Contacts of the helix formed by residues 131 - 148 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 1.3 92.5 - - + +
132A THR* 1.3 67.1 + - + +
133A GLY 3.0 2.7 - - - -
134A LEU* 2.9 36.5 + - + +
135A ARG* 3.2 12.1 + - - +
226A GLU* 6.6 0.2 - - - -
227A ARG* 4.9 22.2 - - - +
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Residues in contact with THR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.1 15.8 + - + +
131A LYS* 1.3 83.3 - - + +
133A GLY* 1.3 67.4 + - - +
135A ARG* 3.1 23.3 + - - +
136A ARG* 2.9 30.2 + - - +
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE 3.3 10.4 + - - +
131A LYS 3.0 1.0 - - - -
132A THR* 1.3 84.3 + - - +
134A LEU* 1.3 56.1 + - - +
136A ARG* 3.2 12.9 + - - +
137A LEU* 2.9 32.7 + - - +
193A ALA* 6.3 1.1 - - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE 4.1 2.3 + - - +
131A LYS* 2.9 34.1 + - + +
133A GLY* 1.3 79.5 - - - +
135A ARG* 1.3 59.1 + - - +
137A LEU* 3.3 13.2 + - + +
138A GLN* 2.7 54.8 + - + +
193A ALA* 6.0 0.2 - - + -
227A ARG* 5.7 3.6 - - + +
230A SER* 4.2 24.7 - - - +
231A LEU* 4.0 28.0 - - + -
234A ILE* 4.6 5.2 - - + -
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS 3.2 8.4 + - - +
132A THR* 3.1 19.9 + - - +
134A LEU* 1.3 76.1 - - - +
136A ARG* 1.3 89.4 + - - +
138A GLN* 3.1 14.3 + - - +
139A HIS* 2.6 62.8 + - + +
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 2.9 26.5 - - - +
133A GLY* 3.5 9.8 - - - +
135A ARG* 1.3 106.5 - - - +
137A LEU* 1.3 59.6 + - - +
139A HIS* 3.4 7.3 + - - +
140A ARG* 3.2 35.9 + - - +
189A GLU* 4.8 16.6 + - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLY 2.9 16.4 + - - +
134A LEU* 3.4 25.1 - - + +
136A ARG* 1.3 75.5 - - - +
138A GLN* 1.3 63.2 + - - +
140A ARG* 3.4 2.6 + - - +
141A VAL* 2.8 31.0 + - - +
186A THR* 3.7 30.3 - - + +
189A GLU* 4.1 31.6 + - + +
190A LEU* 4.1 8.5 - - + +
193A ALA* 4.3 14.6 - - + -
231A LEU* 4.4 5.4 - - + -
234A ILE* 3.6 32.5 - - + -
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Residues in contact with GLN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 2.7 49.6 + - + +
135A ARG* 3.1 17.9 + - - +
137A LEU* 1.3 77.2 - - - +
139A HIS* 1.3 65.1 + - - +
141A VAL* 3.8 4.1 + - - +
142A GLY* 3.6 14.0 + - - -
230A SER* 5.0 5.7 + - - -
234A ILE* 3.9 20.9 - - + +
237A GLN* 6.1 1.1 - - - +
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Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG* 2.6 56.6 + - + +
136A ARG* 3.4 12.1 - - - +
138A GLN* 1.3 79.8 - - + +
140A ARG* 1.3 65.8 + - + +
141A VAL 3.3 0.2 - - - -
142A GLY* 3.2 4.7 + - - -
143A GLU* 3.1 27.3 + - - +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 3.2 21.7 + - - +
137A LEU* 3.4 4.5 + - - +
139A HIS* 1.3 73.0 - - + +
141A VAL* 1.3 63.1 + - - +
