Contacts of the helix formed by residues 174 - 181 (chain B) in PDB entry 4A69
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 GLY 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B HIS* 3.5 13.2 - - - -
166B TYR* 5.1 3.9 - - - -
168B ASP* 3.4 21.7 + - - -
172B HIS 3.5 2.2 + - - -
173B HIS* 1.3 73.1 - - - +
175B ASP* 1.3 63.0 + - - -
176B GLY 3.4 2.8 + - - -
177B VAL* 3.4 6.1 + - - +
178B GLN* 3.1 22.0 + - - +
191B SER* 3.3 17.0 + - - -
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Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B HIS* 2.8 29.9 + - - -
137B LYS* 3.0 27.9 + - - -
142B SER* 4.9 0.9 + - - -
173B HIS* 2.8 31.9 + - + +
174B GLY* 1.3 72.1 - - - +
176B GLY* 1.3 62.1 + - - -
178B GLN* 3.7 2.0 - - - +
179B GLU* 2.9 35.0 + - - +
201B PRO* 3.6 21.6 - - - +
203B THR* 3.8 7.6 + - + +
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.9 3.1 - - - -
134B HIS 3.2 14.1 + - - -
135B HIS 4.2 0.4 - - - -
136B ALA 3.9 9.1 - - - +
137B LYS* 4.0 15.4 - - - -
148B ASN* 3.8 11.6 + - - -
151B VAL* 4.2 1.6 - - - +
175B ASP* 1.3 85.7 + - - +
177B VAL* 1.3 61.5 + - - +
179B GLU* 3.8 2.0 - - - +
180B ALA* 3.1 23.6 + - - +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B HIS* 3.5 13.2 + - + +
148B ASN* 3.9 10.5 - - - +
150B ILE* 3.7 45.5 - - + -
151B VAL* 4.0 7.4 - - + -
154B ILE* 4.4 2.0 - - + -
166B TYR* 3.7 34.1 - - + +
174B GLY 3.4 3.0 + - - +
175B ASP 3.4 0.4 - - - -
176B GLY* 1.3 74.4 - - - +
178B GLN* 1.3 66.3 + - - +
180B ALA* 3.4 0.7 + - - +
181B PHE* 3.3 42.8 + - + +
189B THR* 4.2 4.1 - - + +
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Residues in contact with GLN 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR* 5.7 0.2 - - - -
173B HIS* 2.9 29.6 + - - -
174B GLY 3.1 17.7 + - - +
175B ASP* 3.7 5.2 - - - +
177B VAL* 1.3 76.7 - - - +
179B GLU* 1.3 52.9 + - - +
181B PHE 3.2 3.1 + - - -
182B TYR* 2.8 51.2 + - + -
189B THR* 4.1 18.6 + - - +
191B SER* 5.6 0.6 - - - -
208B GLU* 2.8 23.6 - - - +
218B CYS* 3.1 26.4 - - - +
220B ASN* 2.9 23.0 + - - +
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Residues in contact with GLU 179 (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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137B LYS* 3.9 36.0 - - + +
138B LYS* 5.5 1.6 + - - +
175B ASP* 2.9 17.6 + - - +
176B GLY 3.8 4.0 - - - +
178B GLN* 1.3 75.7 - - - +
180B ALA* 1.3 66.1 + - - +
181B PHE 3.1 0.7 + - - -
182B TYR* 3.4 18.7 + - - +
183B LEU* 5.0 5.2 - - - +
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Residues in contact with ALA 180 (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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61B PHE* 3.9 17.2 - - + -
151B VAL* 3.6 34.8 - - + -
176B GLY 3.1 18.9 + - - +
177B VAL 3.7 3.6 - - - +
178B GLN 3.4 0.2 - - - -
179B GLU* 1.3 77.2 - - - +
181B PHE* 1.3 70.1 + - + +
182B TYR 4.0 0.3 + - - -
183B LEU* 5.4 1.0 + - - +
184B THR* 5.4 0.3 - - - +
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 3.7 34.1 - - + -
154B ILE* 3.8 30.5 - - + -
155B LEU* 3.8 22.7 - - + -
158B LEU* 4.3 5.4 - - + -
177B VAL* 3.3 36.2 + - + +
178B GLN 3.2 4.8 + - - +
179B GLU 3.1 0.4 - - - -
180B ALA* 1.3 84.1 - - + +
182B TYR* 1.3 61.0 + - - +
183B LEU 3.1 4.4 + - - -
184B THR* 3.2 22.2 + - + +
187B VAL* 3.8 41.7 - - + +
189B THR* 4.7 3.4 - - + -
504B K 2.7 27.8 - - - -
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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