Contacts of the helix formed by residues 163 - 176 (chain A) in PDB entry 4AW9
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 VAL 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLY* 2.8 33.7 + - - +
162A HIS* 1.3 72.4 - - + +
164A LYS* 1.3 55.7 + - + +
166A LEU* 3.3 3.3 + - + +
167A ASN* 2.8 38.0 + - + +
193A SER 3.7 19.3 - - - +
194A MET* 3.8 29.6 - - - +
197A HIS* 6.2 4.0 - - + -
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Residues in contact with LYS 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 HIS* 3.3 5.5 - - + +
163A VAL* 1.3 83.5 - - + +
165A ASP* 1.3 65.8 + - - +
167A ASN* 3.2 9.1 - - + +
168A GLU* 3.0 48.9 + - - +
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Residues in contact with ASP 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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114A LEU* 3.8 21.8 - - + +
161A LEU* 4.6 3.1 - - + -
162A HIS* 3.1 33.9 + - - +
164A LYS* 1.3 83.2 - - - +
166A LEU* 1.3 60.0 + - - +
168A GLU* 3.6 13.9 + - - +
169A THR* 3.1 32.2 + - - -
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Residues in contact with LEU 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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113A PHE* 4.4 9.0 - - + -
114A LEU* 4.2 19.7 - - + +
117A LEU* 4.2 15.3 - - + -
154A LEU* 4.8 6.1 - - + -
161A LEU* 4.5 13.2 - - + +
162A HIS 3.2 11.2 + - - +
163A VAL* 3.7 8.3 - - + +
165A ASP* 1.3 73.8 - - - +
167A ASN* 1.3 61.3 + - - +
169A THR* 3.4 0.6 + - - -
170A ILE* 2.9 54.2 + - + +
184A PHE* 4.6 7.4 - - + -
186A ILE* 5.1 1.8 - - + -
194A MET* 3.8 28.3 - - + +
195A MET* 3.8 23.8 - - + -
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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
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163A VAL* 2.8 22.1 + - + +
164A LYS* 3.2 14.8 - - + +
166A LEU* 1.3 74.2 - - - +
168A GLU* 1.3 61.9 + - - +
170A ILE* 4.8 2.7 - - - -
171A HIS* 3.1 26.2 + - - +
197A HIS* 5.6 1.4 - - - +
310A NAG 1.4 75.2 + - - +
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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 LYS* 3.0 43.5 + - + +
165A ASP* 3.6 13.4 + - - +
166A LEU 3.4 0.2 - - - -
167A ASN* 1.3 82.8 - - - +
169A THR* 1.3 57.3 + - - +
171A HIS* 3.5 8.2 + - - +
172A TYR* 2.9 27.4 + - - +
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Residues in contact with THR 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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114A LEU* 3.5 31.2 - - + +
117A LEU* 3.7 36.8 - - + -
118A ARG* 3.8 24.6 + - + +
165A ASP 3.1 18.0 + - - -
166A LEU 3.8 2.9 - - - -
168A GLU* 1.3 76.4 - - - +
170A ILE* 1.3 59.9 + - - +
172A TYR* 3.1 8.2 + - - +
173A MET* 2.9 34.5 + - - +
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Residues in contact with ILE 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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117A LEU* 5.4 1.1 - - + -
166A LEU* 2.9 42.9 + - + +
167A ASN* 3.8 7.2 - - - +
169A THR* 1.3 74.8 - - - +
171A HIS* 1.3 61.0 + - - +
173A MET* 3.3 13.6 + - - +
174A TYR* 3.1 22.0 + - - +
179A TYR* 4.1 3.0 + - + +
182A MET* 5.5 2.0 - - - -
184A PHE* 3.9 30.3 - - + -
194A MET 5.8 0.7 - - - +
195A MET* 4.1 11.0 - - + -
198A LEU* 4.3 12.6 - - + -
202A ILE* 3.7 27.4 - - + -
204A VAL* 4.2 14.8 - - + -
310A NAG 3.9 6.1 - - + +
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Residues in contact with HIS 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* 3.1 19.2 + - - +
168A GLU* 3.7 8.6 + - - +
170A ILE* 1.3 74.4 - - - +
172A TYR* 1.3 60.8 + - - +
174A TYR* 3.4 14.9 + + - +
175A LYS* 3.0 49.3 + - + +
202A ILE* 5.8 4.9 - - + -
310A NAG 3.9 14.8 - - + +
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Residues in contact with TYR 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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118A ARG* 3.5 59.9 + - + +
168A GLU 2.9 15.9 + - - +
169A THR* 3.1 12.8 + - - +
171A HIS* 1.3 80.7 + - - +
173A MET* 1.3 60.6 + - - +
175A LYS* 3.5 2.8 + - - -
176A HIS* 3.0 77.4 + + + +
178A MET* 4.4 4.0 - - - -
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Residues in contact with MET 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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117A LEU* 3.1 54.5 - - + +
118A ARG* 4.8 1.6 - - - -
133A LEU* 3.8 20.6 - - + -
135A SER* 5.1 0.2 - - - +
141A VAL* 4.7 2.5 - - + -
169A THR* 2.9 20.4 + - + +
170A ILE* 3.3 13.0 + - - +
172A TYR* 1.3 76.9 - - - +
174A TYR* 1.3 60.3 + - - +
176A HIS 3.6 0.2 + - - -
177A LYS 3.3 3.1 + - - -
178A MET* 2.9 51.3 + - + +
179A TYR* 3.6 13.1 - - + -
182A MET* 3.2 37.2 - - + +
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Residues in contact with TYR 174 (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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170A ILE 3.1 11.5 + - - +
171A HIS* 3.8 16.4 - + - +
172A TYR 3.3 0.2 - - - -
173A MET* 1.3 74.3 - - - +
175A LYS* 1.3 67.8 + - - +
177A LYS* 3.3 24.3 + - - +
179A TYR* 3.4 22.8 - + - +
201A ASN 3.7 15.1 + - - -
202A ILE* 3.6 48.5 - - + -
203A ASN* 4.1 14.7 + - - -
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Residues in contact with LYS 175 (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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171A HIS* 3.0 39.1 + - + +
172A TYR* 3.9 4.5 - - - +
174A TYR* 1.3 80.3 - - + +
176A HIS* 1.3 75.3 + - + +
177A LYS* 3.2 18.6 + - - +
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Residues in contact with HIS 176 (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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172A TYR* 3.0 69.6 + + + +
173A MET 3.6 0.2 - - - -
174A TYR 3.3 0.2 - - - -
175A LYS* 1.3 97.7 - - + +
177A LYS* 1.3 71.2 + - - +
178A MET* 3.2 19.2 + - + +
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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