Contacts of the helix formed by residues 158 - 168 (chain B) in PDB entry 2JDQ
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 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASP* 3.9 10.5 + - - -
157B GLY* 1.3 78.0 - - - +
159B SER* 1.3 58.4 + - - +
160B LEU* 4.0 6.1 - - + +
161B GLN* 2.8 47.7 + - + +
162B THR* 2.9 27.9 + - - -
752D LYS* 4.3 0.2 - - - -
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Residues in contact with SER 159 (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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158B ASN* 1.3 73.9 - - - +
160B LEU* 1.3 63.7 + - - +
163B ARG* 3.2 26.0 + - - +
199B ASP* 3.0 37.3 + - - +
200B SER* 4.7 7.8 - - - -
203B CYS* 5.8 0.7 - - - -
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Residues in contact with LEU 160 (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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158B ASN* 3.3 6.6 - - + +
159B SER* 1.3 83.2 - - - +
161B GLN* 1.3 60.6 + - - +
163B ARG* 3.8 19.1 - - - +
164B ILE* 3.1 31.5 + - + +
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Residues in contact with GLN 161 (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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118B ILE* 3.4 28.8 - - + +
119B ASP* 3.0 42.5 + - - +
122B ILE* 3.6 19.0 - - + +
154B ILE* 3.7 27.1 - - - +
157B GLY* 3.3 9.9 - - - -
158B ASN* 2.8 49.8 + - - +
160B LEU* 1.3 74.2 - - - +
162B THR* 1.3 65.6 + - - +
163B ARG 3.4 0.3 + - - -
164B ILE* 3.5 13.6 + - + +
165B VAL* 4.1 1.7 + - - +
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Residues in contact with THR 162 (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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155B ALA* 3.0 24.5 + - - +
157B GLY 4.0 0.2 + - - -
158B ASN 2.9 6.5 + - - -
160B LEU 3.4 0.2 - - - -
161B GLN* 1.3 78.7 - - - +
163B ARG* 1.3 60.0 + - - +
165B VAL* 3.3 8.9 + - - +
166B ILE* 3.3 28.1 + - + +
196B ILE* 4.1 26.4 - - + +
199B ASP* 3.4 31.4 - - + +
752D LYS* 2.8 25.6 + - - -
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Residues in contact with ARG 163 (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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159B SER 3.2 18.3 + - - +
160B LEU* 3.6 20.2 + - + +
161B GLN 3.2 0.8 - - - -
162B THR* 1.3 74.0 - - - +
164B ILE* 1.3 58.5 + - - +
165B VAL 3.2 2.0 - - - -
166B ILE* 3.7 22.2 - - + -
167B GLN* 2.8 66.6 + - + +
203B CYS* 6.0 1.8 - - - -
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Residues in contact with ILE 164 (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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122B ILE* 3.1 50.5 - - + +
128B VAL* 3.6 31.4 - - + +
160B LEU* 3.1 22.2 + - + +
161B GLN 3.8 5.6 - - - +
162B THR 3.3 0.4 - - - -
163B ARG* 1.3 78.3 - - - +
165B VAL* 1.3 57.3 + - + +
167B GLN* 4.1 10.0 - - - +
168B ALA* 3.3 24.8 + - - +
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Residues in contact with VAL 165 (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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128B VAL* 4.3 6.5 - - + -
151B LEU* 3.9 35.7 - - + +
154B ILE* 3.9 27.4 - - + -
155B ALA* 4.9 5.4 - - + +
161B GLN 4.3 0.9 - - - +
162B THR* 3.3 10.7 + - - +
163B ARG 3.2 0.2 - - - -
164B ILE* 1.3 76.3 - - - +
166B ILE* 1.3 63.7 + - - +
167B GLN 3.3 0.2 - - - -
168B ALA* 3.3 13.9 + - - +
169B GLY 3.4 8.1 + - - -
170B ALA* 3.4 29.9 + - + +
174B PHE* 4.8 4.0 - - + -
196B ILE* 4.3 19.7 - - + -
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Residues in contact with ILE 166 (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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162B THR* 3.3 17.5 + - + +
163B ARG* 3.4 22.0 + - + +
165B VAL* 1.3 76.5 - - - +
167B GLN* 1.3 61.9 + - + +
169B GLY* 3.3 13.7 + - - -
170B ALA 4.5 2.4 + - - +
171B VAL* 4.8 4.7 - - + -
196B ILE* 4.0 26.5 - - + -
203B CYS* 3.2 35.4 - - + -
206B TYR* 3.5 38.7 + - + -
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Residues in contact with GLN 167 (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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163B ARG* 2.8 71.0 + - + +
164B ILE* 4.4 8.6 - - - +
166B ILE* 1.3 75.0 - - + +
168B ALA* 1.3 59.2 + - - +
169B GLY* 3.1 6.3 + - - -
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Residues in contact with ALA 168 (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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128B VAL* 3.9 11.0 - - + -
129B ALA* 4.4 15.1 - - + +
132B VAL* 3.6 32.6 - - + +
164B ILE 3.3 18.5 + - - +
165B VAL 3.3 7.7 + - - +
167B GLN* 1.3 76.8 - - - +
169B GLY* 1.3 60.0 + - - +
170B ALA 3.7 0.2 - - - -
173B ILE* 5.4 0.2 - - - +
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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