Contacts of the helix formed by residues 132 - 140 (chain K) in PDB entry 1KD1
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 LEU 132 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19K MET* 3.0 44.9 - - + -
41K ALA 3.4 26.2 - - - +
44K ALA* 3.0 22.8 + - + +
46K ILE* 3.9 19.5 - - + -
57K TYR* 5.8 1.1 - - - +
75K PRO* 3.8 23.3 - - + +
78K ILE* 4.4 9.1 - - + +
79K PHE* 3.8 14.8 - - + +
130K VAL 3.9 0.4 + - - -
131K THR* 1.3 71.0 - - - +
133K GLY* 1.3 63.2 + - - +
135K ILE* 3.0 16.4 + - + +
136K SER* 2.9 26.9 + - - -
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Residues in contact with GLY 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K GLU* 3.1 13.4 + - - +
75K PRO* 4.5 0.9 - - - -
131K THR* 2.9 11.6 - - - +
132K LEU* 1.3 78.6 - - - +
134K GLU* 1.3 58.8 + - - +
136K SER* 3.3 4.2 + - - -
137K GLU* 2.8 35.9 + - - +
145K TRP* 3.6 25.3 - - - -
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Residues in contact with GLU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K GLU* 4.8 14.8 - - - +
129K PHE* 4.9 1.9 - - - +
130K VAL* 3.6 15.6 - - + +
131K THR* 2.8 44.9 + - + +
133K GLY* 1.3 76.1 - - - +
135K ILE* 1.3 64.4 + - - +
137K GLU* 3.2 16.8 + - - +
138K THR* 3.1 26.0 + - - -
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Residues in contact with ILE 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K ILE* 4.0 27.6 - - + -
53K ILE* 4.1 21.5 - - + -
54K VAL* 4.8 14.1 - - + -
57K TYR* 4.4 28.0 - - + -
78K ILE* 5.5 4.5 - - + -
130K VAL* 3.6 15.5 - - + -
131K THR 3.0 13.0 + - - +
132K LEU* 3.0 19.9 + - + +
134K GLU* 1.3 77.2 - - - +
136K SER* 1.3 58.5 + - - +
138K THR* 3.2 9.4 + - - -
139K LEU* 2.8 45.1 + - + +
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Residues in contact with SER 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73K LYS 2.7 28.5 + - - -
74K ARG 3.5 0.3 - - - -
75K PRO* 3.1 30.4 - - - +
78K ILE* 4.5 3.6 - - - +
132K LEU 2.9 12.6 + - - -
133K GLY 3.6 7.9 - - - -
135K ILE* 1.3 75.0 - - - +
137K GLU* 1.3 66.4 + - - +
139K LEU* 3.1 9.3 + - - +
140K GLY 3.1 0.2 + - - -
141K ALA* 2.9 31.8 + - - +
145K TRP* 3.8 3.4 - - - -
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Residues in contact with GLU 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2803A C 4.2 3.6 + - - -
133K GLY 2.8 24.8 + - - +
134K GLU* 3.2 17.2 + - - +
136K SER* 1.3 75.7 - - - +
138K THR* 1.3 63.1 + - - +
140K GLY* 3.1 14.6 + - - -
141K ALA* 4.5 9.2 - - - +
143K LYS* 3.6 39.4 + - + +
145K TRP* 4.1 11.9 + - + -
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Residues in contact with THR 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2773A G 6.0 1.6 - - - +
2803A C 4.1 16.1 + - - +
50K GLU* 4.9 6.1 + - - -
54K VAL* 3.5 36.0 - - + +
58K GLU* 4.3 14.3 - - + +
134K GLU 3.1 14.4 + - - -
135K ILE* 3.3 11.0 - - - +
137K GLU* 1.3 79.3 - - - +
139K LEU* 1.3 62.6 + - + +
140K GLY 3.1 1.0 + - - -
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Residues in contact with LEU 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2803A C 3.9 15.1 - - - +
54K VAL* 5.1 1.6 - - + +
57K TYR* 4.0 23.6 - - + +
58K GLU* 3.8 31.2 - - + +
61K VAL* 4.1 17.3 - - + +
71K TYR* 5.2 0.4 - - + -
72K PRO 4.3 6.1 - - - +
73K LYS* 3.8 54.0 + - + +
78K ILE* 4.3 6.7 - - + -
135K ILE* 2.8 33.1 + - + +
136K SER 3.1 7.1 + - - +
138K THR* 1.3 78.4 - - + +
140K GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2803A C 3.1 30.5 - - - -
2804A C 3.7 20.6 + - - +
73K LYS* 5.2 4.3 - - - -
137K GLU 3.1 5.4 + - - -
138K THR 3.0 5.3 - - - -
139K LEU* 1.3 78.4 - - - +
141K ALA* 1.3 69.7 + - - +
142K ASN* 3.7 0.7 + - - +
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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