Contacts of the helix formed by residues 162 - 173 (chain A) in PDB entry 4B23
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A TRP* 2.8 39.9 + - + +
146A MET* 5.4 0.2 - - - -
159A PRO* 2.9 23.6 + - + +
160A ALA 3.2 0.4 - - - +
161A ASP* 1.3 79.1 + - - +
163A SER* 1.3 59.0 + - - +
164A THR* 3.3 11.6 + - - -
165A LEU* 2.9 29.2 + - + +
166A LYS* 2.9 30.6 + - - +
203A TRP* 3.2 24.5 + - - -
7X A 3.8 5.5 + - - -
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASP 3.4 5.3 + - - -
162A ASP* 1.3 75.0 + - - +
164A THR* 1.3 62.8 + - - +
166A LYS* 3.3 4.4 + - - +
167A ASN* 3.1 23.6 + - - -
178A LYS* 2.7 33.1 + - - +
6X 3DR 3.1 45.9 + - - +
7X A 4.4 3.8 + - - -
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Residues in contact with THR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP* 3.3 10.3 + - - -
163A SER* 1.3 75.5 - - - +
165A LEU* 1.3 67.1 + - - +
167A ASN* 3.0 10.6 + - + +
168A GLU* 2.9 41.3 + - - +
203A TRP* 4.3 11.2 - - + +
206A PRO* 5.2 4.9 - - + -
6X 3DR 2.6 30.3 + - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A MET* 4.0 7.2 - - - -
159A PRO* 4.0 23.1 - - + +
160A ALA* 4.4 2.0 - - - +
162A ASP* 2.9 26.1 + - + +
164A THR* 1.3 75.7 - - - +
166A LYS* 1.3 58.1 + - - +
168A GLU* 3.2 5.7 + - - +
169A ALA* 2.8 29.3 + - + +
184A VAL* 3.6 32.1 - - + -
199A ALA* 3.5 44.0 - - + +
202A LEU* 4.0 17.3 - - + -
203A TRP* 3.8 13.6 - - + +
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ALA 3.3 25.6 - - - +
161A ASP* 4.0 10.6 + - - +
162A ASP 2.9 19.8 + - - +
163A SER* 3.5 9.2 - - - +
165A LEU* 1.3 75.4 - - - +
167A ASN* 1.3 65.5 + - - +
169A ALA* 3.7 6.0 - - - +
170A LYS* 3.0 19.4 + - - +
178A LYS* 3.6 24.5 - - + -
179A PRO* 3.4 36.7 + - + +
180A GLN* 4.4 5.9 + - - +
181A THR* 3.2 30.1 + - - +
184A VAL* 4.1 7.6 - - + -
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Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A SER 3.1 17.6 + - - -
164A THR* 3.0 13.1 + - + +
166A LYS* 1.3 76.9 - - - +
168A GLU* 1.3 66.6 + - - +
170A LYS* 3.4 20.3 + - - +
171A GLU* 3.3 17.3 + - - +
178A LYS* 3.3 27.9 + - - +
6X 3DR 3.8 19.8 + - - -
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A THR* 2.9 34.8 + - - +
165A LEU* 3.5 8.3 - - - +
167A ASN* 1.3 79.1 - - - +
169A ALA* 1.3 61.6 + - - +
171A GLU* 3.2 17.9 + - - +
172A PHE* 2.9 30.9 + - - +
202A LEU* 2.8 40.0 - - + +
203A TRP* 4.0 6.2 - - - -
205A ILE* 3.7 19.4 - - + +
206A PRO* 3.4 26.9 - - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 2.8 22.4 + - + +
166A LYS* 3.7 6.7 - - - +
168A GLU* 1.3 73.3 - - - +
170A LYS* 1.3 63.9 + - - +
172A PHE* 4.2 3.6 - - - -
173A PHE* 2.9 51.5 + - + +
175A LEU* 4.1 2.8 - - + +
179A PRO* 4.3 12.1 - - + -
184A VAL* 4.3 15.7 - - + -
187A LEU* 5.6 0.4 - - + -
202A LEU* 4.9 6.2 - - + +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS 3.0 13.1 + - - +
167A ASN* 3.4 14.8 - - - +
168A GLU 3.1 0.2 - - - -
169A ALA* 1.3 77.1 - - - +
171A GLU* 1.3 59.7 + - + +
174A GLY* 3.0 7.1 + - - -
175A LEU* 2.7 59.1 + - + +
176A SER* 3.6 8.9 + - - +
177A SER* 3.5 32.3 - - - +
178A LYS* 3.7 13.7 - - + +
179A PRO* 3.9 7.6 - - + +
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASN* 3.3 19.6 + - - +
168A GLU* 3.2 23.9 + - - +
170A LYS* 1.3 78.5 - - + +
172A PHE* 1.3 68.1 + - - +
174A GLY* 2.9 13.9 + - - -
205A ILE* 4.5 17.3 - - + +
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.4 58.9 - - + +
21A TRP* 3.5 45.8 - + - -
24A LEU* 3.8 27.6 - - + -
168A GLU 2.9 21.2 + - - +
169A ALA* 3.9 2.9 - - - +
171A GLU* 1.3 75.7 - - - +
173A PHE* 1.3 86.0 + + - +
202A LEU* 3.8 14.8 - - + -
205A ILE* 4.2 11.2 - - + +
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP* 5.8 2.2 - - - -
20A LYS* 3.8 23.8 - - - +
21A TRP* 4.1 17.5 - + - -
169A ALA* 2.9 43.3 + - + +
172A PHE* 1.3 101.6 - + - +
174A GLY* 1.3 64.9 + - - +
175A LEU* 3.4 21.4 - - + +
184A VAL* 6.0 0.2 - - + -
187A LEU* 3.7 59.5 - - + -
188A THR* 4.3 9.9 - - + -
202A LEU* 5.1 2.5 - - + -
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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