Contacts of the helix formed by residues 125 - 137 (chain A) in PDB entry 1P4K
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 4.4 11.5 + - + +
49A ARG* 4.9 0.2 + - - -
53A TYR* 3.5 35.9 - - + +
54A GLY* 3.7 19.3 + - - -
123A LEU 3.3 1.8 + - - -
124A LEU* 1.3 78.6 - - - +
126A ALA* 1.3 65.3 + - - +
127A GLU* 3.8 10.5 + - - +
128A SER* 3.1 24.7 + - - -
129A GLU* 3.0 21.7 + - - +
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Residues in contact with ALA 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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124A LEU 4.1 0.2 + - - -
125A THR* 1.3 73.4 - - - +
127A GLU* 1.3 57.6 + - - +
129A GLU* 3.4 12.0 + - - +
130A LYS* 2.9 31.1 + - - +
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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
----------------------------------------------------------
46A PRO 4.6 3.6 - - - +
47A THR* 5.3 2.8 - - - +
49A ARG* 3.4 36.0 + - - +
125A THR* 3.8 8.0 + - - +
126A ALA* 1.3 80.2 - - - +
128A SER* 1.3 61.7 + - - +
130A LYS* 3.4 8.8 + - + +
131A GLU* 3.1 36.9 + - + +
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 2.8 24.0 + - - +
54A GLY 3.1 20.4 + - - -
55A GLY 3.7 5.6 + - - -
56A ARG 4.2 0.2 + - - -
57A PRO* 4.1 13.5 - - - +
124A LEU* 3.6 20.9 - - - -
125A THR* 3.1 15.7 + - - -
127A GLU* 1.3 74.8 - - - +
129A GLU* 1.3 63.2 + - - +
131A GLU* 3.4 2.1 + - - +
132A TRP* 2.9 30.8 + - - +
175A TYR* 4.9 0.5 + - - -
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Residues in contact with GLU 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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124A LEU* 3.7 28.2 - - + +
125A THR 3.0 16.3 + - - +
126A ALA* 3.7 10.7 - - - +
128A SER* 1.3 77.0 - - - +
130A LYS* 1.3 63.7 + - - +
132A TRP* 3.3 10.8 + - + +
133A LYS* 3.0 62.0 + - + +
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Residues in contact with LYS 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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126A ALA 2.9 17.7 + - - +
127A GLU* 3.6 8.5 - - - +
129A GLU* 1.3 78.5 - - - +
131A GLU* 1.3 65.5 + - + +
133A LYS* 3.3 7.1 + - - +
134A GLU* 3.0 24.3 + - + +
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Residues in contact with GLU 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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49A ARG* 2.7 33.3 + - - +
56A ARG* 3.2 28.9 + - - -
127A GLU* 3.1 22.7 + - + +
128A SER* 3.9 3.4 - - - +
130A LYS* 1.3 81.5 - - + +
132A TRP* 1.3 57.9 + - - +
134A GLU* 3.3 7.0 + - - +
135A TRP* 2.9 29.1 + - - +
175A TYR* 3.6 12.3 + - - +
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Residues in contact with TRP 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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57A PRO* 3.9 14.4 - - + -
58A ASP 3.9 5.8 - - - -
59A ARG 3.1 21.4 + - - -
60A ASP* 3.5 10.3 - - - -
61A GLY* 3.4 34.3 - - - +
124A LEU* 5.2 4.3 - - + -
128A SER 2.9 18.6 + - - +
129A GLU* 3.6 13.5 - - + +
130A LYS 3.2 0.2 - - - -
131A GLU* 1.3 74.7 - - - +
133A LYS* 1.3 96.1 + - + +
135A TRP* 3.0 5.0 + + - +
136A LEU* 2.9 48.0 + - + +
175A TYR* 3.7 30.0 + + + -
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Residues in contact with LYS 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 GLU* 3.0 51.4 + - + +
130A LYS* 3.8 5.8 - - - +
132A TRP* 1.3 95.0 - - + +
134A GLU* 1.3 61.9 + - - +
136A LEU* 3.4 26.3 + - + +
137A LYS* 3.8 8.8 + - - +
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Residues in contact with GLU 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 LYS* 3.0 18.0 + - + +
131A GLU* 3.5 9.2 - - - +
132A TRP 3.1 0.2 - - - -
133A LYS* 1.3 78.7 - - - +
135A TRP* 1.3 63.7 + - - +
137A LYS* 3.2 54.4 + - - +
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Residues in contact with TRP 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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59A ARG* 3.6 38.4 - - + -
131A GLU 2.9 14.7 + - - +
132A TRP* 3.0 8.5 + + - +
134A GLU* 1.3 78.3 - - - +
136A LEU* 1.3 86.9 + - + +
137A LYS 3.1 1.2 + - - -
138A THR* 3.3 6.3 + - - -
139A SER* 2.9 53.1 + - - -
140A GLN* 3.0 29.8 + - + +
141A TYR* 4.3 6.7 - - + +
175A TYR* 3.5 58.2 - + + +
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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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59A ARG 3.9 7.9 - - - +
132A TRP* 2.9 56.5 + - + +
133A LYS* 3.5 17.5 - - + +
134A GLU 3.2 0.4 - - - -
135A TRP* 1.3 98.9 - - + +
137A LYS* 1.3 63.7 + - - +
138A THR 3.2 0.4 - - - -
139A SER* 3.1 20.0 + - - +
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Residues in contact with LYS 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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133A LYS 3.9 7.6 - - - +
134A GLU* 3.2 48.7 + - - +
135A TRP 3.1 0.8 + - - -
136A LEU* 1.3 77.9 - - - +
138A THR* 1.3 68.7 + - + +
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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