 85.0 - - - +
131N GLU* 1.4 50.3 - - - +
132N GLU 2.2 6.0 + - - -
133N ILE* 2.0 56.9 + - + -
134N LYS* 4.3 15.3 - - + +
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Residues in contact with GLU 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N THR* 3.7 5.2 + - - +
130N PRO* 1.4 74.5 - - - +
132N GLU* 1.3 66.0 + - + +
133N ILE 3.1 0.4 - - - -
134N LYS* 3.2 26.2 + - + +
135N ASN* 3.2 35.6 + - - +
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Residues in contact with GLU 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821M ARG* 5.2 8.1 + - - +
121N LEU* 5.9 1.1 - - + -
126N GLY 3.5 3.0 - - - +
127N ARG* 3.3 28.0 - - - +
128N PHE* 5.7 0.2 - - - -
129N THR* 3.0 35.6 + - - +
130N PRO 2.2 12.0 + - - +
131N GLU* 1.3 79.3 - - + +
133N ILE* 1.3 55.8 + - + +
135N ASN* 3.3 14.9 + - - +
136N MET* 2.9 42.8 + - + +
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Residues in contact with ILE 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N GLU* 3.5 46.0 - - + +
121N LEU* 4.0 16.6 - - + -
122N THR* 3.3 15.5 - - - +
128N PHE 3.0 22.7 - - - +
129N THR 3.0 14.6 - - - +
130N PRO* 2.0 35.0 + - + +
132N GLU* 1.3 65.5 - - - +
134N LYS* 1.3 58.7 + - + +
136N MET* 3.2 10.2 + - + +
137N TRP* 3.1 37.7 + - + +
145N ALA 5.8 0.2 - - - +
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Residues in contact with LYS 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130N PRO* 4.7 9.3 - - + +
131N GLU* 3.2 33.1 + - + +
133N ILE* 1.3 76.7 - - + +
135N ASN* 1.3 61.9 + - - +
137N TRP* 3.3 9.6 + - - +
138N ALA* 3.0 27.9 + - - +
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Residues in contact with ASN 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824M MET* 5.0 17.7 - - + +
827M MLY 4.9 12.4 - - - -
131N GLU* 3.2 30.1 + - - +
132N GLU* 3.3 17.3 + - - +
134N LYS* 1.3 79.2 - - - +
136N MET* 1.3 65.4 + - + +
138N ALA* 3.2 20.3 + - - +
139N ALA 3.8 3.8 + - - -
140N PHE* 5.7 0.3 - - - -
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Residues in contact with MET 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820M VAL* 2.7 44.4 - - + -
823M PHE* 6.3 0.2 - - - -
824M MET* 4.1 27.1 - - + -
121N LEU* 5.2 10.5 - - + -
127N ARG 5.8 3.1 - - - +
132N GLU* 2.9 34.1 + - + +
133N ILE* 3.2 12.5 + - + +
135N ASN* 1.3 77.4 - - - +
137N TRP* 1.3 60.4 + - + +
138N ALA 3.4 0.2 + - - -
140N PHE* 2.9 48.6 + - + +
145N ALA* 4.2 4.4 - - - +
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Residues in contact with TRP 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114N LYS* 3.3 18.2 - - + -
118N GLU* 3.1 28.3 + - - +
133N ILE* 3.1 28.3 + - + +
134N LYS* 3.3 10.3 + - - +
136N MET* 1.3 79.1 - - + +
138N ALA* 1.3 59.8 + - - +
139N ALA 3.4 1.7 + - - -
140N PHE 3.5 12.0 - - - +
141N PRO* 2.8 13.9 - - - +
142N PRO* 1.5 41.3 - - + -
145N ALA* 1.2 85.3 + - + +
146N GLY* 0.8 126.1 - - - -
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Residues in contact with ALA 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N LYS 3.0 16.6 + - - +
135N ASN* 3.4 13.5 - - - +
136N MET 3.2 1.4 - - - -
137N TRP* 1.3 77.3 - - - +
139N ALA* 1.2 65.6 + - + +
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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