Contacts of the helix formed by residues 164 - 178 (chain A) in PDB entry 1AIS
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 GLU 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 5.2 0.3 - - - +
11A ILE* 4.0 19.3 - - - +
105A MET* 3.8 19.9 - - + +
107A PHE* 3.8 20.4 - - + -
163A SER* 1.3 71.2 - - - +
165A ALA* 1.3 65.2 + - - +
167A ALA* 3.2 4.3 + - - +
168A TRP* 3.1 25.5 + - - +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A SER* 3.4 6.2 + - - +
164A GLU* 1.3 78.4 - - - +
166A ASP* 1.3 65.5 + - - +
168A TRP* 3.8 8.0 - - - +
169A GLU* 3.1 22.0 + - - +
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Residues in contact with ASP 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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144A PRO* 3.4 34.6 - - + +
161A ALA* 4.0 13.6 - - + -
162A LYS* 4.8 6.8 + - - +
163A SER* 3.3 25.2 + - - +
164A GLU 3.1 0.8 - - - -
165A ALA* 1.3 80.8 - - - +
167A ALA* 1.3 59.5 + - - +
169A GLU* 3.1 2.8 + - - +
170A ALA* 2.8 26.0 + - - +
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Residues in contact with ALA 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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9A LEU* 4.1 8.7 - - + -
107A PHE* 3.5 39.3 - - + -
158A CYS* 4.0 13.0 - - - -
161A ALA* 3.8 13.6 - - + +
163A SER 3.4 2.4 + - - +
164A GLU 3.2 7.5 + - - +
166A ASP* 1.3 79.3 - - - +
168A TRP* 1.3 57.4 + - - +
170A ALA* 3.3 3.6 + - - +
171A VAL* 3.0 34.1 + - - +
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Residues in contact with TRP 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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4A MET* 3.3 56.2 - - + +
7A VAL* 3.1 32.6 + - + +
9A LEU* 3.6 33.2 - - + +
164A GLU 3.1 15.9 + - - +
165A ALA* 3.8 9.2 - - - +
166A ASP 3.2 0.2 - - - -
167A ALA* 1.3 77.5 - - - +
169A GLU* 1.3 56.1 + - - +
171A VAL* 3.4 2.1 + - - -
172A ARG* 2.9 31.0 + - + +
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Residues in contact with GLU 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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144A PRO* 3.6 22.7 - - + -
165A ALA 3.1 15.2 + - - +
166A ASP* 3.1 10.7 + - - +
168A TRP* 1.3 73.2 - - - +
170A ALA* 1.3 65.3 + - - +
172A ARG* 3.1 39.0 + - - +
173A LYS* 2.9 47.5 + - + +
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Residues in contact with ALA 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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141A VAL* 3.9 23.8 - - + +
144A PRO* 4.3 4.2 - - + +
146A SER* 3.3 26.5 - - - +
148A ILE* 3.4 15.8 - - + +
158A CYS* 4.4 3.8 - - - -
166A ASP 2.8 15.6 + - - +
167A ALA* 3.5 9.4 - - - +
169A GLU* 1.3 78.4 - - - +
171A VAL* 1.3 60.6 + - - +
173A LYS* 3.3 4.0 + - - +
174A LEU* 3.2 16.6 + - - +
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Residues in contact with VAL 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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4A MET* 4.1 7.6 - - + -
7A VAL* 3.9 23.8 - - + -
9A LEU* 4.2 18.4 - - + -
111A ILE* 3.9 21.8 - - + -
148A ILE* 3.9 16.8 - - + -
156A ILE* 4.0 17.5 - - + -
158A CYS* 4.9 4.7 - - + -
167A ALA 3.0 21.8 + - - +
168A TRP* 3.8 5.4 - - - +
170A ALA* 1.3 73.3 - - - +
