Contacts of the helix formed by residues 154 - 169 (chain Z) in PDB entry 5WTI
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 154 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Z LEU* 4.7 6.2 - - - +
152Z ASP* 2.2 30.1 + - - +
153Z PRO* 1.3 76.0 - - - +
155Z TRP* 1.3 63.3 + - - +
156Z GLU 3.1 3.5 + - - +
157Z GLU* 3.4 16.1 + - - +
158Z GLU* 3.0 27.6 + - - +
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Residues in contact with TRP 155 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Z TRP* 3.5 24.9 - + - +
147Z LEU* 3.9 9.3 - - + +
148Z LYS* 3.4 72.5 - - + +
151Z GLY 5.7 0.2 - - - -
152Z ASP* 3.2 23.0 + - - +
153Z PRO* 3.2 8.6 - - + -
154Z SER* 1.3 77.7 + - - +
156Z GLU* 1.3 88.5 + - + +
158Z GLU* 3.4 5.3 + - - +
159Z LYS* 2.8 58.7 + - + +
160Z LYS* 5.6 1.8 - - - -
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Residues in contact with GLU 156 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Z PRO 3.9 14.1 + - - +
154Z SER 3.1 0.6 - - - -
155Z TRP* 1.3 118.8 + - + +
157Z GLU* 1.3 63.9 + - - +
159Z LYS* 2.9 11.4 + - - +
160Z LYS* 3.0 36.1 + - - +
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Residues in contact with GLU 157 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154Z SER* 3.4 16.0 + - - +
156Z GLU* 1.3 78.3 - - - +
158Z GLU* 1.3 70.4 + - - +
160Z LYS* 3.3 11.7 + - + +
161Z LYS* 3.1 56.0 + - + +
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Residues in contact with GLU 158 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Z ARG* 3.6 29.9 + - - +
144Z TRP* 3.9 15.2 - - + +
147Z LEU* 3.6 21.5 - - + -
154Z SER* 3.0 22.6 + - - +
155Z TRP 3.7 3.8 - - - +
157Z GLU* 1.3 80.3 - - - +
159Z LYS* 1.3 64.3 + - - +
161Z LYS* 3.2 38.4 + - - +
162Z TRP* 2.9 21.1 + - - +
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Residues in contact with LYS 159 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Z TRP* 3.5 61.4 - - + +
155Z TRP* 2.8 37.6 + - + +
156Z GLU 2.9 6.5 + - - +
158Z GLU* 1.3 72.2 - - - +
160Z LYS* 1.3 68.4 + - + +
162Z TRP* 3.1 9.9 - - + +
163Z GLU* 2.9 52.8 + - - +
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Residues in contact with LYS 160 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155Z TRP* 5.6 1.6 - - - -
156Z GLU* 3.0 40.3 + - - +
157Z GLU* 3.6 10.1 - - + +
158Z GLU 3.1 0.2 - - - -
159Z LYS* 1.3 93.6 - - - +
161Z LYS* 1.3 60.0 + - - +
162Z TRP 3.1 1.1 - - - -
163Z GLU* 3.7 20.9 + - - +
164Z GLU* 2.9 36.7 + - + +
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Residues in contact with LYS 161 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Z GLU* 3.1 39.8 + - + +
158Z GLU* 3.2 38.0 + - - +
160Z LYS* 1.3 75.2 - - - +
162Z TRP* 1.3 61.2 + - - +
164Z GLU* 3.9 5.4 - - - +
165Z ASP* 3.1 24.9 + - - +
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Residues in contact with TRP 162 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H T 5.0 0.9 - - - -
10H C 2.8 31.4 + - - -
11H C 5.5 3.8 + - - -
142Z PRO* 3.4 20.3 - - + +
143Z ARG 5.8 0.2 - - - -
144Z TRP* 2.9 46.9 - + + -
158Z GLU 2.9 12.6 + - - +
159Z LYS* 3.1 19.1 - - + +
161Z LYS* 1.3 74.3 - - - +
163Z GLU* 1.3 80.7 + - + +
165Z ASP* 3.1 15.2 + - + +
166Z LYS* 3.0 51.8 + - + +
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Residues in contact with GLU 163 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159Z LYS* 2.9 44.1 + - - +
160Z LYS* 3.5 26.8 + - - +
162Z TRP* 1.3 87.6 - - + +
164Z GLU* 1.3 62.4 + - - +
166Z LYS* 3.5 13.7 + - - +
167Z LYS* 3.4 20.3 + - - +
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Residues in contact with GLU 164 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Z LYS* 2.9 22.1 + - + +
161Z LYS* 3.9 6.1 - - - +
163Z GLU* 1.3 77.9 - - - +
165Z ASP* 1.3 61.6 + - - +
167Z LYS* 3.4 27.0 + - - +
168Z LYS* 3.5 18.0 + - + +
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Residues in contact with ASP 165 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H C 2.9 45.6 + - - -
161Z LYS 3.1 17.6 + - - +
162Z TRP* 3.1 9.0 + - + +
164Z GLU* 1.3 77.4 - - - +
166Z LYS* 1.3 69.5 + - - +
168Z LYS* 3.2 39.0 + - - +
169Z ASP* 3.3 6.2 + - - +
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Residues in contact with LYS 166 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H C 5.5 5.8 - - - +
162Z TRP* 3.0 74.3 + - + +
163Z GLU* 3.5 12.1 + - - +
164Z GLU 3.3 0.2 - - - -
165Z ASP* 1.3 82.2 - - - +
167Z LYS* 1.3 65.5 + - - +
169Z ASP* 3.1 25.9 + - + +
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Residues in contact with LYS 167 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Z GLU 3.4 10.3 + - - +
164Z GLU* 3.7 23.1 - - - +
165Z ASP 3.3 0.6 - - - -
166Z LYS* 1.3 77.2 - - - +
168Z LYS* 1.3 61.3 + - + +
169Z ASP 3.4 4.7 + - - +
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Residues in contact with LYS 168 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Z LYS* 6.3 0.4 - - - +
164Z GLU* 3.5 14.7 + - + +
165Z ASP* 3.2 28.0 + - - +
166Z LYS 3.1 0.6 - - - -
167Z LYS* 1.3 76.5 - - - +
169Z ASP* 1.3 62.8 + - - +
170Z PRO* 3.2 11.3 - - - +
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Residues in contact with ASP 169 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H C 4.0 16.0 + - - +
101Z GLU* 4.1 4.5 - - - +
119Z LYS* 2.9 34.5 + - - -
165Z ASP 3.3 5.8 + - - +
166Z LYS* 3.1 23.3 + - + +
167Z LYS 4.0 3.6 - - - +
168Z LYS* 1.3 77.0 - - - +
170Z PRO* 1.3 71.2 - - - +
171Z LEU* 3.3 16.6 + - - +
172Z ALA* 4.5 6.6 + - - +
173Z LYS 5.2 1.0 + - - -
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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