Contacts of the helix formed by residues 138 - 151 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136J ARG 3.8 1.3 + - - +
137J PRO* 1.3 74.9 - - - +
139J LEU* 1.3 69.3 + - - +
140J GLY 3.5 3.1 - - - +
141J VAL* 3.1 13.7 - - + +
142J SER* 3.0 20.3 + - - -
190J ILE* 5.3 1.5 - - - +
191J ASP* 5.4 4.3 + - - +
194J ILE* 3.5 13.6 - - + +
195J LEU 5.3 0.2 + - - -
198J ASP* 2.8 26.0 + - - +
212J GLU* 4.0 8.9 - - - +
213J TRP* 2.9 36.8 + - - +
216J ASP* 3.1 30.4 + - - +
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Residues in contact with LEU 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J ASN* 1.3 84.6 + - - +
140J GLY* 1.3 62.6 + - - +
141J VAL 3.4 0.7 - - - -
142J SER* 3.3 4.9 + - - -
143J LEU* 2.9 52.5 + - + +
161J LEU* 4.7 6.1 - - + -
179J LEU* 4.3 7.9 - - + -
180J VAL* 3.7 16.8 - - + -
183J LEU* 5.6 0.9 - - + -
190J ILE* 3.5 28.7 - - + -
195J LEU* 3.6 24.9 - - + -
198J ASP* 5.3 0.4 - - - +
213J TRP* 3.9 42.0 - - + -
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Residues in contact with GLY 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J ASN* 4.3 5.3 - - - +
139J LEU* 1.3 83.2 - - - +
141J VAL* 1.3 57.2 + - - +
143J LEU* 3.2 5.7 + - - -
144J ALA 2.9 24.9 + - - -
161J LEU* 5.6 1.6 - - - -
213J TRP* 3.5 28.9 + - - +
216J ASP* 4.4 1.1 - - - -
217J TYR* 3.3 24.1 - - - -
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Residues in contact with VAL 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J PRO* 3.5 18.4 - - + -
138J ASN 3.1 33.2 - - - +
140J GLY* 1.3 76.3 - - - +
142J SER* 1.3 60.3 + - - +
144J ALA* 4.0 0.7 - - - +
145J GLN* 2.9 33.4 + - - +
216J ASP* 3.6 24.6 - - + +
220J THR* 3.0 39.2 - - + +
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Residues in contact with SER 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J PRO* 4.9 4.9 - - - +
138J ASN 3.0 15.5 + - - -
139J LEU* 3.3 11.4 + - - -
140J GLY 3.2 0.4 - - - -
141J VAL* 1.3 83.6 - - - +
143J LEU* 1.3 56.1 + - - +
145J GLN* 2.7 27.9 + - - -
146J ALA* 2.9 15.4 + - - +
183J LEU* 4.5 6.7 - - - -
188J VAL* 3.8 0.7 - - - +
189J HIS* 3.2 28.0 + - - -
190J ILE* 4.3 13.0 - - - +
191J ASP 4.8 2.3 + - - -
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Residues in contact with LEU 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J LEU* 2.9 40.5 + - + +
140J GLY* 3.6 4.5 - - - +
142J SER* 1.3 74.8 - - - +
144J ALA* 1.3 60.3 - - - +
146J ALA* 3.1 6.7 + - + +
147J VAL* 2.9 32.8 + - + +
152J LEU* 5.7 5.2 - - + -
157J THR* 3.8 20.2 - - + -
161J LEU* 3.4 31.9 - - + -
179J LEU* 4.2 13.9 - - + +
183J LEU* 3.6 28.0 - - + -
217J TYR* 3.8 13.0 - - + -
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Residues in contact with ALA 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J GLY 2.9 11.7 + - - +
141J VAL 4.0 2.9 - - - +
143J LEU* 1.3 75.2 - - - +
145J GLN* 1.3 59.0 + - - +
147J VAL* 3.1 4.9 + - - +
148J PHE* 2.9 29.6 + - - +
217J TYR* 3.3 42.0 - - + +
220J THR* 4.3 5.6 - - - -
221J LEU* 3.7 27.3 - - + +
224J LEU* 4.7 1.6 - - - -
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Residues in contact with GLN 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J VAL 2.9 25.7 + - - +
142J SER* 2.7 23.8 + - - +
144J ALA* 1.3 77.3 - - - +
146J ALA* 1.3 58.8 + - - +
148J PHE* 4.5 0.4 - - - +
149J ASP* 2.8 46.5 + - - +
150J LYS* 4.6 6.6 + - - +
188J VAL* 3.1 24.4 - - - +
189J HIS* 4.1 14.0 + - - +
220J THR* 5.3 1.3 - - + -
224J LEU* 3.8 24.5 - - + +
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Residues in contact with ALA 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J SER 2.9 19.8 + - - +
143J LEU* 3.1 9.4 + - + +
145J GLN* 1.3 77.1 - - - +
147J VAL* 1.3 63.0 + - - +
150J LYS* 3.0 36.1 + - - +
151J GLY 3.4 1.4 + - - -
152J LEU* 3.9 16.1 + - + +
183J LEU* 4.5 2.9 - - + -
188J VAL* 3.4 31.2 - - + -
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Residues in contact with VAL 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J LEU* 2.9 19.9 + - + +
144J ALA* 3.1 8.3 + - - +
146J ALA* 1.3 75.0 - - + +
148J PHE* 1.3 66.8 + - - +
151J GLY* 3.1 22.9 + - - -
152J LEU* 3.9 20.8 - - + +
153J ASN 4.1 15.5 - - - +
154J ALA* 3.5 28.3 - - + -
157J THR* 4.7 9.4 - - + -
217J TYR* 4.0 17.5 - - + +
221J LEU* 4.6 11.4 - - + -
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Residues in contact with PHE 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J ALA 2.9 15.0 + - - +
145J GLN 4.2 1.8 - - - +
147J VAL* 1.3 80.2 - - - +
149J ASP* 1.3 78.9 + - - +
151J GLY* 4.2 2.1 + - - -
221J LEU* 4.5 9.6 - - + -
224J LEU* 3.8 46.4 - - + -
225J THR* 4.4 21.3 - - + -
228J ALA* 4.1 17.3 - - + -
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Residues in contact with ASP 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J GLN* 2.8 37.4 + - - +
148J PHE* 1.3 94.4 - - - +
150J LYS* 1.3 78.0 + - + +
151J GLY* 3.1 5.7 + - - -
224J LEU* 5.7 1.4 - - - +
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Residues in contact with LYS 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J GLN* 4.6 8.9 + - - -
146J ALA* 3.0 20.1 + - - +
149J ASP* 1.3 91.2 + - - +
151J GLY* 1.3 60.3 + - - +
152J LEU* 4.5 15.6 - - + +
186J ASP* 3.6 22.7 - - + +
187J GLN* 3.5 27.0 + - - -
188J VAL* 4.1 15.5 - - + +
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Residues in contact with GLY 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J ALA 3.4 0.2 + - - -
147J VAL 3.1 16.3 + - - -
148J PHE 4.7 1.3 - - - -
149J ASP 3.1 5.6 + - - -
150J LYS* 1.3 79.1 - - - +
152J LEU* 1.3 69.0 + - - +
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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