Contacts of the helix formed by residues 159 - 171 (chain B) in PDB entry 3HB8
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 ASP 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ARG* 2.5 66.2 + - - +
141B HIS* 5.8 0.5 - - - -
157B GLY 3.9 2.8 + - - -
158B VAL* 1.3 71.1 - - - +
160B GLN* 1.3 62.2 + - - +
162B GLN* 3.0 21.7 + - + +
163B LYS* 2.9 23.6 + - - +
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Residues in contact with GLN 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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182A TRP* 4.8 0.9 + - - -
184A PRO* 3.9 21.2 - - + +
138B GLN 2.9 22.6 + - - -
139B TRP* 3.1 9.7 + - - +
142B PHE* 3.5 15.2 - - + +
158B VAL* 2.8 21.2 + - + +
159B ASP* 1.3 69.2 - - - +
161B LEU* 1.3 66.1 + - - +
163B LYS* 3.0 8.1 + - - +
164B VAL* 2.9 25.7 + - - +
178B ILE 3.7 8.0 - - - +
179B MET* 3.2 20.6 - - + -
180B CYS* 2.6 49.7 + - - +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 4.0 17.3 - - + -
139B TRP* 3.1 13.2 + - + +
140B ARG* 3.5 42.0 - - - +
160B GLN* 1.3 80.6 - - - +
162B GLN* 1.3 62.4 + - - +
164B VAL* 3.2 4.4 + - + +
165B ILE* 3.0 26.8 + - + +
179B MET* 3.9 32.3 - - + -
233B LEU* 4.6 7.6 - - + -
237B ILE* 4.4 20.2 - - + -
288B ILE* 3.9 28.9 - - + -
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Residues in contact with GLN 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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140B ARG* 4.2 6.8 - - - +
159B ASP* 3.0 29.2 + - + +
161B LEU* 1.3 77.5 - - - +
163B LYS* 1.3 57.5 + - - +
165B ILE* 3.4 21.3 + - - +
166B ASP* 2.7 56.0 + - - +
169B LYS* 5.8 1.0 + - - -
287B LYS* 5.4 11.5 - - - +
288B ILE* 4.3 19.4 - - - +
289B ASP* 5.0 2.8 + - - -
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Residues in contact with LYS 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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187A LEU* 5.4 10.7 - - - +
188A PRO* 6.2 2.3 - - - +
158B VAL* 4.2 23.5 - - + +
159B ASP 2.9 17.2 + - - +
160B GLN* 3.5 7.0 - - - +
162B GLN* 1.3 73.2 - - - +
164B VAL* 1.3 62.3 + - + +
166B ASP* 3.2 11.5 + - + +
167B THR* 2.9 37.7 + - - +
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Residues in contact with VAL 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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160B GLN 2.9 15.2 + - - +
161B LEU* 3.4 11.0 - - + +
163B LYS* 1.3 73.0 - - + +
165B ILE* 1.3 73.6 + - + +
167B THR* 3.1 5.0 + - - -
168B ILE* 3.0 33.3 + - + +
177B ILE* 3.6 23.1 - - + +
178B ILE 3.8 25.4 - - - +
179B MET* 3.9 13.9 - - + -
201B PHE* 3.5 29.8 - - + -
237B ILE* 4.7 3.1 - - + -
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Residues in contact with ILE 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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161B LEU* 3.0 26.5 - - + +
162B GLN* 3.5 26.0 - - - +
164B VAL* 1.3 78.8 - - - +
166B ASP* 1.3 65.8 + - - +
168B ILE* 3.3 7.1 + - - +
169B LYS* 3.3 34.4 + - - +
237B ILE* 3.4 46.2 - - + -
240B ILE* 3.7 28.0 - - + -
241B THR* 4.0 12.1 - - + +
288B ILE* 5.1 2.0 - - + -
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Residues in contact with ASP 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 GLN* 2.7 50.1 + - - +
163B LYS* 3.3 14.2 - - + +
164B VAL 3.1 0.2 - - - -
165B ILE* 1.3 76.4 - - - +
167B THR* 1.3 62.1 + - - +
169B LYS* 3.0 21.8 + - - +
170B THR* 3.2 19.0 + - + +
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Residues in contact with THR 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 LYS* 2.9 26.9 + - - +
164B VAL* 3.7 5.5 - - - -
166B ASP* 1.3 66.7 - - - +
168B ILE* 1.3 67.8 + - - +
169B LYS 2.9 2.6 + - - -
170B THR* 3.1 6.5 + - - -
171B ASN* 2.8 39.4 + - + +
174B ASP* 3.6 37.9 - - + +
177B ILE* 4.0 14.3 - - + -
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Residues in contact with ILE 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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164B VAL* 3.0 29.3 + - + +
165B ILE 3.6 7.4 - - - +
167B THR* 1.3 76.9 - - - +
169B LYS* 1.3 59.2 + - - +
172B PRO* 3.6 21.3 - - - +
177B ILE* 3.9 23.3 - - + -
201B PHE* 4.2 6.1 - - + -
203B VAL* 3.8 8.1 - - + -
208B LEU* 3.6 24.9 - - + -
237B ILE* 3.7 22.9 - - + -
241B THR* 4.0 13.0 - - + +
243B LEU* 3.5 31.4 - - + +
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Residues in contact with LYS 169 (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 GLN* 5.8 1.2 + - - -
165B ILE* 3.3 28.5 + - + +
166B ASP* 3.0 13.8 + - - +
167B THR 2.9 1.4 + - - -
168B ILE* 1.3 79.7 - - - +
170B THR* 1.3 65.9 + - + +
172B PRO* 4.4 4.1 - - - +
240B ILE* 3.4 26.6 + - - +
241B THR* 4.2 17.9 - - + +
286B GLU 5.2 4.9 + - - -
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 3.2 14.6 + - + +
167B THR* 3.1 5.3 + - - -
169B LYS* 1.3 82.2 - - + +
171B ASN* 1.3 87.7 + - - +
172B PRO* 3.7 5.2 - - - +
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Residues in contact with ASN 171 (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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167B THR* 2.8 28.5 + - + +
170B THR* 1.3 102.6 + - - +
172B PRO* 1.3 66.4 - - - +
173B ASP* 3.2 4.5 - - + -
174B ASP* 3.1 28.7 + - + +
177B ILE* 4.5 0.5 - - - +
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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