172A ARG* 1.3 59.9 + - - +
174A LEU* 3.2 3.6 + - + +
175A LEU* 2.9 32.7 + - + +
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Residues in contact with ARG 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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1A MET* 4.2 23.1 - - - +
2A VAL* 3.2 41.0 - - + +
4A MET* 3.5 28.0 - - + +
168A TRP* 2.9 17.2 + - + +
169A GLU* 3.1 39.3 + - - +
171A VAL* 1.3 76.8 - - - +
173A LYS* 1.3 66.1 + - - +
175A LEU* 3.3 1.9 + - - -
176A ARG* 3.0 31.4 + - - +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A TYR* 4.4 6.0 + - + +
141A VAL* 4.3 13.7 - - + -
142A LYS* 6.1 0.4 - - - +
143A GLU* 2.9 39.3 + - - +
144A PRO* 4.8 0.9 - - + -
169A GLU* 2.9 41.0 + - - +
170A ALA* 3.6 6.3 - - - +
172A ARG* 1.3 84.9 - - - +
174A LEU* 1.3 63.6 + - - +
176A ARG* 3.5 19.5 + - - +
177A GLU* 3.6 13.2 + - - +
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Residues in contact with LEU 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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111A ILE* 5.2 5.4 - - + -
124A LEU* 3.9 21.5 - - + -
139A TYR* 3.8 30.2 - - + -
148A ILE* 3.6 39.7 - - + -
150A LEU* 4.7 13.9 - - + -
156A ILE* 4.8 5.2 - - + -
170A ALA 3.2 13.6 + - - +
171A VAL* 3.2 8.3 + - + +
173A LYS* 1.3 73.0 - - - +
175A LEU* 1.3 68.1 + - + +
176A ARG 3.1 0.2 - - - -
177A GLU* 3.0 12.7 + - - +
178A LEU* 3.0 39.2 + - + +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A VAL* 3.9 11.6 - - + +
3A ASP 4.0 19.3 - - - +
4A MET* 4.0 16.4 - - - -
7A VAL* 4.8 6.5 - - + -
111A ILE* 4.1 39.7 - - + +
113A ARG* 4.2 10.5 - - - +
171A VAL* 2.9 20.5 + - + +
172A ARG 3.8 4.3 - - - +
174A LEU* 1.3 79.1 - - + +
176A ARG* 1.3 55.8 + - - +
178A LEU* 3.9 19.3 - - + -
179A ASP* 3.0 50.9 + - - +
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Residues in contact with ARG 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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2A VAL* 4.3 19.5 - - + +
172A ARG* 3.0 16.3 + - - +
173A LYS* 3.5 14.1 - - - +
174A LEU 3.1 0.2 - - - -
175A LEU* 1.3 77.5 - - - +
177A GLU* 1.3 89.6 + - - +
179A ASP* 3.9 3.1 + - - +
180A LYS* 3.3 44.0 + - - +
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Residues in contact with GLU 177 (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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124A LEU* 3.3 26.0 - - + -
125A PRO* 4.0 19.4 - - + +
139A TYR* 3.7 18.2 - - - +
173A LYS 3.7 12.1 - - - +
174A LEU 3.0 4.6 + - - +
176A ARG* 1.3 113.3 + - - +
178A LEU* 1.3 65.1 + - - +
180A LYS* 3.2 40.9 + - - +
181A TYR* 4.0 9.5 - - - -
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Residues in contact with LEU 178 (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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111A ILE* 3.7 17.5 - - + -
113A ARG* 3.5 16.4 + - - +
115A PHE* 3.6 32.5 - - + -
120A VAL* 4.1 21.1 - - + -
124A LEU* 4.3 8.5 - - + -
150A LEU* 3.9 17.0 - - + -
174A LEU* 3.0 42.3 + - + +
175A LEU* 4.0 9.6 - - + +
177A GLU* 1.3 75.5 - - - +
179A ASP* 1.3 58.2 + - - +
180A LYS 3.3 1.3 + - - -
181A TYR* 3.2 24.7 + - - +
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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