Contacts of the helix formed by residues 162 - 170 (chain B) in PDB entry 4BPU
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 ARG 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ILE* 3.9 5.0 - - - +
158B GLU* 3.3 46.6 + - - +
159B LYS 3.3 5.4 + - - -
161B LEU* 1.3 98.6 - - + +
163B GLU* 1.3 62.7 + - - +
164B GLN 3.3 2.7 - - - -
165B GLU* 3.3 19.3 + - + -
166B ILE* 2.9 34.7 + - + +
201B TYR* 4.2 5.8 - - + -
203B GLU* 3.0 41.1 + - - +
208B TYR* 3.6 36.4 + - - -
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Residues in contact with GLU 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 LYS* 3.2 11.3 + - - +
160B THR* 3.6 34.5 + - - +
161B LEU 3.6 1.4 - - - -
162B ARG* 1.3 78.2 - - - +
164B GLN* 1.3 62.0 + - + +
166B ILE* 3.3 1.2 + - - +
167B VAL* 2.9 39.5 + - + +
178B LEU* 3.4 44.9 + - + +
179B GLY* 4.3 4.6 + - - -
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Residues in contact with GLN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 6.0 1.1 - - - +
162B ARG* 3.3 0.4 - - - +
163B GLU* 1.3 81.1 - - + +
165B GLU* 1.3 63.4 + - + +
167B VAL* 3.3 5.6 + - - +
168B ALA* 2.8 37.7 + - - +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PRO* 3.9 13.6 - - + +
213A ARG* 3.2 34.7 + - - +
214A LYS* 4.4 3.3 + - - -
161B LEU 5.0 3.0 - - - +
162B ARG* 3.3 25.8 + - + +
164B GLN* 1.3 86.5 - - + +
166B ILE* 1.3 54.1 + - - +
168B ALA* 3.3 3.2 + - - +
169B SER* 2.5 39.2 + - - -
201B TYR* 3.7 34.9 + - + +
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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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154B ILE* 5.3 0.4 - - + -
159B LYS* 4.4 12.3 - - - +
162B ARG* 2.9 37.0 + - + +
163B GLU 3.8 2.9 - - - +
165B GLU* 1.3 76.6 - - - +
167B VAL* 1.3 57.3 + - - +
169B SER* 4.3 2.5 - - - -
170B SER* 3.0 33.1 + - - +
173B LEU* 3.9 19.5 - - + +
178B LEU* 4.4 11.0 - - + -
183B ILE* 4.1 37.2 - - + -
201B TYR* 4.3 9.2 - - + -
208B TYR* 4.2 30.5 - - + +
210B PRO* 5.3 2.0 - - + -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LYS* 3.2 34.2 + - + +
163B GLU* 2.9 26.4 + - + +
164B GLN* 3.7 6.3 - - - +
166B ILE* 1.3 72.8 - - - +
168B ALA* 1.3 65.1 + - - +
170B SER 3.2 6.2 - - - +
173B LEU* 4.5 21.3 - - + -
178B LEU* 4.3 24.0 - - + +
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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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207A LYS* 3.9 26.1 - - + +
208A ILE 3.5 19.3 - - - +
209A HIS* 4.0 12.6 + - - +
210A PRO* 4.1 9.4 - - + -
213A ARG* 5.2 4.7 - - - +
164B GLN 2.8 22.2 + - - +
165B GLU* 3.7 4.7 - - - +
167B VAL* 1.3 74.3 - - - +
169B SER* 1.3 63.0 + - - +
171B PRO* 5.7 0.3 - - - +
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Residues in contact with SER 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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209A HIS* 3.6 14.8 - - - -
210A PRO* 3.3 14.9 - - - +
165B GLU 2.5 23.2 + - - -
166B ILE 3.9 1.8 - - - -
168B ALA* 1.3 80.5 - - - +
170B SER* 1.3 59.5 + - - +
171B PRO* 3.2 13.5 - - - +
198B ARG 3.4 16.1 - - - +
199B LYS 3.5 3.8 - - - -
200B VAL 3.5 4.3 - - - -
201B TYR* 3.2 39.8 - - - +
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LYS* 3.2 15.4 + - - -
166B ILE* 3.0 19.1 + - - +
167B VAL 3.2 5.5 - - - +
169B SER* 1.3 74.1 - - - +
171B PRO* 1.3 61.7 - - - +
172B SER* 3.1 16.0 + - - -
173B LEU* 3.5 24.7 + - - +
199B LYS 3.4 15.5 + - - -
200B VAL* 3.9 8.8 - - - +
201B TYR 4.7 0.2 + - - -
208B TYR 4.6 0.7 + - - -
210B PRO* 3.9 17.1 - - - +
213B ASP* 4.3 3.1 - - - -
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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