Contacts of the helix formed by residues 114 - 119 (chain k) 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 k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160j LYS* 3.8 28.4 - - + +
79k VAL* 3.7 29.8 - - + -
83k GLY 5.7 0.4 - - - +
84k LYS* 6.3 0.4 - - - -
85k ILE* 4.9 2.9 - - + -
113k THR* 1.4 73.9 - - - +
115k GLU* 1.4 56.6 + - - +
117k ALA* 3.4 7.1 + - - +
118k LEU* 3.1 32.1 + - + +
150k LEU* 4.1 24.2 - - + +
153k TYR* 4.8 7.2 - - + -
154k LYS* 3.5 35.0 - - + +
157k GLN* 5.1 1.6 - - - +
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Residues in contact with GLU 115 (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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160j LYS* 3.9 24.2 - - + +
161j LYS* 3.8 31.8 + - + +
164j ALA* 5.6 5.4 - - + -
113k THR* 3.3 5.6 + - - +
114k VAL* 1.4 72.2 - - - +
116k GLU* 1.4 66.5 + - + +
118k LEU* 3.5 7.2 + - - +
119k THR* 3.0 24.2 + - - -
154k LYS* 2.9 33.8 + - - -
162k GLY* 3.7 11.1 - - - +
165k GLU* 4.2 0.2 - - - +
166k LYS* 3.2 45.0 + - - +
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Residues in contact with GLU 116 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172K ASN* 5.0 10.4 + - - -
180K VAL* 5.5 1.6 - - - +
184K GLU* 4.7 9.2 - - - +
206K SER 5.3 4.8 - - - +
207K GLY* 5.3 4.1 - - - -
71Q PRO* 4.1 22.2 - - + -
112k LYS* 3.6 42.8 + - + -
113k THR* 3.5 20.3 + - - +
115k GLU* 1.4 78.2 - - + +
117k ALA* 1.3 65.3 + - - +
119k THR* 3.1 30.4 + - - +
120k ILE 3.7 0.3 + - - -
166k LYS* 6.2 0.3 - - - -
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Residues in contact with ALA 117 (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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85k ILE* 3.9 11.7 - - + -
109k VAL* 3.7 31.5 - - + +
112k LYS* 4.1 4.2 - - + +
113k THR 2.9 20.6 + - - +
114k VAL 3.7 2.9 - - - +
115k GLU 3.3 0.2 - - - -
116k GLU* 1.3 76.8 - - - +
118k LEU* 1.4 54.9 + - - +
120k ILE* 3.2 30.1 + - - +
150k LEU* 3.5 22.6 - - + +
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Residues in contact with LEU 118 (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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178K ASP* 4.3 3.5 - - - +
114k VAL* 3.1 23.6 + - + +
115k GLU* 3.7 6.5 - - - +
116k GLU 3.3 0.2 - - - -
117k ALA* 1.4 70.7 - - - +
119k THR* 1.4 56.3 + - - +
120k ILE* 3.2 8.1 + - - +
147k LYS* 3.5 49.5 - - + +
150k LEU* 3.9 17.9 - - + -
151k ALA 4.5 2.9 - - - +
154k LYS* 3.8 15.5 - - + +
162k GLY 3.2 26.7 - - - +
163k GLU* 3.9 12.8 - - + -
166k LYS* 3.5 23.7 - - + +
167k LYS* 4.4 18.4 - - + -
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Residues in contact with THR 119 (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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178K ASP* 3.1 42.5 + - - +
179K GLY 4.4 1.7 - - - -
180K VAL* 3.9 31.4 - - + +
112k LYS* 5.4 3.5 + - - +
115k GLU 3.0 15.2 + - - -
116k GLU* 3.1 25.5 + - - +
118k LEU* 1.4 74.7 - - - +
120k ILE* 1.4 62.9 + - - +
121k LYS* 3.4 9.2 + - - -
124k ASP* 3.9 2.3 - - - +
166k LYS* 4.1 12.1 - - - +
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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