Contacts of the helix formed by residues 138 - 149 (chain B) in PDB entry 5U07
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 ASN 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B ARG 3.8 0.8 + - - +
137B PRO* 1.3 74.8 - - - +
139B LEU* 1.3 70.4 + - - +
140B GLY 3.5 3.1 - - - +
141B VAL* 3.1 13.9 - - + +
142B SER* 3.0 20.3 + - - -
190B ILE* 5.3 0.9 - - - +
191B ASP* 5.4 5.0 + - - +
194B ILE* 3.5 12.9 - - + +
195B LEU 5.3 0.2 + - - -
198B ASP* 2.8 25.7 - - - +
212B GLU* 4.0 9.5 - - - +
213B TRP* 2.9 35.4 + - - +
216B ASP* 3.1 30.5 + - - +
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Residues in contact with LEU 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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138B ASN* 1.3 85.1 + - - +
140B GLY* 1.3 62.2 + - - +
141B VAL 3.4 0.4 - - - -
142B SER* 3.3 5.5 + - - -
143B LEU* 2.9 53.1 + - + +
161B LEU* 4.7 5.6 - - + -
179B LEU* 4.3 7.6 - - + -
180B VAL* 3.7 16.4 - - + -
183B LEU* 5.6 1.1 - - + -
190B ILE* 3.5 28.5 - - + -
195B LEU* 3.6 25.1 - - + -
198B ASP* 5.3 0.2 - - - +
213B TRP* 3.9 41.1 - - + -
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASN* 3.5 5.3 - - - +
139B LEU* 1.3 82.8 - - - +
141B VAL* 1.3 56.7 + - - +
143B LEU* 3.2 5.6 + - - -
144B ALA 2.9 24.8 + - - -
161B LEU* 5.6 1.6 - - - -
213B TRP* 3.5 26.7 + - - +
216B ASP* 4.4 0.9 - - - -
217B TYR* 3.3 23.6 - - - -
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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
----------------------------------------------------------
137B PRO* 3.5 18.6 - - + -
138B ASN 3.1 33.4 - - - +
140B GLY* 1.3 75.9 - - - +
142B SER* 1.3 60.9 + - - +
144B ALA* 4.0 1.3 - - - +
145B GLN* 2.9 32.8 + - - +
216B ASP* 3.6 25.1 - - + +
220B THR* 3.0 39.4 - - + +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PRO* 4.9 4.9 - - - +
138B ASN 3.0 15.2 + - - -
139B LEU* 3.3 11.2 + - - -
140B GLY 3.2 0.2 - - - -
141B VAL* 1.3 83.6 - - - +
143B LEU* 1.3 57.0 + - - +
145B GLN* 2.7 29.2 + - - +
146B ALA* 2.9 16.3 + - - +
183B LEU* 4.5 5.8 - - - -
188B VAL* 3.8 0.5 - - - +
189B HIS* 3.2 28.2 + - - -
190B ILE* 4.3 12.8 - - - +
191B ASP 4.8 2.3 + - - -
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Residues in contact with LEU 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 LEU* 2.9 40.9 + - + +
140B GLY* 3.6 4.9 - - - +
142B SER* 1.3 74.3 - - - +
144B ALA* 1.3 60.2 + - - +
146B ALA* 3.1 6.5 + - + +
147B VAL* 2.9 33.5 + - + +
152B LEU* 5.7 5.2 - - + -
157B THR* 3.8 20.4 - - + -
161B LEU* 3.4 31.4 - - + -
179B LEU* 4.2 13.7 - - + +
183B LEU* 3.6 27.6 - - + -
217B TYR* 3.8 13.5 - - + -
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Residues in contact with ALA 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 GLY 2.9 12.1 + - - +
141B VAL 4.0 2.9 - - - +
143B LEU* 1.3 74.8 - - - +
145B GLN* 1.3 57.1 + - - +
147B VAL* 3.1 4.5 + - - +
148B PHE* 2.9 29.5 + - - +
217B TYR* 3.3 42.7 - - + +
220B THR* 4.3 5.2 - - - -
221B LEU* 3.7 27.2 - - + +
224B LEU* 4.7 1.6 - - - -
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Residues in contact with GLN 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 2.9 26.3 + - - +
142B SER* 2.7 23.4 + - - +
144B ALA* 1.3 77.1 - - - +
146B ALA* 1.3 57.3 + - - +
148B PHE 4.5 0.2 - - - +
149B ASP* 2.8 45.7 + - - +
150B LYS* 4.6 7.5 + - - +
188B VAL* 3.1 24.4 - - - +
189B HIS* 4.1 13.6 + - - +
220B THR* 5.3 1.1 - - + -
224B LEU* 3.8 24.8 - - + +
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Residues in contact with ALA 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 SER 2.9 19.6 + - - +
143B LEU* 3.1 10.1 + - + +
145B GLN* 1.3 78.2 - - - +
147B VAL* 1.3 61.2 + - - +
150B LYS* 3.0 37.0 + - - +
151B GLY 3.4 1.7 + - - -
152B LEU* 3.9 15.3 + - + +
183B LEU* 4.5 2.7 - - + -
188B VAL* 3.4 31.4 - - + -
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Residues in contact with VAL 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 LEU* 2.9 20.1 + - + +
144B ALA* 3.1 8.5 + - - +
146B ALA* 1.3 75.8 - - + +
148B PHE* 1.3 68.1 + - - +
151B GLY* 3.1 21.8 + - - -
152B LEU* 3.9 20.1 - - + +
153B ASN 4.1 15.3 - - - +
154B ALA* 3.5 27.4 - - + -
157B THR* 4.7 9.4 - - + +
217B TYR* 4.0 18.2 - - + +
221B LEU* 4.6 11.2 - - + -
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Residues in contact with PHE 148 (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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144B ALA 2.9 15.4 + - - +
145B GLN 4.2 1.8 - - - +
147B VAL* 1.3 80.4 - - - +
149B ASP* 1.3 78.6 + - - +
151B GLY* 4.2 2.1 + - - -
221B LEU* 4.5 9.6 - - + -
224B LEU* 3.8 45.8 - - + -
225B THR* 4.4 20.2 - - + -
228B ALA* 4.1 17.5 - - + -
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Residues in contact with ASP 149 (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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145B GLN* 2.8 37.6 + - - +
148B PHE* 1.3 94.2 - - - +
150B LYS* 1.3 76.6 + - + +
151B GLY* 3.1 6.1 + - - -
224B LEU* 5.7 1.6 - - - +
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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