Contacts of the helix formed by residues 157 - 168 (chain T) 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 LYS 157 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155T GLU 3.7 1.0 + - - -
156T HIS* 1.4 69.7 - - - +
158T CYS* 1.3 59.9 + - - +
160T LEU* 4.2 10.5 - - + +
161T ASP* 3.0 57.9 + - - +
380T ALA* 3.9 17.3 - - + -
384T ALA* 3.5 36.6 - - + -
385T SER* 3.8 5.8 - - - -
387T GLU* 3.2 27.2 + - - +
388T PRO 3.3 15.0 + - - -
389T SER* 3.9 20.1 + - - +
390T TYR* 5.6 1.0 + - - -
391T VAL* 5.1 0.6 - - - +
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Residues in contact with CYS 158 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128T THR* 3.9 35.9 - - + -
132T ASN* 4.1 9.0 + - - +
156T HIS* 5.1 0.9 - - - -
157T LYS* 1.3 76.8 - - - +
159T VAL* 1.4 60.3 + - - +
161T ASP* 3.6 2.9 + - - +
162T SER* 3.2 24.4 + - - -
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Residues in contact with VAL 159 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128T THR* 3.8 14.6 - - - +
131T ASN* 3.6 34.8 - - + +
132T ASN* 3.6 12.1 - - - +
135T ILE* 3.5 32.5 - - + -
155T GLU* 3.6 20.0 - - + +
156T HIS* 3.0 21.5 + - + +
158T CYS* 1.4 72.5 - - - +
160T LEU* 1.4 56.6 + - - +
162T SER* 3.4 4.2 + - - -
163T CYS* 3.0 34.8 + - - -
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Residues in contact with LEU 160 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152T THR 3.6 15.7 - - - +
153T GLN* 3.8 14.1 - - - +
155T GLU* 3.2 50.7 - - + +
156T HIS 3.0 9.0 + - - +
157T LYS* 3.9 7.9 - - + +
158T CYS 3.4 0.2 - - - -
159T VAL* 1.4 74.2 - - - +
161T ASP* 1.3 60.4 + - - +
163T CYS* 3.4 2.8 + - - -
164T ARG* 3.0 23.9 + - - +
175T TYR* 3.4 23.6 + - + -
389T SER* 4.1 5.4 - - - +
390T TYR* 3.6 43.0 - - + +
391T VAL* 4.0 4.9 - - + -
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Residues in contact with ASP 161 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157T LYS* 3.0 46.9 + - - +
158T CYS* 4.3 2.9 - - - +
160T LEU* 1.3 76.4 - - - +
162T SER* 1.4 60.7 + - - +
164T ARG* 3.5 7.7 - - - +
165T SER* 3.2 24.4 + - - -
385T SER* 3.1 24.8 + - - -
387T GLU* 3.8 16.9 - - - +
390T TYR* 5.0 6.1 - - - -
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Residues in contact with SER 162 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132T ASN* 3.6 22.2 + - - +
136T LYS* 3.3 25.7 - - - +
158T CYS 3.2 18.1 + - - -
159T VAL 3.6 2.2 - - - -
161T ASP* 1.4 75.6 - - - +
163T CYS* 1.4 59.7 + - - +
165T SER* 3.4 8.9 + - - -
166T LEU* 3.3 17.2 + - - +
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Residues in contact with CYS 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135T ILE* 4.1 22.7 - - - -
136T LYS* 3.9 10.3 - - - +
151T THR* 3.8 21.8 - - + -
155T GLU* 3.8 11.9 - - - -
159T VAL* 3.0 27.8 + - - -
160T LEU* 3.6 6.1 - - - +
161T ASP 3.3 0.2 - - - -
162T SER* 1.4 71.6 - - - +
164T ARG* 1.4 58.7 + - - +
166T LEU* 3.1 5.6 + - - +
167T GLU 3.1 23.2 + - - -
173T VAL* 3.7 18.0 - - + +
175T TYR* 3.5 16.6 - - + +
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Residues in contact with ARG 164 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160T LEU 3.0 13.2 + - - +
161T ASP* 3.5 15.5 - - - +
163T CYS* 1.4 75.6 - - - +
165T SER* 1.3 60.4 + - - +
167T GLU* 3.4 24.9 + - - +
168T ALA* 3.2 19.2 + - - +
175T TYR* 3.4 32.1 + - - -
387T GLU* 3.9 24.1 + - - +
390T TYR* 3.6 31.3 + - - +
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Residues in contact with SER 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161T ASP 3.2 13.4 + - - -
162T SER* 3.5 13.0 - - - -
164T ARG* 1.3 72.8 - - - +
166T LEU* 1.3 64.8 + - - +
168T ALA* 3.3 11.0 + - - +
169T GLU* 3.2 19.1 + - - +
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Residues in contact with LEU 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136T LYS* 3.6 37.0 - - + +
139T ALA* 5.9 1.3 - - + -
140T ARG* 3.8 32.8 - - - +
149T LEU* 4.6 8.5 - - + -
162T SER 3.3 3.5 + - - +
163T CYS 3.1 10.9 + - - +
165T SER* 1.3 77.0 - - - +
167T GLU* 1.3 62.6 + - - +
169T GLU* 3.1 33.1 + - - +
171T PHE* 3.3 52.1 + - + -
173T VAL* 4.7 5.8 - - + -
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Residues in contact with GLU 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163T CYS 3.1 7.4 + - - +
164T ARG* 3.4 37.2 + - - +
166T LEU* 1.3 75.0 - - - +
168T ALA* 1.3 57.2 + - - +
170T GLY* 3.2 11.1 + - - -
171T PHE 2.9 30.6 - - - +
172T GLN* 4.5 1.8 - - - +
173T VAL* 3.5 41.4 + - + +
175T TYR* 3.9 11.8 - - - -
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Residues in contact with ALA 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164T ARG 3.2 9.5 + - - +
165T SER* 3.3 14.1 - - - +
166T LEU 3.2 0.2 - - - -
167T GLU* 1.3 74.6 - - - +
169T GLU* 1.4 53.9 + - - +
170T GLY* 3.1 10.3 + - - -
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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