Contacts of the helix formed by residues 155 - 167 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D SER* 1.3 77.0 + - - +
156D ALA* 1.3 62.2 + - - +
158D CYS* 3.2 19.5 + - - +
159D GLU* 4.3 2.1 + - - +
180D ASP 4.1 1.4 + - - -
181D ILE* 3.4 27.7 - - - +
182D ASN* 5.2 4.9 - - + +
184D ALA* 4.5 10.1 - - + -
185D GLY* 3.9 15.7 - - - +
188D VAL* 5.3 3.0 - - + +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ASP* 3.6 19.1 - - + +
130D GLN* 5.3 7.1 + - - +
154D SER* 3.0 13.4 + - - +
155D ALA* 1.3 78.9 - - - +
157D SER* 1.3 57.2 + - - +
158D CYS 3.4 0.3 + - - -
159D GLU* 3.7 5.0 + - - +
160D PRO* 3.1 21.7 - - - +
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ASP* 2.4 37.4 + - - -
129D LEU* 3.5 21.7 - - - +
153D LEU* 3.7 21.9 - - - +
154D SER 3.2 8.1 + - - -
156D ALA* 1.3 76.3 - - - +
158D CYS* 1.3 60.6 + - - +
159D GLU 3.3 0.4 - - - -
160D PRO* 3.2 8.1 - - - +
161D LEU* 3.0 33.3 + - - +
181D ILE* 6.1 0.2 - - - -
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Residues in contact with CYS 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D SER 4.2 0.9 - - - -
155D ALA* 3.2 13.1 + - - +
157D SER* 1.3 77.6 - - - +
159D GLU* 1.3 60.4 + - - +
161D LEU* 3.8 3.4 - - - -
162D ALA* 2.8 29.3 + - - +
181D ILE* 3.8 28.9 - - - -
185D GLY* 3.4 44.0 - - - +
188D VAL* 3.7 9.1 - - + +
189D LEU* 3.5 21.3 - - + +
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ALA 4.3 1.8 + - - +
156D ALA 3.7 5.5 + - - +
158D CYS* 1.3 75.9 - - - +
160D PRO* 1.3 75.6 - - + +
162D ALA* 2.9 13.7 + - - +
163D SER* 2.9 18.2 + - - +
166D ARG* 3.6 20.3 + - - -
188D VAL* 3.6 24.2 - - + +
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Residues in contact with PRO 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ASP 6.0 0.2 - - - +
129D LEU* 4.6 5.2 - - + +
130D GLN* 4.5 24.2 - - + +
133D CYS* 3.9 25.2 - - + +
156D ALA 3.1 20.2 - - - +
157D SER* 3.2 12.6 - - - +
159D GLU* 1.3 93.5 - - + +
161D LEU* 1.3 62.8 + - - +
163D SER* 2.9 19.9 + - - +
164D VAL* 3.1 15.2 + - - +
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LEU* 3.7 14.1 - - + -
133D CYS* 3.9 17.5 - - - -
136D LEU* 5.0 2.5 - - + -
146D LEU* 4.6 12.6 - - + -
148D LEU* 4.2 19.5 - - + -
153D LEU* 5.0 1.8 - - + -
157D SER* 3.0 26.1 + - - +
158D CYS* 3.8 5.8 - - - +
160D PRO* 1.3 75.5 - - - +
162D ALA* 1.3 62.9 + - - +
164D VAL* 3.3 8.3 + - + +
165D LEU* 3.0 27.3 + - - +
171D PHE* 6.5 0.4 - - + -
174D LEU* 4.7 13.2 - - + -
176D VAL* 4.0 27.1 - - + -
189D LEU* 3.9 16.6 - - + -
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D CYS 2.8 19.7 + - - +
159D GLU* 2.9 10.1 + - - +
161D LEU* 1.3 76.0 - - - +
163D SER* 1.3 58.6 + - - +
165D LEU* 3.4 11.6 + - - +
166D ARG* 2.8 54.4 + - - +
188D VAL* 4.3 11.7 - - + +
189D LEU* 4.2 2.7 - - + +
192D GLY* 4.1 14.3 - - - -
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Residues in contact with SER 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 3.5 19.4 - - - +
159D GLU* 2.9 15.0 + - - +
160D PRO* 2.9 15.9 + - - +
162D ALA* 1.3 74.6 - - - +
164D VAL* 1.3 66.2 + - - +
166D ARG* 3.6 13.8 + - - +
167D ALA* 3.1 23.4 + - - +
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Residues in contact with VAL 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D CYS* 3.9 20.4 - - + +
136D LEU* 3.7 41.1 - - + +
137D LEU* 3.7 23.8 - - + +
160D PRO 3.1 5.9 + - - +
161D LEU* 3.7 12.1 - - + +
163D SER* 1.3 71.9 - - - +
165D LEU* 1.3 61.2 + - + +
167D ALA* 2.8 21.3 + - - +
168D LYS* 2.9 18.3 + - + +
171D PHE* 4.3 27.8 - - + -
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 3.0 17.2 + - + +
162D ALA* 3.5 11.9 - - - +
164D VAL* 1.3 79.5 - - + +
166D ARG* 1.3 61.1 + - - +
167D ALA 2.9 1.7 + - - -
168D LYS 3.4 13.6 + - - +
171D PHE* 3.8 32.8 - - + -
174D LEU* 4.4 24.0 - - + -
189D LEU* 4.4 17.5 - - + +
192D GLY 4.4 6.5 - - - +
193D LEU* 3.9 37.9 - - + +
196D SER* 2.6 23.5 + - - -
198D CYS* 4.5 7.8 - - - -
200D LEU* 4.7 4.9 - - + -
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Residues in contact with ARG 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLU* 3.6 15.0 + - - -
162D ALA* 2.8 42.6 + - - +
163D SER* 3.8 12.7 + - - +
165D LEU* 1.3 72.7 - - - +
167D ALA* 1.3 59.0 + - - +
188D VAL* 5.3 1.0 + - - +
191D GLN* 4.2 5.7 - - - +
192D GLY* 3.5 19.4 - - - +
195D ASP* 3.2 44.8 + - - +
196D SER* 3.7 11.2 - - - +
197D PRO* 3.7 14.4 - - - +
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Residues in contact with ALA 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 3.6 21.3 - - + +
163D SER 3.1 16.1 + - - +
164D VAL 2.8 7.5 + - - +
166D ARG* 1.3 80.0 - - - +
168D LYS* 1.3 58.6 + - - +
169D PRO* 3.2 12.5 - - - +
197D PRO* 5.4 1.1 - - - +
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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