143A GLU* 3.1 33.4 + - - +
144A ILE* 2.8 25.6 + - - +
182A LEU* 6.0 2.0 - - - +
183A LEU* 3.9 21.2 - - + +
185A GLU* 3.7 29.7 + - - +
186A THR* 3.3 30.4 + - - +
189A GLU* 3.4 36.5 + - - -
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 2.8 22.4 + - + +
138A GLN* 4.1 5.4 - - - +
139A HIS 3.3 0.2 - - - -
140A ARG* 1.3 77.0 - - - +
142A GLY* 1.3 61.1 + - - +
144A ILE* 3.6 15.3 + - + +
145A HIS* 3.6 11.4 + - - +
186A THR* 3.9 11.7 - - + -
234A ILE* 4.1 14.8 - - + +
237A GLN* 3.8 33.4 - - + +
238A LEU* 3.3 35.2 - - + +
241A GLU* 5.0 5.7 - - + +
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLN 3.6 7.8 + - - -
139A HIS* 3.2 8.5 + - - -
140A ARG 3.2 0.6 - - - -
141A VAL* 1.3 77.7 - - - +
143A GLU* 1.3 63.3 + - - +
145A HIS* 3.1 20.7 + - - +
146A LEU* 3.5 14.2 + - - +
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A HIS* 3.1 17.4 + - - +
140A ARG* 3.1 39.4 + - - +
142A GLY* 1.3 76.2 - - - +
144A ILE* 1.3 61.9 + - - +
146A LEU* 3.6 8.6 + - - +
147A LEU* 3.3 24.3 + - + +
183A LEU* 4.0 21.1 - - + +
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG 2.8 21.5 - - - +
141A VAL* 3.9 9.9 - - + +
142A GLY 3.1 0.2 - - - -
143A GLU* 1.3 74.8 - - - +
145A HIS* 1.3 61.3 + - - +
147A LEU* 3.5 7.4 - - + +
148A ARG* 2.9 29.2 + - + +
181A MET* 4.3 15.9 - - + +
183A LEU* 3.7 32.3 - - + +
184A GLN* 4.1 21.3 - - - +
186A THR* 4.8 4.9 - - + +
238A LEU* 5.7 3.1 - - + -
241A GLU* 3.4 45.3 - - + +
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Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL 3.6 9.1 + - - +
142A GLY* 3.1 11.8 + - - +
144A ILE* 1.3 83.2 - - - +
146A LEU* 1.3 85.9 + - + +
148A ARG* 3.4 30.8 + - - +
149A GLU* 3.6 33.1 + - - -
241A GLU* 4.1 16.2 - - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 3.5 11.1 + - - +
143A GLU* 3.9 9.9 - - - +
144A ILE 3.3 0.4 - - - -
145A HIS* 1.3 97.9 - - + +
147A LEU* 1.3 65.9 + - - +
149A GLU* 2.9 33.7 + - - +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLU* 3.3 13.9 + - + +
144A ILE* 3.5 7.4 - - - +
146A LEU* 1.3 75.5 - - - +
148A ARG* 1.3 58.7 + - - +
149A GLU 2.8 18.7 + - - +
150A ALA* 3.7 9.4 + - - +
179A LEU* 3.6 33.7 - - + +
180A ALA 4.8 0.9 - - - -
181A MET* 3.8 32.7 - - + +
183A LEU* 3.6 28.0 - - + -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 2.9 18.3 + - + +
145A HIS* 3.8 24.1 + - - +
146A LEU 3.2 0.8 - - - -
147A LEU* 1.3 75.3 - - - +
149A GLU* 1.3 75.2 + - - +
150A ALA* 3.0 8.0 + - - +
151A LEU* 4.0 5.5 - - - -
153A LYS 4.4 20.1 + - - +
154A GLY* 5.7 1.8 - - - +
181A MET* 3.9 17.7 - - + -
240A GLN* 5.0 5.5 + - - +
241A GLU* 3.2 42.0 + - - +
243A GLY 4.1 20.1 + - - +
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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