Contacts of the helix formed by residues 181 - 192 (chain D) in PDB entry 6PB4
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 GLY 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D VAL* 3.7 8.5 - - - +
139D LEU* 3.5 13.0 - - - -
141D PHE* 4.0 10.5 - - - -
180D MET* 1.3 75.5 - - - +
182D ALA* 1.3 57.6 + - - -
183D GLU* 3.0 7.0 - - - -
184D ALA* 2.7 27.8 + - - +
185D ILE* 3.0 14.3 - - - +
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Residues in contact with ALA 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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110D PRO* 3.4 38.6 + - + +
111D THR* 5.1 1.6 - - - -
112D ALA* 5.7 2.5 - - + +
139D LEU* 3.8 6.5 - - + +
141D PHE* 5.7 0.4 - - - -
181D GLY* 1.3 71.8 - - - -
183D GLU* 1.3 57.0 + - - +
185D ILE* 2.9 13.4 + - + -
186D GLN* 2.6 39.8 + - + +
238D ILE* 4.2 14.4 - - + -
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Residues in contact with GLU 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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109D SER* 4.7 13.9 - - - -
110D PRO* 4.4 18.8 - - + +
147D ILE* 5.2 1.0 - - - +
179D LYS* 5.9 3.1 - - + +
181D GLY* 3.0 3.6 - - - -
182D ALA* 1.3 78.2 - - - +
184D ALA* 1.3 60.0 - - - +
185D ILE 3.1 1.0 + - - -
186D GLN* 4.9 1.7 - - - +
187D ALA* 3.3 20.6 + - - +
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Residues in contact with ALA 184 (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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145D VAL* 5.1 7.2 - - + -
147D ILE* 3.6 39.9 - - + +
179D LYS* 3.9 6.4 - - + +
180D MET* 3.9 13.5 - - - +
181D GLY* 2.7 29.7 + - - +
183D GLU* 1.3 75.0 - - - +
185D ILE* 1.3 60.0 + - + +
187D ALA* 4.0 3.1 - - - +
188D LEU* 3.7 17.0 + - - +
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Residues in contact with ILE 185 (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 LEU* 5.4 7.4 - - + -
135D ILE* 5.3 3.6 - - + -
138D VAL* 4.3 9.4 - - + -
139D LEU* 3.5 37.7 - - + -
145D VAL* 6.2 1.6 - - + -
181D GLY 3.0 19.7 - - - +
182D ALA* 2.9 10.2 + - + +
183D GLU 3.0 0.4 - - - -
184D ALA* 1.3 82.0 - - + +
186D GLN* 1.3 67.5 + - - +
187D ALA 3.1 0.7 - - - -
188D LEU* 2.9 17.8 + - + +
189D LEU* 2.7 37.9 + - + +
238D ILE* 6.2 2.2 - - + -
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Residues in contact with GLN 186 (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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110D PRO* 4.9 8.7 - - + +
182D ALA* 2.6 26.0 + - + +
183D GLU* 4.9 2.5 - - - +
185D ILE* 1.3 74.4 - - - +
187D ALA* 1.3 49.0 + - - +
189D LEU* 3.0 21.6 + - - +
190D LYS* 2.4 43.1 + - + +
235D GLU* 2.6 45.0 + - + +
238D ILE* 2.9 39.1 + - + +
240D THR* 6.3 0.8 - - - +
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Residues in contact with ALA 187 (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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147D ILE* 4.6 15.3 - - + -
183D GLU 3.3 21.5 + - - +
184D ALA 4.0 5.6 - - - +
186D GLN* 1.3 77.5 - - - +
188D LEU* 1.3 52.9 + - - +
190D LYS* 2.9 14.8 + - + +
191D SER* 2.4 37.9 + - - -
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Residues in contact with LEU 188 (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 LEU* 4.1 33.4 - - + -
130D MET* 5.7 4.3 - - + -
146D VAL 6.0 1.6 - - - +
147D ILE* 5.2 3.8 - - - +
156D ARG* 3.7 39.5 - - + +
157D GLN* 5.4 10.5 - - + +
184D ALA 3.7 12.8 + - - +
185D ILE* 2.9 18.4 + - + +
187D ALA* 1.3 77.5 - - - +
189D LEU* 1.3 60.3 + - + +
191D SER* 2.1 34.7 + - - +
192D MET* 2.9 21.7 + - + +
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Residues in contact with LEU 189 (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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124D ILE* 5.7 10.3 - - + +
127D LEU* 5.4 3.6 - - + -
128D LEU* 4.4 18.8 - - + -
185D ILE* 2.7 24.8 + - + +
186D GLN* 3.3 30.7 - - - +
188D LEU* 1.3 74.3 - - + +
190D LYS* 1.3 61.8 + - - +
191D SER 3.2 1.4 + - - -
192D MET* 3.4 36.5 + - - +
234D PRO* 3.5 43.2 - - + +
235D GLU* 2.9 18.6 - - + +
237D MET* 5.3 3.4 - - + -
238D ILE* 5.3 1.3 - - + -
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Residues in contact with LYS 190 (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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186D GLN* 2.4 32.7 + - + +
187D ALA* 3.1 14.8 - - - +
189D LEU* 1.3 67.9 - - - +
191D SER* 1.3 60.0 + - - +
235D GLU* 2.9 16.3 + - + +
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Residues in contact with SER 191 (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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156D ARG* 4.2 17.9 + - - -
187D ALA 2.4 15.6 + - - -
188D LEU* 2.1 39.4 + - - +
190D LYS* 1.3 77.8 - - - +
192D MET* 1.3 71.1 + - - +
193D ASP* 3.5 4.5 + - - +
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Residues in contact with MET 192 (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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127D LEU* 3.9 22.9 - - + -
128D LEU* 3.8 26.5 - - + -
156D ARG* 6.4 0.7 - - - -
188D LEU* 2.9 23.0 + - + +
189D LEU* 3.4 27.2 + - + +
191D SER* 1.3 81.0 + - - +
193D ASP* 1.3 61.3 + - - +
194D LEU* 4.0 19.7 + - + +
197D GLU* 3.4 35.0 - - - +
220D ARG* 5.4 5.8 - - - +
224D LEU* 5.7 0.9 - - + -
234D PRO* 5.9 2.7 - - + -
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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