Contacts of the helix formed by residues 164 - 179 (chain A) in PDB entry 3NRN
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A GLU* 6.0 3.6 - - - -
128A ILE 3.8 9.9 - - - -
129A PRO* 4.6 1.3 - - - -
130A ALA* 3.8 5.0 - - - +
162A ASP 5.5 1.3 - - - +
163A LEU* 1.3 78.0 - - - +
165A ALA* 1.3 64.7 + - - +
166A LEU* 3.6 9.3 + - - +
167A GLU* 3.0 27.7 + - + +
168A LEU 3.1 17.3 + - - -
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Residues in contact with ALA 165 (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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124A PRO* 3.8 9.6 - - + +
126A GLU* 4.5 7.2 + - + +
127A GLU* 6.0 0.2 - - - +
128A ILE* 2.9 25.2 + - + +
130A ALA* 3.9 9.4 - - - +
133A TRP* 3.4 44.4 - - + -
164A THR* 1.3 73.6 - - - +
166A LEU* 1.3 57.8 + - - +
168A LEU* 3.5 1.7 + - - +
169A ALA* 2.9 30.1 + - - +
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Residues in contact with LEU 166 (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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123A LEU* 3.8 28.9 - - + -
124A PRO* 3.9 21.2 - - - +
126A GLU 4.8 5.8 + - - +
164A THR* 3.1 8.0 + - - +
165A ALA* 1.3 77.3 - - - +
167A GLU* 1.3 61.0 + - - +
169A ALA* 3.2 1.6 + - - +
170A LYS* 2.9 68.4 + - + +
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Residues in contact with GLU 167 (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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163A LEU* 3.7 18.2 - - + -
164A THR* 3.0 28.6 + - + +
166A LEU* 1.3 76.9 - - - +
168A LEU* 1.3 63.5 + - - +
170A LYS* 3.2 4.3 + - - +
171A GLU* 2.5 49.6 + - - +
384A PRO* 3.5 15.5 - - - +
385A GLY* 3.1 28.8 + - - -
386A GLY 4.7 1.0 + - - +
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Residues in contact with LEU 168 (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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130A ALA* 3.9 20.0 - - + -
133A TRP* 3.8 21.3 - - - +
134A ILE* 4.0 18.2 - - + -
148A LEU* 4.7 9.6 - - + -
151A PHE* 4.1 31.0 - - + -
160A LEU* 4.2 11.4 - - + -
163A LEU* 4.6 15.6 - - + +
164A THR 3.1 12.8 + - - +
165A ALA 3.8 3.4 - - - +
167A GLU* 1.3 79.1 - - - +
169A ALA* 1.3 58.8 + - - +
171A GLU* 3.2 5.9 + - - +
172A ILE* 2.8 49.1 + - + +
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Residues in contact with ALA 169 (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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118A ILE* 3.6 12.9 - - + +
123A LEU* 3.7 11.7 - - + -
124A PRO* 3.5 28.5 - - + -
133A TRP* 4.3 7.6 - - + -
165A ALA 2.9 19.4 + - - +
166A LEU 3.5 5.2 - - - +
167A GLU 3.2 0.2 - - - -
168A LEU* 1.3 77.0 - - - +
170A LYS* 1.3 58.0 + - - +
172A ILE* 3.1 11.1 + - - +
173A ARG* 2.8 27.5 + - - +
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Residues in contact with LYS 170 (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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123A LEU* 3.8 22.9 - - + -
166A LEU* 2.9 52.2 + - + +
167A GLU* 3.6 5.2 - - - +
169A ALA* 1.3 77.9 - - - +
171A GLU* 1.3 57.0 + - - +
173A ARG* 3.2 23.8 + - - +
174A ALA* 3.0 26.7 + - - +
384A PRO* 3.8 35.5 - - + +
385A GLY* 3.8 16.3 - - - +
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Residues in contact with GLU 171 (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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151A PHE* 3.6 26.1 - - + -
156A ASP* 2.7 40.1 - - - +
163A LEU* 4.2 2.8 - - - +
167A GLU* 2.5 50.5 + - - +
168A LEU* 3.7 7.2 - - - +
170A LYS* 1.3 74.3 - - - +
172A ILE* 1.3 66.1 + - - +
174A ALA* 3.4 3.8 + - - +
175A ALA* 3.1 22.0 + - - +
385A GLY* 3.7 19.7 - - - +
386A GLY 5.7 0.8 - - - +
387A ILE* 3.9 21.1 - - + +
