Contacts of the helix formed by residues 171 - 183 (chain D) in PDB entry 5AIS
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 HIS 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D PRO* 4.7 3.8 + - - +
128D MET* 3.7 19.0 - - + +
129D GLN* 3.6 41.9 + - + -
132D ASP* 2.9 28.4 + - - +
167D LEU 3.7 22.0 - - - -
168D LEU* 3.2 15.5 + - + +
170D ASN* 1.3 91.0 + - + +
172D PRO* 1.3 67.6 - - - +
173D ARG 3.2 2.9 - - - -
174D LEU* 3.1 29.9 + - + +
175D VAL* 3.2 12.6 + - - +
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Residues in contact with PRO 172 (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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132D ASP* 5.2 1.3 - - - +
168D LEU 4.4 0.6 - - - +
169D ASP 5.0 2.2 - - - +
170D ASN* 3.4 9.6 - - - +
171D HIS* 1.3 88.7 - - - +
173D ARG* 1.3 63.1 + - + +
175D VAL* 3.3 12.0 + - + +
176D THR* 2.8 32.6 + - - +
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Residues in contact with ARG 173 (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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132D ASP* 2.9 51.8 + - - +
133D THR* 4.7 2.6 - - - +
135D LEU* 3.6 20.8 - - + +
136D GLY* 2.7 33.6 + - - -
137D GLY* 5.0 4.7 - - - -
171D HIS 3.1 1.4 + - - -
172D PRO* 1.3 81.3 - - + +
174D LEU* 1.3 60.1 + - - +
176D THR* 3.5 9.3 + - - +
177D LEU* 3.2 18.9 + - - +
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Residues in contact with LEU 174 (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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128D MET* 3.5 27.4 - - - +
131D LEU* 4.0 17.7 - - + +
132D ASP* 3.9 24.7 - - + +
135D LEU* 4.1 14.6 - - + -
141D LEU* 5.8 2.5 - - + -
153D TRP* 3.2 45.6 + - + +
168D LEU* 3.9 23.8 - - + -
171D HIS* 3.1 21.9 + - + +
173D ARG* 1.3 74.5 - - - +
175D VAL* 1.3 63.7 + - - +
177D LEU* 3.5 5.0 + - + -
178D ARG* 3.3 12.3 + - - +
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Residues in contact with VAL 175 (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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168D LEU* 3.6 38.8 - - + +
171D HIS 3.2 8.4 + - - +
172D PRO* 3.3 12.3 + - + +
174D LEU* 1.3 74.3 - - - +
176D THR* 1.3 64.7 + - - +
178D ARG* 3.1 15.3 + - + +
179D LYS* 3.0 48.9 + - + +
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Residues in contact with THR 176 (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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172D PRO* 2.8 24.5 + - - +
173D ARG* 3.6 10.7 - - - +
174D LEU 3.3 0.2 - - - -
175D VAL* 1.3 75.5 - - - +
177D LEU* 1.3 57.2 + - - +
179D LYS* 3.2 16.8 + - + +
180D LYS* 3.0 44.4 + - + +
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Residues in contact with LEU 177 (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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135D LEU* 4.4 14.8 - - + -
139D GLU 3.8 22.0 - - - +
140D TRP* 3.9 15.5 - - + -
141D LEU* 3.6 34.1 - - + -
150D ASP* 3.5 22.0 - - + +
153D TRP* 3.5 26.0 - - + +
173D ARG 3.2 11.4 + - - +
174D LEU* 3.6 11.9 - - + +
175D VAL 3.2 0.2 - - - -
176D THR* 1.3 80.2 - - - +
178D ARG* 1.3 61.5 + - - +
180D LYS* 3.2 7.2 + - + +
181D VAL* 3.1 24.3 + - + +
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Residues in contact with ARG 178 (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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153D TRP* 3.7 10.3 - - + +
154D GLU* 3.3 14.3 + - - +
157D SER* 2.8 38.8 + - - +
158D THR* 3.1 29.3 + - - +
161D LEU* 3.6 22.8 - - - +
168D LEU* 3.5 27.7 - - - +
174D LEU 3.3 8.2 + - - +
175D VAL* 3.1 14.3 + - + +
177D LEU* 1.3 78.1 - - - +
179D LYS* 1.3 57.0 + - - +
181D VAL* 3.2 3.8 + - - +
182D GLN* 2.9 59.0 + - - +
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Residues in contact with LYS 179 (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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175D VAL* 3.0 39.5 + - + +
176D THR* 3.2 19.0 + - + +
178D ARG* 1.3 76.4 - - + +
180D LYS* 1.3 58.5 + - + +
182D GLN* 3.3 11.4 + - - +
183D ALA* 2.8 32.9 + - - +
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Residues in contact with LYS 180 (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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139D GLU* 2.6 51.7 + - - +
140D TRP* 3.7 32.5 - - + -
176D THR* 3.0 32.3 + - + +
177D LEU* 3.4 10.8 - - - +
178D ARG 3.2 0.2 - - - -
179D LYS* 1.3 77.2 - - + +
181D VAL* 1.3 62.0 + - - +
183D ALA* 3.4 14.2 + - - +
184D ILE* 3.6 14.9 + - - +
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Residues in contact with VAL 181 (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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20D TYR* 4.5 2.5 - - + -
140D TRP* 4.4 7.9 - - + -
146D VAL* 5.0 0.7 - - + -
150D ASP* 3.6 37.2 - - + +
151D PHE* 3.9 26.2 - - + +
154D GLU* 3.8 24.5 - - + -
177D LEU* 3.1 15.1 + - + +
178D ARG 3.2 6.0 + - - +
180D LYS* 1.3 75.9 - - - +
182D GLN* 1.3 63.2 + - - +
184D ILE* 3.3 25.5 + - - +
187D VAL* 3.5 20.2 - - + +
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Residues in contact with GLN 182 (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 GLU* 2.7 32.7 + - - +
158D THR* 4.7 0.6 + - - -
178D ARG* 2.9 50.9 + - - +
179D LYS* 3.9 9.2 - - - +
181D VAL* 1.3 75.8 - - - +
183D ALA* 1.3 58.6 + - - +
184D ILE 3.3 0.7 - - - -
187D VAL* 4.4 6.7 - - - -
188D ALA* 3.3 27.9 - - - +
191D ILE* 3.8 17.0 - - + +
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Residues in contact with ALA 183 (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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179D LYS 2.8 17.9 + - - +
180D LYS* 3.6 9.4 - - - +
181D VAL 3.2 0.6 - - - -
182D GLN* 1.3 74.8 - - - +
184D ILE* 1.3 63.6 + - - +
185D PRO* 3.3 9.0 - - - +
188D ALA* 4.8 2.5 - - - +
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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