Contacts of the helix formed by residues 135 - 145 (chain B) in PDB entry 5NET
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 LEU 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B TYR* 4.2 13.5 - - + -
131B THR 4.8 4.0 - - - +
132B ILE* 2.8 46.2 + - + +
134B GLU* 1.3 71.7 - - - +
136B GLY* 1.3 57.1 + - - +
137B SER 3.1 2.0 - - - -
138B ARG* 2.7 12.1 + - - +
139B LEU* 2.7 44.5 + - + -
203B PHE* 4.8 6.1 - - + -
204B ASN* 2.9 1.4 + - - -
340B ILE* 4.2 27.1 - - + -
341B LEU* 3.7 41.5 - - + +
344B ILE* 5.4 0.4 - - + -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 1.3 75.9 - - - +
137B SER* 1.3 55.8 + - - +
139B LEU* 3.8 3.2 - - - +
140B SER* 3.0 30.0 + - - -
152B LEU* 4.0 13.9 - - - +
200B ALA* 3.7 8.1 - - - +
203B PHE* 3.5 29.5 - - - -
204B ASN* 2.9 12.6 + - - -
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLU* 3.6 34.1 + - - +
136B GLY* 1.3 76.2 - - - +
138B ARG* 1.3 67.2 + - - +
140B SER* 3.9 1.2 - - - -
141B LYS* 3.0 29.8 + - - +
200B ALA* 4.4 10.5 - - - -
201B GLU* 5.7 4.9 - - - -
204B ASN* 3.3 18.0 - - - +
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1721 ARG* 4.9 12.9 - - - +
131B THR* 4.9 14.3 + - - +
134B GLU* 3.1 49.3 + - - +
135B LEU* 2.7 15.4 + - - +
137B SER* 1.3 82.0 + - - +
139B LEU* 1.3 59.1 + - - +
141B LYS* 3.7 6.0 + - - +
142B GLU* 3.4 28.2 + - - +
341B LEU* 3.6 29.9 - - + +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 4.0 10.5 - - + -
117B TYR* 5.7 2.0 - - + -
135B LEU* 2.7 29.2 + - + +
136B GLY* 3.9 6.5 - - - +
138B ARG* 1.3 72.4 - - - +
140B SER* 1.3 60.1 + - - +
141B LYS 3.3 0.2 + - - -
142B GLU* 3.3 3.1 + - - +
143B MET* 3.0 43.8 + - + +
150B PHE* 3.8 15.0 - - + -
152B LEU* 3.8 20.9 - - + -
203B PHE* 6.0 1.6 - - + -
341B LEU* 3.9 20.1 - - + +
344B ILE* 3.9 42.4 - - + -
345B ILE* 4.4 7.2 - - + -
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLY 3.0 19.6 + - - -
137B SER 4.1 2.0 - - - -
139B LEU* 1.3 76.6 - - - +
141B LYS* 1.3 51.5 + - - +
143B MET* 3.8 0.5 - - - +
144B SER* 2.4 40.2 + - - -
150B PHE* 3.6 30.8 + - - +
152B LEU* 4.2 2.0 - - - +
198B ASN 5.2 2.1 + - - -
200B ALA* 3.6 21.5 - - - +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B SER 3.0 18.7 + - - +
138B ARG* 3.7 9.9 - - - +
139B LEU 3.2 0.2 - - - -
140B SER* 1.3 77.8 - - - +
142B GLU* 1.3 72.3 + - - +
144B SER* 3.3 21.0 - - - +
145B LYS* 3.4 26.2 - - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ARG 3.4 16.6 + - - +
139B LEU 3.3 2.9 + - - +
141B LYS* 1.3 80.9 - - + +
143B MET* 1.3 63.6 + - - +
144B SER 3.2 1.8 - - - -
145B LYS* 3.3 41.9 + - - +
146B LEU* 3.7 14.8 - - - +
341B LEU* 4.4 7.0 - - + -
345B ILE* 3.6 28.5 - - + -
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Residues in contact with MET 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL* 4.4 9.6 - - + -
115B LEU* 6.1 0.2 - - + -
139B LEU* 3.0 30.4 + - + +
140B SER 4.0 0.7 - - - +
142B GLU* 1.3 76.9 - - - +
144B SER* 1.3 59.1 + - - +
145B LYS 3.3 0.2 - - - -
146B LEU* 3.1 20.3 + - + +
147B THR* 2.9 36.9 + - - +
150B PHE* 3.6 52.4 - - + +
245B LEU* 5.6 1.8 - - + -
344B ILE* 5.6 4.0 - - - -
345B ILE* 4.6 14.8 - - + -
348B TYR* 4.2 38.8 - - + -
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 1.0 100.2 + - - -
110B ASP* 3.2 5.7 - - - +
140B SER* 2.4 29.7 + - - -
141B LYS* 3.3 15.8 + - - +
142B GLU 3.2 0.4 - - - -
143B MET* 1.3 72.8 - - - +
145B LYS* 1.3 47.4 - - - +
147B THR 3.2 10.7 - - - +
150B PHE* 6.0 0.7 - - - -
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 2.2 30.3 + - - +
141B LYS* 3.4 33.6 - - - +
142B GLU* 3.3 46.2 + - - +
144B SER* 1.3 63.0 - - - +
146B LEU* 1.3 65.4 + - + +
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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