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Residues in contact with ILE 172 (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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114A LEU* 5.8 3.1 - - + -
115A LEU* 3.9 23.1 - - + -
118A ILE* 3.3 33.9 - - + -
133A TRP* 5.1 4.7 - - + -
134A ILE* 5.4 5.2 - - + -
148A LEU* 6.0 4.0 - - + -
151A PHE* 5.8 2.7 - - + -
168A LEU* 2.8 50.2 + - + +
169A ALA* 3.3 8.1 - - - +
171A GLU* 1.3 75.8 - - - +
173A ARG* 1.3 64.4 + - - +
175A ALA* 3.1 8.5 + - + +
176A LEU* 3.0 26.8 + - + +
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Residues in contact with ARG 173 (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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118A ILE* 3.7 30.9 - - + +
121A ASN* 3.7 33.5 + - - +
123A LEU* 3.7 27.8 - - + +
169A ALA 2.8 13.9 + - - +
170A LYS* 3.4 24.0 + - - +
172A ILE* 1.3 77.4 - - - +
174A ALA* 1.3 57.5 + - - +
176A LEU* 3.0 7.2 + - + +
177A ARG* 2.8 60.5 + - + +
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Residues in contact with ALA 174 (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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59A HIS* 3.6 13.3 - - - +
170A LYS 3.0 13.8 + - - +
171A GLU 3.6 8.7 - - - +
172A ILE 3.3 0.4 - - - -
173A ARG* 1.3 76.8 - - - +
175A ALA* 1.3 58.0 + - - +
177A ARG* 4.5 3.6 - - - -
178A TRP* 2.8 65.3 + - + +
385A GLY 3.9 14.4 - - - +
387A ILE* 5.4 0.2 - - + -
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Residues in contact with ALA 175 (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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59A HIS* 3.8 13.2 - - + -
84A LYS* 4.9 2.4 - - - -
151A PHE* 6.1 4.7 - - + -
171A GLU 3.1 14.5 + - - +
172A ILE* 3.1 11.2 + - - +
174A ALA* 1.3 76.1 - - - +
176A LEU* 1.3 61.4 + - + +
179A GLY* 2.9 34.3 + - - +
387A ILE* 6.2 0.7 - - + -
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Residues in contact with LEU 176 (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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115A LEU* 3.5 43.3 - - + +
118A ILE* 4.0 14.1 - - + -
119A ARG* 3.5 57.8 + - + +
172A ILE* 3.0 24.1 + - + +
173A ARG* 3.0 7.3 + - + +
175A ALA* 1.3 79.7 - - + +
177A ARG* 1.3 68.6 + - - +
179A GLY* 4.4 1.4 + - - -
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Residues in contact with ARG 177 (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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62A ASP* 5.3 0.7 - - - +
118A ILE 4.4 3.6 + - - -
119A ARG* 2.9 53.3 + - - +
121A ASN* 4.7 6.1 - - - +
173A ARG* 2.8 39.8 + - + +
174A ALA* 3.9 4.3 - - - +
176A LEU* 1.3 82.9 + - - +
178A TRP* 1.3 78.9 + - + +
179A GLY 3.9 0.2 + - - -
411A TRP* 3.3 57.5 - - + +
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Residues in contact with TRP 178 (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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59A HIS* 3.5 41.6 - + + +
62A ASP* 3.1 52.8 + - + +
63A GLY* 3.9 2.9 - - - -
64A PRO* 3.6 29.2 - - + -
174A ALA* 2.8 38.2 + - + +
177A ARG* 1.3 88.3 - - + +
179A GLY* 1.3 62.2 + - - +
385A GLY 5.3 3.6 - - - -
386A GLY* 5.8 4.5 - - - -
387A ILE 6.3 0.2 - - - -
390A ASP* 5.5 1.1 - - + -
394A LEU* 5.2 6.5 - - + -
411A TRP* 3.1 45.7 + + - +
412A TYR* 3.5 23.7 - - - -
413A LEU 5.5 3.4 - - - -
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Residues in contact with GLY 179 (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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58A PRO 4.3 0.2 - - - +
59A HIS* 3.0 23.9 + - - -
62A ASP* 5.0 0.9 - - - -
84A LYS* 3.4 22.9 - - - -
175A ALA* 2.9 27.3 + - - +
176A LEU 4.4 1.3 + - - -
177A ARG 3.5 2.0 - - - -
178A TRP* 1.3 79.1 - - - +
180A GLY* 1.3 58.4 + - - -
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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