Contacts of the helix formed by residues 123 - 135 (chain D) in PDB entry 4F2N
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 PRO 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D PRO 3.3 9.9 - - - +
122D MET* 1.3 91.6 - - + +
124D LYS* 1.3 61.7 + - - +
125D THR* 3.3 3.1 - - - +
126D LEU* 3.2 4.1 + - + -
127D GLU* 3.0 23.6 + - - +
218D TRP 3.6 18.8 - - - +
219D GLU* 4.3 13.9 - - + -
222D CYS* 3.8 30.5 - - + -
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Residues in contact with LYS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D MET 3.7 1.0 + - - -
123D PRO* 1.3 69.9 - - - +
125D THR* 1.3 59.7 + - - +
127D GLU* 3.6 32.8 + - - +
128D ASN* 2.9 68.9 + - - +
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Residues in contact with THR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO* 3.3 2.1 - - - +
124D LYS* 1.3 77.6 - - - +
126D LEU* 1.3 62.1 + - - +
128D ASN* 3.6 7.9 + - - +
129D ALA* 3.2 21.7 + - - +
222D CYS* 4.1 13.7 - - - -
225D TYR* 4.4 13.9 - - + -
226D GLU* 3.9 25.6 + - + +
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D MET* 3.9 8.5 - - + -
123D PRO 3.2 8.7 + - - +
125D THR* 1.3 78.5 - - - +
127D GLU* 1.3 67.5 + - - +
129D ALA* 3.1 4.5 + - + +
130D ILE* 2.9 43.9 + - + +
168D LEU* 5.3 0.4 - - + -
187D ILE* 4.3 13.7 - - + -
218D TRP* 3.7 36.8 - - + +
221D VAL* 3.7 12.3 - - + -
222D CYS* 3.8 26.6 - - + +
225D TYR* 4.2 28.7 - - + -
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D MET* 3.6 27.3 - - + +
123D PRO 3.0 15.2 + - - +
124D LYS* 3.6 35.1 + - - +
126D LEU* 1.3 77.7 - - - +
128D ASN* 1.3 59.4 + - - +
130D ILE* 3.9 1.4 - - - +
131D ALA* 2.9 31.9 + - + +
137D VAL* 3.9 18.8 - - + +
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Residues in contact with ASN 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LYS* 2.9 52.4 + - - +
125D THR* 3.8 7.3 - - - +
127D GLU* 1.3 77.1 - - - +
129D ALA* 1.3 57.1 - - - +
131D ALA* 3.4 5.0 + - - +
132D LYS* 2.8 33.2 + - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR 3.2 13.5 + - - +
126D LEU* 3.1 7.7 + - + +
128D ASN* 1.3 80.5 - - - +
130D ILE* 1.3 60.3 + - - +
132D LYS* 3.4 14.3 + - - +
133D GLN* 3.2 17.8 + - - +
168D LEU* 3.7 13.3 - - + +
225D TYR* 3.4 42.6 - - + +
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D MET* 3.8 23.1 - - + -
126D LEU* 2.9 49.5 + - + +
127D GLU 4.0 2.7 - - - +
129D ALA* 1.3 69.8 - - - +
131D ALA* 1.3 62.1 + - - +
133D GLN 3.2 1.6 + - - -
134D PHE* 2.9 34.3 + - + +
136D SER 4.9 0.2 - - - -
137D VAL* 4.0 15.5 - - + -
140D PHE* 3.5 38.4 - - + -
159D LEU* 4.3 16.6 - - + -
168D LEU* 4.0 15.5 - - + -
218D TRP* 4.5 5.8 - - + -
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Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLU* 2.9 21.5 + - + +
128D ASN* 3.8 6.1 - - - +
130D ILE* 1.3 79.0 - - - +
132D LYS* 1.3 58.4 + - - +
135D GLY* 2.8 39.2 + - - +
136D SER* 4.0 17.7 - - - +
137D VAL* 4.6 3.3 - - + +
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Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ASN 2.8 21.6 + - - +
129D ALA* 3.7 13.9 - - - +
130D ILE 3.3 0.2 - - - -
131D ALA* 1.3 74.9 - - - +
133D GLN* 1.3 61.6 + - - +
135D GLY* 4.7 0.7 + - - -
225D TYR* 5.6 4.3 + - - -
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Residues in contact with GLN 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA 3.2 13.0 + - - +
130D ILE 3.2 2.2 + - - -
132D LYS* 1.3 80.4 - - + +
134D PHE* 1.3 85.5 + - + +
135D GLY 3.6 0.6 + - - -
167D GLU* 3.5 20.5 - - - +
168D LEU* 3.0 48.3 + - + +
169D LEU* 5.4 2.6 - - - +
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Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ILE* 2.9 39.7 + - + +
133D GLN* 1.3 97.9 - - + +
135D GLY* 1.3 57.7 + - - +
136D SER 3.1 10.1 + - - +
139D ASP* 3.3 18.3 - - - +
140D PHE* 3.8 33.4 - + + +
143D SER* 5.4 5.2 - - - -
159D LEU* 3.9 22.9 - - + -
168D LEU* 3.8 18.6 - - + -
169D LEU* 5.1 0.4 - - - -
170D ILE* 3.9 33.2 - - + -
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Residues in contact with GLY 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ALA* 2.8 24.8 + - - +
132D LYS 4.6 0.8 + - - -
133D GLN 3.6 2.0 + - - -
134D PHE* 1.3 75.2 - - - +
136D SER* 1.3 60.5 + - - +
139D ASP* 4.4 5.8 - - - -
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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