Contacts of the helix formed by residues 153 - 165 (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 153 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147J VAL* 4.1 3.5 - - - +
152J LEU* 1.3 76.0 - - - +
154J ALA* 1.3 77.5 + - - +
155J ASP* 3.3 14.3 + - - +
156J SER* 3.5 30.0 + - - +
157J THR* 3.0 26.8 + - - +
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Residues in contact with ALA 154 (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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147J VAL* 3.5 27.6 - - + -
152J LEU 3.3 2.4 + - - +
153J ASN* 1.3 78.6 + - - +
155J ASP* 1.3 70.1 + - - +
156J SER 3.2 1.8 - - - -
157J THR* 3.4 1.4 + - - -
158J GLU* 2.9 23.9 + - - +
217J TYR* 3.8 10.8 + - - +
221J LEU* 5.6 5.6 - - + -
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Residues in contact with ASP 155 (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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153J ASN* 3.3 6.9 + - - +
154J ALA* 1.3 79.7 - - - +
156J SER* 1.3 55.7 + - - +
158J GLU* 2.7 29.2 - - - +
159J GLN* 3.2 7.4 + - - +
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Residues in contact with SER 156 (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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153J ASN* 3.5 30.6 + - - -
154J ALA 3.2 0.4 - - - -
155J ASP* 1.3 73.2 - - - +
157J THR* 1.3 64.7 + - - +
158J GLU 2.9 5.0 + - - -
159J GLN* 3.1 14.6 + - - +
160J ARG* 3.1 27.2 + - - +
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Residues in contact with THR 157 (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* 3.8 24.7 - - + -
147J VAL* 4.7 10.5 - - + +
152J LEU* 4.8 9.7 - - + +
153J ASN* 3.0 23.9 + - - +
154J ALA 3.4 3.6 + - - -
156J SER* 1.3 77.8 - - - +
158J GLU* 1.3 56.1 + - - +
160J ARG* 3.4 17.8 + - + +
161J LEU* 2.9 45.3 + - + +
179J LEU* 5.5 3.4 - - + -
217J TYR* 5.0 5.2 - - + -
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Residues in contact with GLU 158 (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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527C LYS* 3.4 17.1 - - - +
154J ALA 2.9 13.4 + - - +
155J ASP* 2.7 23.6 - - - +
156J SER 2.9 0.2 - - - -
157J THR* 1.3 74.6 - - - +
159J GLN* 1.3 62.5 + - - +
161J LEU* 3.2 7.9 + - - +
162J HIS* 2.5 60.6 + - + +
217J TYR* 3.0 27.9 + - - -
218J HIS* 2.6 28.9 + - - -
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Residues in contact with GLN 159 (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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155J ASP 3.2 5.6 + - - +
156J SER* 3.1 9.4 + - - +
158J GLU* 1.3 79.1 - - - +
160J ARG* 1.3 59.2 + - - +
162J HIS* 3.1 11.8 + - + +
163J LEU* 2.9 32.9 + - + +
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Residues in contact with ARG 160 (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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21G ASP* 4.5 12.3 + - - -
156J SER* 3.1 20.9 + - - -
157J THR* 3.8 26.5 + - - +
159J GLN* 1.3 77.2 - - - +
161J LEU* 1.3 62.9 + - - +
163J LEU* 3.0 22.9 - - + +
164J ILE* 3.0 24.8 + - + +
178J ARG* 3.4 37.6 - - - +
179J LEU* 3.4 41.2 - - + +
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Residues in contact with LEU 161 (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* 4.7 9.6 - - + -
140J GLY* 5.6 1.3 - - - -
143J LEU* 3.4 34.1 - - + -
157J THR* 2.9 35.1 + - + +
158J GLU* 3.5 14.4 - - - +
160J ARG* 1.3 76.6 - - - +
162J HIS* 1.3 63.0 + - + +
163J LEU 3.2 0.2 + - - -
164J ILE* 3.2 7.3 + - + +
165J ALA* 3.0 25.2 + - - +
179J LEU* 3.8 13.5 - - + -
213J TRP* 5.0 16.6 - - + -
214J VAL* 5.0 19.7 - - + -
217J TYR* 5.0 17.9 - - + -
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Residues in contact with HIS 162 (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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523C PRO* 2.8 65.3 - - + +
524C ARG* 3.4 8.2 + - + +
527C LYS* 3.7 16.6 - - + +
158J GLU* 2.5 62.9 + - + +
159J GLN* 3.1 11.0 + - + +
161J LEU* 1.3 76.6 - - + +
163J LEU* 1.3 56.4 + - - +
165J ALA 3.9 0.9 + - - -
166J ARG* 2.4 35.4 + - - +
214J VAL* 4.8 3.6 - - + -
218J HIS* 4.4 2.0 - + - -
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Residues in contact with LEU 163 (chain J).
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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201H VAL* 4.5 18.8 - - + -
159J GLN* 2.9 11.8 + - + +
160J ARG* 3.0 33.0 - - + +
161J LEU 3.1 0.4 - - - -
162J HIS* 1.3 77.0 - - - +
164J ILE* 1.3 79.5 + - + +
165J ALA 3.2 0.2 - - - -
166J ARG* 3.2 32.7 + - - +
167J GLN* 3.6 9.4 + - - +
175J HIS* 3.6 33.0 - - + +
178J ARG* 3.2 25.4 - - - +
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Residues in contact with ILE 164 (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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160J ARG* 3.0 12.1 + - + +
161J LEU* 4.0 6.3 - - + +
163J LEU* 1.3 84.7 - - + +
165J ALA* 1.3 63.8 + - - +
166J ARG 2.9 6.7 + - - -
167J GLN* 3.1 17.5 + - + +
172J VAL* 4.5 24.0 - - + -
175J HIS* 4.0 20.0 - - + +
176J LEU* 4.1 13.5 - - + -
179J LEU* 3.3 39.5 - - + -
202J TRP* 3.7 9.2 - - + -
213J TRP* 4.2 26.2 - - + -
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Residues in contact with ALA 165 (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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521C GLU 5.4 1.9 - - - +
523C PRO* 3.8 23.4 - - + +
161J LEU 3.0 16.1 + - - +
163J LEU 3.2 0.8 - - - -
164J ILE* 1.3 76.4 - - - +
166J ARG* 1.3 59.3 + - - +
167J GLN 3.7 0.2 - - - -
202J TRP* 4.6 3.5 - - - -
207J ARG* 5.4 2.4 - - - -
210J ALA* 3.2 35.3 - - + +
213J TRP* 6.4 1.6 - - - -
214J VAL* 3.8 24.5 - - + -
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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