Contacts of the helix formed by residues 155 - 167 (chain A) in PDB entry 1A4Y
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 ALA 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A SER* 1.3 74.9 + - - +
156A ALA* 1.3 62.3 + - - +
158A CYS* 3.2 19.0 + - - +
159A GLU* 4.3 1.7 + - - +
180A ASP 4.1 1.6 + - - -
181A ILE* 3.4 27.3 - - - +
182A ASN* 5.7 2.9 - - + +
184A ALA* 4.3 10.1 - - + -
185A GLY* 3.7 18.9 - - - +
188A VAL* 5.8 1.6 - - - +
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Residues in contact with ALA 156 (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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126A ASP* 3.6 16.4 - - + +
130A GLN* 3.9 9.8 + - - +
154A SER* 2.9 14.5 + - - +
155A ALA* 1.3 78.9 - - - +
157A SER* 1.3 56.4 + - - +
158A CYS 3.4 0.3 + - - -
159A GLU* 3.8 4.9 + - - +
160A PRO* 3.2 19.8 - - - +
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Residues in contact with SER 157 (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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126A ASP* 2.6 29.0 + - - -
129A LEU* 3.1 31.0 - - - +
130A GLN* 4.6 1.6 - - - +
153A LEU* 3.4 20.8 - - - +
154A SER 3.0 9.2 + - - -
156A ALA* 1.3 78.4 - - - +
158A CYS* 1.3 61.6 + - - +
159A GLU 3.4 0.2 - - - -
160A PRO* 3.2 14.2 - - - +
161A LEU* 3.2 20.1 + - - +
181A ILE* 5.8 0.9 - - - -
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Residues in contact with CYS 158 (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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154A SER 4.3 0.4 - - - -
155A ALA* 3.2 13.7 + - - +
157A SER* 1.3 77.1 - - - +
159A GLU* 1.3 60.8 + - - +
161A LEU* 3.9 7.5 - - - +
162A ALA* 2.8 31.5 + - - +
181A ILE* 3.9 29.4 - - - -
185A GLY* 3.3 42.2 - - - +
188A VAL* 3.3 11.4 - - + +
189A LEU* 4.1 12.7 - - + +
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Residues in contact with GLU 159 (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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155A ALA 4.3 2.0 + - - +
156A ALA 3.8 5.0 + - - +
158A CYS* 1.3 79.7 - - - +
160A PRO* 1.3 70.4 - - + +
162A ALA* 3.2 2.3 + - - +
163A SER* 3.0 21.3 + - - -
166A ARG* 3.2 23.5 + - - -
188A VAL* 3.8 21.2 - - + +
191A GLN* 5.7 0.7 - - - +
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Residues in contact with PRO 160 (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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129A LEU* 5.1 1.1 - - + -
130A GLN* 3.8 36.1 - - + +
133A CYS* 3.7 27.1 - - + +
137A LEU* 5.6 0.9 - - + +
156A ALA 3.2 11.7 - - - +
157A SER* 3.2 14.1 - - - +
159A GLU* 1.3 95.4 - - + +
161A LEU* 1.3 59.6 + - - +
163A SER* 3.2 8.5 + - - -
164A VAL* 3.1 25.5 + - - +
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Residues in contact with LEU 161 (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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129A LEU* 3.8 28.5 - - + -
133A CYS* 4.5 7.4 - - - -
136A LEU* 5.2 3.4 - - + -
146A LEU* 4.5 13.5 - - + -
148A LEU* 4.5 4.3 - - + -
153A LEU* 5.3 3.1 - - + -
157A SER* 3.2 24.8 + - - +
158A CYS* 3.9 2.2 - - - +
160A PRO* 1.3 76.2 - - - +
162A ALA* 1.3 64.2 + - - +
164A VAL* 3.0 9.6 + - + +
165A LEU* 3.0 27.9 + - + +
171A PHE* 6.5 0.2 - - + -
174A LEU* 4.2 18.8 - - + -
176A VAL* 4.0 26.5 - - + -
189A LEU* 3.9 23.3 - - + -
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Residues in contact with ALA 162 (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 CYS 2.8 19.9 + - - +
159A GLU* 3.6 5.2 - - - +
161A LEU* 1.3 76.0 - - - +
163A SER* 1.3 56.7 + - - +
165A LEU* 3.5 10.0 + - - +
166A ARG* 3.0 44.3 + - - +
188A VAL* 4.0 18.2 - - + +
189A LEU* 4.4 6.0 - - - +
192A GLY* 3.9 22.1 - - - -
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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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137A LEU* 3.6 16.1 - - - +
159A GLU* 3.0 15.4 + - - -
160A PRO* 3.5 12.8 - - - -
161A LEU 3.1 0.2 - - - -
162A ALA* 1.3 76.5 - - - +
164A VAL* 1.3 63.4 + - - +
166A ARG* 3.6 20.0 + - - +
167A ALA* 3.3 22.9 + - - +
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Residues in contact with VAL 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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133A CYS* 4.1 13.9 - - - +
136A LEU* 3.7 41.7 - - + +
137A LEU* 3.7 24.5 - - + +
146A LEU* 6.2 0.4 - - + -
160A PRO 3.1 13.8 + - - +
161A LEU* 3.0 14.6 + - + +
163A SER* 1.3 75.5 - - - +
165A LEU* 1.3 64.5 + - + +
167A ALA* 3.0 4.0 + - - +
168A LYS* 2.9 31.9 + - + +
171A PHE* 4.6 21.8 - - + -
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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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161A LEU* 3.0 16.4 + - + +
162A ALA* 3.6 11.9 - - - +
164A VAL* 1.3 81.1 - - + +
166A ARG* 1.3 57.8 + - - +
167A ALA 3.2 0.7 + - - -
168A LYS* 3.5 14.2 + - - +
171A PHE* 3.4 43.1 - - + -
174A LEU* 3.9 24.7 - - + -
189A LEU* 4.6 8.5 - - + +
192A GLY 4.6 2.0 - - - +
193A LEU* 3.4 40.6 - - + +
196A SER* 2.6 30.8 + - - -
197A PRO* 4.1 0.5 - - - +
198A CYS* 4.4 3.9 - - - +
200A LEU* 4.8 1.6 - - + -
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Residues in contact with ARG 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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159A GLU* 3.2 26.7 + - - -
162A ALA* 3.0 24.2 + - - +
163A SER* 3.9 19.2 + - - +
164A VAL 3.3 0.2 - - - -
165A LEU* 1.3 76.1 - - - +
167A ALA* 1.3 57.7 + - + +
191A GLN* 4.2 4.9 + - - +
192A GLY* 3.5 34.0 - - - +
195A ASP* 3.5 37.5 + - + +
196A SER* 3.7 8.0 - - - +
197A PRO* 3.5 17.8 - - - +
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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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137A LEU* 4.2 15.3 - - + +
163A SER 3.3 15.0 + - - +
164A VAL 3.0 5.1 + - - +
166A ARG* 1.3 81.9 - - - +
168A LYS* 1.3 59.5 + - - +
169A PRO* 3.4 11.0 - - - +
197A PRO* 5.6 0.4 - - - -
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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