Contacts of the helix formed by residues 133 - 141 (chain A) in PDB entry 5TKM
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 ARG 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLU 4.9 1.8 + - - -
129A ARG* 3.2 38.2 + - - +
130A ASP* 3.1 4.3 + - - +
131A TYR 3.3 0.4 + - - -
132A ARG* 1.3 87.4 - - + +
134A ALA* 1.3 61.6 + - - +
135A LEU 3.6 1.3 - - - -
136A CYS* 3.3 4.1 + - - +
137A ARG* 2.8 69.4 + - - +
190A ARG* 5.6 1.1 - - - +
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Residues in contact with ALA 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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98A PRO* 4.4 12.3 - - + -
101A VAL* 3.2 28.9 - - + +
126A TYR* 3.9 25.4 - - + -
130A ASP* 2.9 28.9 + - + +
133A ARG* 1.3 75.3 - - - +
135A LEU* 1.3 63.4 + - - +
137A ARG* 3.2 8.7 + - - +
138A LEU 3.2 15.4 + - - -
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Residues in contact with LEU 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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95A THR* 4.2 7.0 - - + +
96A PRO* 4.3 17.0 - - + -
101A VAL* 4.4 10.3 - - + -
123A LEU* 4.1 14.6 - - + -
126A TYR* 3.3 40.8 - - + +
130A ASP 4.7 0.6 + - - -
131A TYR 5.1 0.2 + - - -
134A ALA* 1.3 79.9 - - - +
136A CYS* 1.3 58.0 + - - +
138A LEU* 3.3 10.7 + - + +
139A SER* 2.9 30.3 + - - -
145A VAL* 4.3 15.1 - - + +
185A LEU* 3.8 23.3 - - + -
188A ILE* 3.8 20.8 - - + +
189A LEU* 3.7 9.8 - - + +
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Residues in contact with CYS 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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132A ARG 3.8 15.3 - - - +
133A ARG* 3.3 9.7 + - - +
134A ALA 3.2 0.4 - - - -
135A LEU* 1.3 77.7 - - - +
137A ARG* 1.3 57.9 + - - +
139A SER* 3.3 3.6 + - - -
140A GLN* 2.9 47.2 + - - +
188A ILE* 4.0 12.9 + - - +
189A LEU* 4.0 14.8 - - - +
190A ARG* 4.3 29.8 - - - -
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Residues in contact with ARG 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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98A PRO* 5.8 4.8 + - - +
101A VAL* 4.4 9.6 - - + +
105A ALA* 4.6 6.4 - - + +
130A ASP* 4.7 10.7 + - - -
133A ARG* 2.8 59.3 + - - +
134A ALA* 3.5 10.9 - - - +
136A CYS* 1.3 73.6 - - - +
138A LEU* 1.3 62.7 + - - +
140A GLN* 3.3 8.2 + - - +
141A ALA* 3.1 22.2 + - - +
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Residues in contact with LEU 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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96A PRO* 4.6 4.9 - - + -
101A VAL* 4.0 22.8 - - + +
104A LEU* 4.1 26.2 - - + -
105A ALA* 4.2 12.8 - - - +
108A LEU* 4.3 8.3 - - + -
116A LEU* 5.1 1.3 - - + -
118A ILE* 3.8 29.6 - - + -
134A ALA 3.2 10.0 + - - +
135A LEU* 3.7 15.3 - - + +
136A CYS 3.3 0.2 - - - -
137A ARG* 1.3 80.1 - - - +
139A SER* 1.3 62.1 + - - +
141A ALA* 3.2 11.9 + - - +
142A GLY 3.5 0.3 + - - -
143A ALA* 3.3 31.2 + - + -
145A VAL* 4.2 11.4 - - + -
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Residues in contact with SER 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 LEU 2.9 16.6 + - - -
136A CYS* 3.8 4.5 - - - -
138A LEU* 1.3 77.7 - - - +
140A GLN* 1.3 58.3 + - - +
142A GLY* 3.0 20.4 + - - -
143A ALA 3.4 17.8 + - - +
145A VAL* 4.7 6.8 + - - +
189A LEU* 4.2 22.5 - - - +
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Residues in contact with GLN 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 CYS* 2.9 32.7 + - - +
137A ARG* 3.6 8.1 - - - +
138A LEU 3.2 0.4 - - - -
139A SER* 1.3 72.3 - - - +
141A ALA* 1.3 60.0 + - - +
142A GLY 3.1 6.4 + - - -
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Residues in contact with ALA 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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105A ALA* 3.9 35.0 - - + +
108A LEU* 4.1 19.9 - - + +
109A SER* 5.4 4.9 - - - +
137A ARG 3.1 13.6 + - - +
138A LEU 3.2 9.8 + - - +
140A GLN* 1.3 75.2 - - - +
142A GLY* 1.3 56.9 + - - +
143A ALA 3.6 1.3 - - - -
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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