Contacts of the helix formed by residues 129 - 141 (chain X) in PDB entry 5CQL
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 PHE 129 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125X LYS* 4.4 12.1 - - + -
126X TYR* 3.1 48.4 + + - +
127X VAL 3.1 1.4 - - - -
128X ALA* 1.3 82.6 - - + +
130X LEU* 1.3 63.0 + - - +
131X LYS 3.4 2.2 + - - -
132X LEU* 3.6 8.2 + - + +
133X PHE* 3.1 23.4 + - - +
212X VAL* 3.4 19.1 - - - +
213X ASP* 3.7 25.4 - - + -
214X MET 4.9 0.7 - - - +
344X VAL* 4.0 37.2 - - + -
345X PRO 4.9 5.8 - - - -
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Residues in contact with LEU 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X VAL* 4.3 5.8 - - + -
122X ALA* 3.9 23.6 - - + -
127X VAL* 3.2 28.3 + - + +
128X ALA 3.3 0.2 - - - -
129X PHE* 1.3 75.8 - - - +
131X LYS* 1.3 67.2 + - - +
133X PHE* 4.2 3.4 - - + -
134X LEU* 2.9 37.3 + - + +
151X VAL* 3.9 36.3 - - + -
153X THR* 5.3 0.2 - - - +
159X VAL* 4.1 13.5 - - + -
160X PRO* 3.6 24.9 - - + -
212X VAL* 3.7 18.8 - - + -
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Residues in contact with LYS 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X VAL 4.8 0.4 + - - -
128X ALA 4.5 6.3 + - - +
129X PHE 3.4 0.8 - - - -
130X LEU* 1.3 78.1 - - - +
132X LEU* 1.3 58.4 + - - +
134X LEU* 4.0 0.7 - - - +
135X GLU* 2.6 68.9 + - + +
160X PRO* 3.7 25.6 - - + +
161X ARG 4.8 10.7 + - - -
162X VAL* 4.3 8.0 - - + +
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Residues in contact with LEU 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X ALA 5.4 0.8 + - - -
129X PHE* 3.6 9.2 + - + +
131X LYS* 1.3 76.8 - - - +
133X PHE* 1.3 64.1 + - - +
135X GLU* 4.5 11.9 - - - +
136X THR* 2.8 46.9 + - + +
214X MET 5.3 0.4 - - - +
215X GLU* 3.9 38.1 - - + +
344X VAL* 4.0 24.2 - - + -
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Residues in contact with PHE 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X LEU* 3.8 25.4 - - + -
120X VAL* 3.4 30.3 - - + -
129X PHE 3.1 19.9 + - - +
130X LEU* 3.6 4.5 - - + +
132X LEU* 1.3 77.7 - - - +
134X LEU* 1.3 78.9 + - + +
136X THR* 3.2 3.8 + - - -
137X ALA* 2.9 29.5 + - + +
149X TYR* 4.9 1.1 - + - -
210X VAL* 3.5 25.1 - - + -
211X ASP 3.6 10.3 - - - -
212X VAL* 3.7 28.7 - - + +
214X MET 3.8 16.5 + - - +
216X PHE* 4.1 7.8 - + - -
341X PHE* 3.9 16.2 - + - -
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Residues in contact with LEU 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X VAL* 5.9 0.2 - - + -
130X LEU* 2.9 39.3 + - + +
133X PHE* 1.3 85.1 - - + +
135X GLU* 1.3 67.3 + - - +
137X ALA* 3.2 4.0 + - - +
138X GLU* 2.9 27.0 + - - +
149X TYR* 3.7 36.0 + - + -
151X VAL* 4.9 5.8 - - + -
159X VAL* 5.2 2.0 - - + -
160X PRO* 4.6 9.2 - - + +
162X VAL* 4.1 30.3 - - + -
164X LEU* 5.5 2.5 - - + -
170X LEU* 3.8 29.2 - - + -
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Residues in contact with GLU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X LYS* 2.6 64.4 + - + +
132X LEU* 4.1 11.4 - - - +
134X LEU* 1.3 77.5 - - - +
136X THR* 1.3 64.5 + - + +
138X GLU* 3.4 12.6 + - - +
139X LYS* 3.4 23.3 + - - +
162X VAL* 3.9 19.9 - - + -
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Residues in contact with THR 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X LEU* 2.8 42.2 + - + +
133X PHE 3.2 6.8 + - - -
135X GLU* 1.3 74.8 - - + +
137X ALA* 1.4 65.1 + - - +
139X LYS* 3.0 19.4 + - + +
140X HIS* 3.0 22.1 + - + +
215X GLU* 3.7 11.8 - - + +
216X PHE* 3.0 44.0 + - - +
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Residues in contact with ALA 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X LEU* 4.7 2.5 - - + -
133X PHE* 2.9 20.2 + - + +
134X LEU* 3.2 4.2 + - - +
136X THR* 1.4 75.4 + - - +
138X GLU* 1.3 58.7 + - - +
141X PHE* 2.8 32.5 + - + +
149X TYR* 3.4 30.3 - - + +
168X ARG* 3.3 8.1 + - - -
216X PHE* 3.5 25.2 - - + -
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Residues in contact with GLU 138 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134X LEU 2.9 18.7 + - - +
135X GLU* 3.5 10.8 - - - +
136X THR 3.2 0.2 - - - -
137X ALA* 1.3 76.3 - - - +
139X LYS* 1.3 62.2 + - + +
143X VAL* 3.6 13.9 - - - +
149X TYR* 2.5 30.6 + - - +
162X VAL* 4.7 2.5 - - + -
163X THR 3.8 15.8 - - - +
164X LEU* 3.5 13.9 - - + +
165X GLY* 2.8 30.9 + - - -
168X ARG* 2.7 25.6 + - - +
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Residues in contact with LYS 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X GLU* 3.4 15.9 + - - +
136X THR* 3.0 14.4 + - + +
138X GLU* 1.3 81.6 - - + +
140X HIS* 1.3 80.7 + - + +
143X VAL* 3.5 11.7 - - - +
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Residues in contact with HIS 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X THR* 3.0 20.1 + - + +
137X ALA 3.2 0.2 + - - -
139X LYS* 1.3 98.7 + - + +
141X PHE* 1.3 61.0 + - - +
142X MET 3.7 1.1 + - - -
143X VAL* 4.1 5.6 + - - -
216X PHE* 3.5 34.2 + - + -
217X ARG* 3.6 21.6 + - - -
218X ASP* 3.3 31.8 - - - +
219X HIS* 3.7 8.8 + - - +
220X VAL 2.9 25.0 + - - +
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Residues in contact with PHE 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116X ILE* 4.0 18.2 - - + -
118X LEU* 3.9 43.7 - - + -
137X ALA* 2.8 30.3 + - + +
140X HIS* 1.3 70.0 - - - +
142X MET* 1.3 95.5 + - + +
143X VAL* 3.1 2.2 + - - +
147X VAL* 4.2 13.9 - - + -
149X TYR* 5.0 0.9 - + - -
168X ARG* 2.8 36.2 + - - -
208X VAL* 4.4 11.9 - - + -
216X PHE* 3.8 28.9 - + + -
220X VAL* 3.3 19.5 - - + -
224X ILE* 4.7 1.1 - - + -
269X PHE* 5.4 1.3 - + - -
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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