Contacts of the helix formed by residues 123 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PRO 3.3 10.1 - - - +
122A MET* 1.4 86.7 - - + +
124A LYS* 1.3 66.5 + - - +
125A THR* 3.3 2.7 - - - +
126A LEU* 3.1 4.4 + - + +
127A GLU* 3.0 19.2 + - - +
218A TRP* 3.5 19.5 - - + +
219A GLU* 4.3 14.1 - - + -
222A CYS* 3.7 31.4 - - + -
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Residues in contact with LYS 124 (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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122A MET 3.8 0.6 + - - -
123A PRO* 1.3 73.2 - - - +
125A THR* 1.3 57.9 + - - +
127A GLU* 3.2 37.6 + - - +
128A ASN* 2.8 55.2 + - - +
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Residues in contact with THR 125 (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 PRO* 3.3 1.9 - - - +
124A LYS* 1.3 79.0 - - - +
126A LEU* 1.3 57.1 + - - +
128A ASN* 3.5 6.9 + - - +
129A ALA* 3.1 26.2 + - - +
222A CYS* 4.3 11.2 - - - -
225A TYR* 4.4 21.5 - - + -
226A GLU* 4.4 17.8 + - + +
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Residues in contact with LEU 126 (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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122A MET* 3.9 8.5 - - + -
123A PRO* 3.1 9.5 + - + +
125A THR* 1.3 77.5 - - - +
127A GLU* 1.3 67.7 + - - +
129A ALA* 3.2 4.5 + - + -
130A ILE* 2.9 48.4 + - + +
168A LEU* 5.2 0.7 - - + -
187A ILE* 4.2 23.1 - - + -
218A TRP* 3.6 37.9 - - + +
221A VAL* 3.6 13.5 - - + -
222A CYS* 3.8 28.4 - - + +
225A TYR* 4.2 17.7 - - + -
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Residues in contact with GLU 127 (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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122A MET* 3.5 26.5 - - + +
123A PRO 3.0 13.2 + - - +
124A LYS* 3.2 47.1 + - - +
126A LEU* 1.3 77.4 - - - +
128A ASN* 1.3 60.0 + - - +
130A ILE* 3.4 2.1 + - - +
131A ALA* 3.0 32.3 + - + +
137A VAL* 3.8 18.9 - - + +
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Residues in contact with ASN 128 (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 LYS* 2.8 49.0 + - - +
125A THR* 3.8 7.1 - - - +
127A GLU* 1.3 74.9 - - - +
129A ALA* 1.3 59.6 + - - +
131A ALA* 3.4 5.1 + - - +
132A LYS* 2.9 31.1 + - - +
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Residues in contact with ALA 129 (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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125A THR 3.1 16.7 + - - +
126A LEU* 3.2 5.4 + - + +
128A ASN* 1.3 77.0 - - - +
130A ILE* 1.3 61.8 + - - +
132A LYS* 3.4 8.0 + - - +
133A GLN* 3.0 23.9 + - - +
168A LEU* 3.8 8.2 - - + +
225A TYR* 3.4 41.3 - - + +
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Residues in contact with ILE 130 (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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122A MET* 3.8 22.2 - - + -
126A LEU* 2.9 47.5 + - + +
127A GLU 3.8 2.9 - - - +
129A ALA* 1.3 73.7 - - - +
131A ALA* 1.3 58.8 + - - +
133A GLN 3.2 1.2 + - - -
134A PHE* 2.9 37.5 + - + +
137A VAL* 3.9 17.7 - - + -
140A PHE* 3.4 38.4 - - + -
159A LEU* 4.4 13.5 - - + -
168A LEU* 4.0 15.5 - - + -
218A TRP* 4.4 9.0 - - + -
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Residues in contact with ALA 131 (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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127A GLU* 3.0 18.9 + - + +
128A ASN* 3.9 6.1 - - - +
130A ILE* 1.3 77.3 - - - +
132A LYS* 1.3 58.6 + - - +
135A GLY* 2.9 32.2 + - - +
136A SER* 3.8 24.9 - - - +
137A VAL* 4.3 6.5 - - + +
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Residues in contact with LYS 132 (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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128A ASN 2.9 18.7 + - - +
129A ALA* 3.7 8.1 - - - +
131A ALA* 1.3 79.2 - - - +
133A GLN* 1.3 62.7 + - - +
135A GLY* 4.3 1.7 + - - -
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Residues in contact with GLN 133 (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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129A ALA 3.0 15.8 + - - +
132A LYS* 1.3 79.8 - - - +
134A PHE* 1.3 87.7 + - + +
167A GLU* 3.0 33.8 + - - +
168A LEU* 3.0 46.8 + - + +
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Residues in contact with PHE 134 (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 ILE* 2.9 27.9 + - + +
133A GLN* 1.3 101.6 - - + +
135A GLY* 1.3 56.2 - - - +
136A SER 3.4 5.6 - - - +
139A ASP* 3.7 14.9 - - - +
140A PHE* 3.8 43.1 - + + +
143A SER* 5.2 4.9 - - - -
159A LEU* 3.7 21.3 - - + -
168A LEU* 3.8 14.8 - - + -
169A LEU* 4.1 10.8 - - - -
170A ILE* 3.7 32.3 - - + -
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Residues in contact with GLY 135 (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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131A ALA* 2.9 19.5 + - - +
132A LYS 4.3 1.9 + - - -
133A GLN 3.6 1.6 + - - -
134A PHE* 1.3 76.9 - - - +
136A SER* 1.3 62.0 + - - +
139A ASP* 4.3 5.4 - - - -
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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