Contacts of the helix formed by residues 135 - 141 (chain A) in PDB entry 3N51
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 GLU 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLY 4.6 0.7 - - - +
134A GLY* 1.3 74.4 - - - -
136A LEU* 1.3 68.0 + - - +
137A PHE* 3.3 3.8 - - + +
138A ASP* 3.2 31.9 + - - +
139A GLU* 3.5 8.7 + - - +
177A PRO 4.6 6.2 - - - +
178A GLU* 3.9 22.4 - - - +
180A LEU 3.5 7.4 - - - +
181A LEU* 4.0 6.1 - - + -
182A LEU* 4.4 0.7 - - - +
334A GLN* 4.2 4.8 + - - +
338A LYS* 2.9 34.2 + - - -
701A BK3 2.6 47.8 + - - -
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Residues in contact with LEU 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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134A GLY 3.7 1.0 + - - -
135A GLU* 1.3 72.0 - - - +
137A PHE* 1.3 81.5 + - + +
139A GLU* 3.0 19.5 + - - +
140A ILE* 3.0 31.2 + - + +
143A ARG* 4.9 1.3 - - - +
154A ILE* 3.7 40.4 - - + -
177A PRO 4.6 1.5 + - - +
180A LEU* 2.8 45.0 + - + +
182A LEU* 3.9 26.9 - - + +
191A ILE* 4.2 13.5 - - + -
239A ILE* 5.5 0.4 - - + -
243A LEU* 4.8 0.7 - - + -
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Residues in contact with PHE 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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135A GLU* 3.3 3.1 - - + +
136A LEU* 1.3 96.9 - - + +
138A ASP* 1.3 57.3 + - - +
139A GLU 3.0 0.2 - - - -
140A ILE* 3.1 9.3 + - + +
141A ILE* 3.0 35.2 + - + +
177A PRO* 3.6 43.4 + - + -
217A TYR* 4.6 0.4 - - - -
239A ILE* 4.4 12.8 - - + -
242A ILE* 3.9 30.7 - - + -
243A LEU* 3.8 24.2 - - + -
330A ILE* 4.0 19.3 - - + -
333A PHE* 4.4 11.9 - + - -
334A GLN* 3.4 34.5 - - + +
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Residues in contact with ASP 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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134A GLY* 6.0 0.7 - - - -
135A GLU* 3.2 36.1 + - + +
137A PHE* 1.3 75.7 - - - +
139A GLU* 1.3 59.6 + - - +
141A ILE* 3.4 23.7 - - + +
142A SER* 4.4 4.2 + - - -
185A LYS* 4.2 17.6 + - - +
334A GLN* 2.9 27.1 + - - +
338A LYS* 3.7 15.0 - - - +
449A MET* 6.2 0.3 - - - +
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Residues in contact with GLU 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 GLU 3.5 2.9 + - - +
136A LEU* 3.0 11.5 + - - +
138A ASP* 1.3 78.4 - - - +
140A ILE* 1.3 67.4 + - - +
141A ILE 3.2 0.2 - - - -
142A SER* 2.7 31.0 + - - +
143A ARG* 2.7 51.2 + - - +
182A LEU* 3.5 26.4 - - + +
185A LYS* 4.3 17.9 - - + +
186A SER* 3.9 17.8 - - - +
187A LYS* 3.7 18.3 + - - +
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Residues in contact with ILE 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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136A LEU* 3.0 37.2 + - + +
137A PHE* 3.1 15.0 + - + +
139A GLU* 1.3 76.2 - - - +
141A ILE* 1.3 56.9 + - - +
142A SER 3.1 0.2 - - - -
143A ARG* 3.0 51.7 + - - +
146A PHE* 4.1 22.7 - - + -
154A ILE* 3.8 11.4 - - + -
243A LEU* 3.7 25.6 - - + -
327A ILE* 4.7 7.0 - - + +
330A ILE* 4.2 26.7 - - + -
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Residues in contact with ILE 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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137A PHE* 3.0 18.6 + - - +
138A ASP* 3.4 26.7 - - - +
140A ILE* 1.3 75.8 - - - +
142A SER* 1.3 56.3 + - - +
143A ARG 3.4 0.7 - - - -
327A ILE* 5.3 0.7 - - - -
330A ILE* 4.0 14.1 - - + -
331A ARG* 2.8 59.2 + - + +
334A GLN* 3.7 31.4 - - + -
335A GLY* 6.0 1.6 - - - +
449A MET* 4.7 27.8 - - + -
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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