Contacts of the helix formed by residues 135 - 143 (chain A) in PDB entry 2K5U
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 SER 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLN* 4.3 2.9 - - - -
133A ALA 3.8 2.7 + - - -
134A MET* 1.3 74.3 - - - +
136A ALA* 1.3 56.0 + - - +
137A ALA* 3.1 10.0 + - - -
138A GLU* 3.1 14.5 + - - +
139A ILE* 2.7 38.0 + - - +
157A ALA* 5.3 0.9 - - - -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ALA* 5.0 0.2 - - - -
135A SER* 1.3 73.4 - - - +
137A ALA* 1.3 51.4 + - - +
139A ILE* 4.2 6.9 - - - +
140A THR* 2.5 42.3 + - - -
155A ILE* 3.1 31.8 - - + +
156A GLN* 4.6 0.9 - - - -
157A ALA* 3.5 33.1 - - + +
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Residues in contact with ALA 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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135A SER* 3.1 6.8 - - - -
136A ALA* 1.3 79.2 - - - +
138A GLU* 1.3 61.8 + - - +
140A THR* 3.3 6.3 + - - +
141A GLU* 3.1 29.6 + - - +
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Residues in contact with GLU 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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134A MET* 4.9 9.6 - - + -
135A SER* 3.1 20.7 + - - +
137A ALA* 1.3 75.4 - - - +
139A ILE* 1.3 57.4 + - - +
141A GLU* 2.9 30.4 - - - +
142A LYS* 2.7 47.1 + - + +
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Residues in contact with ILE 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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92A VAL* 4.3 10.1 - - + -
94A SER* 3.5 22.7 - - - +
100A ILE* 4.1 17.0 - - + -
123A VAL* 5.9 1.1 - - + -
125A ALA* 3.9 19.3 - - + -
134A MET* 3.1 47.8 - - + +
135A SER 2.7 27.4 + - - +
136A ALA* 3.8 4.3 - - - +
138A GLU* 1.3 70.4 - - - +
140A THR* 1.3 60.8 + - - +
142A LYS* 3.7 5.6 - - - +
143A LEU* 2.8 44.7 + - + +
155A ILE* 5.5 4.7 - - + -
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Residues in contact with THR 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ALA 2.5 28.0 + - - -
137A ALA* 3.5 7.8 - - - +
139A ILE* 1.3 75.1 - - - +
141A GLU* 1.3 58.7 + - + +
143A LEU* 4.1 3.4 - - - -
144A GLY 3.5 0.2 + - - -
145A LEU* 2.7 64.7 + - + +
146A HIS* 3.6 11.1 + - + +
155A ILE* 2.9 30.7 - - + +
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Residues in contact with GLU 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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137A ALA* 3.1 13.7 + - - +
138A GLU* 2.9 50.3 - - - +
140A THR* 1.3 78.9 - - + +
142A LYS* 1.3 71.3 + - + +
144A GLY* 3.3 11.1 + - - -
145A LEU 4.8 0.4 - - - +
146A HIS* 4.9 12.2 - - + +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ARG* 5.8 2.2 - - + -
100A ILE* 4.7 28.1 - - + +
101A GLY* 5.9 1.0 - - - -
104A ARG* 5.1 5.9 + - - -
134A MET* 4.7 14.4 - - - -
138A GLU* 2.7 37.3 + - + +
139A ILE* 3.7 6.5 - - - +
141A GLU* 1.3 82.7 + - + +
143A LEU* 1.3 57.3 + - - +
144A GLY 3.1 3.4 + - - -
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Residues in contact with LEU 143 (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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90A PHE* 5.7 4.9 - - + -
92A VAL* 5.5 3.8 - - + -
100A ILE* 4.2 20.2 - - + +
103A ALA* 5.6 2.7 - - + -
104A ARG* 3.2 40.3 - - + +
107A MET* 4.5 9.1 - - + +
123A VAL* 4.3 10.8 - - + -
139A ILE* 2.8 36.3 + - + +
142A LYS* 1.3 75.6 - - - +
144A GLY* 1.3 57.7 + - - +
145A LEU* 3.2 32.3 - - + +
153A TRP* 3.3 30.5 - - + -
155A ILE* 5.4 0.2 - - + -
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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