Contacts of the helix formed by residues 131 - 147 (chain B) in PDB entry 4Y5U
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 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B PHE* 1.3 80.2 - - + +
132B THR* 1.3 58.1 + - + +
133B GLY 3.4 0.2 - - - -
134B LEU* 3.5 36.0 + - + +
135B ARG* 2.9 25.8 + - - +
138B GLN* 4.8 6.9 - - - +
226B GLU* 4.6 17.7 - - - -
227B ARG* 5.7 12.3 - - + +
230B SER* 4.2 11.5 + - - -
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE* 3.7 20.3 + - + +
131B LYS* 1.3 76.4 - - + +
133B GLY* 1.3 62.5 + - - +
135B ARG* 3.0 49.6 + - - +
136B ARG* 3.2 6.8 + - - +
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE 3.5 13.7 - - - +
131B LYS 3.4 0.2 - - - -
132B THR* 1.3 81.0 + - - +
134B LEU* 1.3 58.2 + - - +
136B ARG* 3.1 40.0 + - - +
137B LEU* 3.4 7.3 + - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE 3.9 8.2 + - - +
131B LYS* 3.5 53.9 + - + +
132B THR 3.2 0.6 - - - -
133B GLY* 1.3 72.7 - - - +
135B ARG* 1.3 59.3 + - - +
136B ARG 3.1 0.4 - - - -
137B LEU* 3.1 11.0 + - + +
138B GLN* 2.3 51.1 + - - +
193B ALA* 6.4 2.2 - - + -
227B ARG* 5.2 2.7 - - + +
230B SER* 3.7 34.3 - - - +
231B LEU* 4.0 22.9 - - + -
234B ILE* 4.6 6.5 - - + -
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS 2.9 14.6 + - - +
132B THR* 3.0 36.3 + - - +
134B LEU* 1.3 76.9 - - - +
136B ARG* 1.3 61.1 + - - +
138B GLN* 2.9 14.1 + - + +
139B HIS* 3.2 46.7 + - + +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B THR* 3.2 4.9 + - - +
133B GLY* 3.1 27.4 + - - +
134B LEU 3.1 0.2 - - - -
135B ARG* 1.3 83.0 - - - +
137B LEU* 1.3 62.0 + - - +
139B HIS* 3.1 8.0 + - - +
140B ARG* 3.1 40.6 + - + +
189B GLU* 3.9 32.7 + - + +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 3.4 5.5 + - - +
134B LEU* 3.1 14.9 + - + +
136B ARG* 1.3 81.8 - - - +
138B GLN* 1.3 58.4 + - - +
140B ARG* 4.0 2.2 - - - +
141B VAL* 2.9 30.7 + - - +
186B THR* 3.8 35.7 - - + +
189B GLU* 4.0 20.0 - - + +
190B LEU* 3.7 26.2 - - + -
193B ALA* 4.6 3.1 - - + -
231B LEU* 4.4 11.4 - - + -
234B ILE* 3.7 37.0 - - + +
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Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS* 4.8 6.7 - - - +
134B LEU* 2.3 60.3 + - - +
135B ARG* 2.9 13.7 - - + +
137B LEU* 1.3 77.2 - - - +
139B HIS* 1.3 67.8 + - + +
141B VAL* 3.4 5.8 + - - +
142B GLY* 3.3 17.0 + - - -
230B SER* 5.4 2.6 + - - -
234B ILE* 3.9 17.9 - - + +
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Residues in contact with HIS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ARG* 3.2 36.8 + - + +
136B ARG* 3.1 11.3 + - - +
138B GLN* 1.3 84.2 - - + +
140B ARG* 1.3 63.0 + - + +
142B GLY* 3.4 2.8 + - - -
143B GLU* 3.2 28.5 + - - +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 3.1 30.9 + - + +
137B LEU* 4.2 3.8 - - - +
138B GLN 3.3 0.2 - - - -
139B HIS* 1.3 75.0 - - + +
141B VAL* 1.3 65.4 + - - +
142B GLY 3.1 1.3 - - - -
143B GLU* 3.1 15.4 + - - +
144B ILE* 3.0 29.5 + - - +
182B LEU 4.7 0.4 + - - -
183B LEU* 3.9 32.7 + - + +
185B GLU* 3.5 30.8 + - - +
186B THR* 3.7 20.7 + - + -
189B GLU* 2.2 47.0 + - - -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU 2.9 21.1 - - - +
138B GLN* 3.4 6.5 + - - +
140B ARG* 1.3 74.2 - - - +
142B GLY* 1.3 63.3 + - - +
144B ILE* 3.1 13.8 - - + +
145B HIS* 3.0 24.8 + - + +
186B THR* 4.9 4.0 - - + -
234B ILE* 4.2 18.6 - - + -
237B GLN* 3.6 39.5 - - + +
238B LEU* 3.8 23.8 - - + -
241B GLU* 6.1 1.8 - - + +
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B GLN 3.3 9.3 + - - -
139B HIS* 3.8 4.7 - - - -
140B ARG 3.1 0.8 - - - -
141B VAL* 1.3 81.8 - - - +
143B GLU* 1.3 55.1 - - - +
145B HIS* 3.0 14.3 - - - +
146B LEU* 2.9 33.3 + - - +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B HIS* 3.2 17.2 + - - +
140B ARG* 3.1 23.9 + - - +
142B GLY* 1.3 72.8 - - - +
144B ILE* 1.3 56.1 + - + +
145B HIS 3.0 1.8 - - - -
146B LEU* 2.8 15.4 + - + +
147B LEU* 2.6 39.6 + - + +
183B LEU* 4.1 15.6 - - + +
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ARG 3.0 8.9 + - - +
141B VAL* 3.1 23.6 - - + +
143B GLU* 1.3 74.9 - - - +
145B HIS* 1.3 59.5 + - - +
147B LEU* 3.5 16.9 + - - +
148B ARG* 3.6 17.2 + - - +
181B MET* 4.6 11.4 - - + +
183B LEU* 2.6 51.6 - - + -
184B GLN* 3.8 22.4 - - - +
186B THR* 4.7 4.0 - - + +
238B LEU* 4.6 12.8 - - + -
241B GLU* 3.3 37.4 - - + +
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Residues in contact with HIS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B VAL* 3.0 16.1 + - + +
142B GLY* 3.0 20.9 - - - +
144B ILE* 1.3 78.2 - - - +
146B LEU* 1.3 65.4 + - + +
148B ARG* 3.2 42.3 + - - +
149B GLU* 3.7 7.9 - - - +
241B GLU* 3.4 15.2 + - - +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLY 2.9 17.4 + - - +
143B GLU* 2.8 19.8 + - + +
145B HIS* 1.3 84.4 - - + +
147B LEU* 1.3 58.4 + - + +
148B ARG 2.9 5.5 + - - -
149B GLU* 2.5 24.1 + - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLU* 2.6 19.6 + - + +
144B ILE* 3.8 10.3 - - - +
145B HIS 3.3 0.6 - - - -
146B LEU* 1.3 76.0 - - + +
148B ARG* 1.3 55.9 + - - +
149B GLU 3.4 10.8 + - - +
150B ALA* 5.4 0.5 - - - +
180B ALA* 4.1 20.6 - - - +
181B MET* 4.2 18.2 - - + +
183B LEU* 4.9 16.8 - - + -
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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