Contacts of the helix formed by residues 114 - 119 (chain d) in PDB entry 5KZ5
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 VAL 114 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79d VAL* 4.0 22.2 - - + -
80d ASP 4.3 4.0 - - - +
81d GLU 4.7 2.7 - - - +
83d GLY 3.5 26.7 + - - +
85d ILE* 4.9 4.0 - - + -
112d LYS 4.1 0.2 + - - -
113d THR* 1.4 72.7 - - - +
115d GLU* 1.4 58.8 + - - +
117d ALA* 3.4 8.6 + - - +
118d LEU* 2.9 43.4 + - + +
150d LEU* 4.5 13.5 - - + -
153d TYR* 6.2 1.1 - - + -
154d LYS* 5.6 3.6 - - + +
157d GLN* 4.7 15.9 - - - +
160f LYS* 4.1 19.7 - - + +
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Residues in contact with GLU 115 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113d THR* 3.2 6.4 - - - +
114d VAL* 1.4 73.5 - - - +
116d GLU* 1.4 63.7 + - - +
118d LEU* 3.5 22.7 + - - +
119d THR* 3.3 24.0 + - - +
154d LYS* 4.4 5.0 + - - -
165d GLU* 5.4 1.0 - - - +
160f LYS* 3.5 38.1 - - + +
161f LYS* 4.3 23.1 + - - +
164f ALA* 4.8 14.7 - - + +
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Residues in contact with GLU 116 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694 LEU* 5.3 1.7 - - - +
208D LYS* 3.1 33.3 + - + +
108d TRP* 3.5 28.3 + - - +
112d LYS* 3.4 35.1 + - + +
113d THR* 3.2 20.8 + - - +
115d GLU* 1.4 76.4 - - - +
117d ALA* 1.3 62.0 + - - +
119d THR* 3.2 16.4 - - + +
120d ILE* 3.2 22.3 + - + +
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Residues in contact with ALA 117 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85d ILE* 3.5 32.1 - - + -
109d VAL* 4.6 14.8 - - + -
112d LYS* 5.3 1.7 - - + +
113d THR 3.1 7.9 + - - +
114d VAL 3.4 9.0 - - - +
116d GLU* 1.3 76.9 - - - +
118d LEU* 1.4 55.0 + - - +
120d ILE* 3.1 34.2 - - - +
146d ILE* 4.2 1.2 - - + +
147d LYS* 4.8 1.2 - - - +
150d LEU* 3.6 21.2 - - + +
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Residues in contact with LEU 118 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114d VAL* 2.9 27.4 + - + +
115d GLU* 3.7 24.0 - - - +
116d GLU 3.4 0.2 - - - -
117d ALA* 1.4 73.0 - - - +
119d THR* 1.4 56.6 + - - +
120d ILE 3.4 0.2 - - - -
147d LYS* 3.0 22.0 + - - +
150d LEU* 3.8 31.0 - - + -
151d ALA 5.3 0.4 - - - +
154d LYS* 3.5 34.8 - - + +
162d GLY 5.3 0.2 - - - +
163d GLU* 5.8 1.3 - - - +
166d LYS* 3.8 34.3 - - + +
167d LYS 4.4 21.5 - - - -
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Residues in contact with THR 119 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ASP* 2.8 45.2 + - - +
179D GLY 4.3 8.1 + - - +
180D VAL* 4.7 2.4 - - - +
184D GLU* 4.8 13.3 + - - +
115d GLU 3.3 14.1 + - - +
116d GLU* 3.2 22.4 - - + +
118d LEU* 1.4 74.6 - - - +
120d ILE* 1.4 65.9 + - - +
121d LYS* 3.6 5.5 - - - +
124d ASP* 3.9 4.4 - - - +
147d LYS* 4.2 0.4 - - - -
166d LYS* 5.1 1.6 - - - -
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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