Contacts of the helix formed by residues 132 - 144 (chain D) in PDB entry 6IY6
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 PRO 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D ALA* 3.7 23.3 - - + -
130D SER 3.3 7.1 - - - +
131D PRO* 1.4 77.5 - - + +
133D LEU* 1.3 64.3 - - - +
134D SER 3.2 2.9 - - - -
135D LEU* 3.1 38.7 + - + +
136D LEU* 3.4 16.0 + - + +
187D LEU* 5.3 3.4 - - + -
189D TRP* 3.8 22.2 - - + -
195D THR* 4.3 7.4 - - + +
210D GLU* 3.7 28.7 - - + +
287D GLN* 4.9 0.2 - - - +
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Residues in contact with LEU 133 (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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131D PRO 2.9 7.7 + - - -
132D PRO* 1.3 68.5 - - - +
134D SER* 1.3 63.9 + - - +
136D LEU* 3.2 14.1 + - + -
137D VAL* 3.0 35.0 + - + +
210D GLU* 5.1 0.4 + - - -
282D TRP* 4.2 5.6 - - + -
283D SER* 3.7 31.4 - - - +
286D GLN* 3.9 17.0 - - + -
287D GLN* 3.3 29.7 + - + +
315D ALA* 4.4 24.2 - - + +
316D LEU* 4.2 11.0 - - + -
319D LEU* 4.1 19.5 - - + -
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Residues in contact with SER 134 (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 PRO 4.1 0.3 - - - -
133D LEU* 1.3 79.1 - - - +
135D LEU* 1.3 54.7 + - - +
138D LEU* 3.2 33.4 + - - +
210D GLU* 2.4 44.9 + - - +
214D ALA* 4.9 2.5 - - - -
279D VAL* 3.7 6.3 - - - +
280D VAL* 4.0 28.5 - - - -
283D SER* 3.4 24.0 - - - -
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Residues in contact with LEU 135 (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* 3.8 22.0 - - + -
132D PRO* 3.1 25.8 + - + +
134D SER* 1.3 76.7 + - - +
136D LEU* 1.3 59.4 + - + +
137D VAL 3.3 0.2 - - - -
138D LEU* 3.4 4.9 + - + +
139D HIS* 2.8 33.5 + - - +
185D PHE* 4.3 7.5 - - + -
187D LEU* 6.4 0.9 - - + -
195D THR* 3.6 30.5 - - + -
210D GLU* 4.0 10.5 - - + +
213D ILE* 3.5 29.4 - - + -
214D ALA* 4.0 16.6 - - + +
217D LEU* 3.8 14.7 - - + +
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Residues in contact with LEU 136 (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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131D PRO* 5.3 6.7 - - + -
132D PRO* 3.6 16.2 - - + +
133D LEU* 3.2 21.4 + - + +
135D LEU* 1.3 75.6 - - + +
137D VAL* 1.3 63.8 + - - +
139D HIS* 3.5 7.6 + - + +
140D ARG* 3.3 26.5 + - - +
165D LEU* 5.6 2.5 - - + -
168D CYS* 4.4 15.7 - - + -
169D PHE* 4.1 18.2 - - + -
185D PHE* 5.8 1.6 - - + -
187D LEU* 3.9 30.1 - - + -
189D TRP* 5.2 11.9 - - + -
315D ALA* 4.1 19.5 - - + +
319D LEU* 5.5 9.4 - - + -
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Residues in contact with VAL 137 (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 LEU* 3.0 22.7 + - + +
134D SER 3.9 4.5 - - - +
136D LEU* 1.3 75.1 - - - +
138D LEU* 1.3 62.0 + - - +
140D ARG* 3.2 7.4 + - - +
141D LEU* 3.1 26.0 + - + +
279D VAL* 3.6 19.7 - - + -
282D TRP* 4.0 18.6 - - + -
283D SER* 3.9 12.1 - - - +
311D PRO* 4.0 8.3 - - - +
312D PHE* 3.9 31.6 - - + -
315D ALA* 4.0 19.3 - - + -
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Residues in contact with LEU 138 (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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134D SER 3.2 20.7 + - - +
135D LEU* 3.4 5.8 + - - +
137D VAL* 1.3 74.8 - - - +
139D HIS* 1.3 54.8 + - - +
141D LEU* 3.3 13.4 + - + +
142D LEU* 2.8 38.2 + - - +
214D ALA* 3.4 44.2 - - + +
217D LEU* 4.1 18.2 - - + -
218D PHE* 3.6 41.5 - - + -
221D PHE* 4.4 3.0 - - + -
276D VAL* 4.7 2.0 - - + -
279D VAL* 3.8 19.5 - - + -
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Residues in contact with HIS 139 (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 2.8 18.0 + - - +
136D LEU* 3.5 7.3 + - - +
137D VAL 3.2 0.2 - - - -
138D LEU* 1.3 72.2 - - - +
140D ARG* 1.3 80.8 + - - +
142D LEU* 3.0 9.0 + - + +
143D CYS* 3.0 45.4 + - - -
148D VAL* 4.4 1.8 - - + +
150D SER* 3.1 29.0 - - - -
169D PHE* 3.0 39.6 - + + -
185D PHE* 3.4 46.0 - + + +
217D LEU* 5.1 0.4 - - - +
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Residues in contact with ARG 140 (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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136D LEU 3.3 12.9 + - - +
137D VAL 3.2 9.3 + - - +
139D HIS* 1.3 90.3 + - - +
141D LEU* 1.3 61.9 + - - +
143D CYS* 3.5 10.5 + - - +
144D GLU* 3.3 28.6 + - - +
168D CYS 4.0 1.2 + - - -
169D PHE* 3.8 33.6 + - - +
170D GLY* 4.1 1.6 - - - +
311D PRO* 3.9 22.2 - - + +
314D THR* 3.7 26.7 + - - +
315D ALA* 4.6 6.2 - - + +
318D LEU* 3.2 30.7 - - - +
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Residues in contact with LEU 141 (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 VAL* 3.1 22.9 + - + +
138D LEU* 3.3 29.4 - - + +
140D ARG* 1.3 75.0 - - - +
142D LEU* 1.3 61.8 + - - +
144D GLU* 3.2 17.6 + - - +
145D HIS* 3.0 30.5 + - + -
218D PHE* 4.6 10.1 - - + -
221D PHE* 3.6 17.5 - - + -
274D LEU* 5.2 9.2 - - + -
279D VAL* 4.2 17.0 - - + -
311D PRO* 3.7 24.5 - - + -
312D PHE* 4.8 4.9 - - + -
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Residues in contact with LEU 142 (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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122D ILE* 4.5 5.2 - - + -
138D LEU 2.8 17.7 + - - +
139D HIS* 3.0 10.7 + - + +
141D LEU* 1.3 72.6 - - - +
143D CYS* 1.3 51.0 + - - +
145D HIS* 3.1 5.0 + - - +
146D PHE* 2.9 67.8 + - + +
148D VAL* 4.0 10.1 - - + -
183D LEU* 4.2 7.6 - - + -
185D PHE* 4.4 18.8 - - + -
217D LEU* 3.7 35.7 - - + +
220D LEU* 3.7 22.4 - - + -
221D PHE* 3.7 15.8 - - + -
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Residues in contact with CYS 143 (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 HIS* 3.0 40.8 + - - +
140D ARG* 3.7 13.7 - - - +
142D LEU* 1.3 75.8 - - - +
144D GLU* 1.3 59.9 + - + +
145D HIS 3.2 0.6 - - - -
146D PHE 2.8 23.5 + - - +
148D VAL* 3.6 30.1 - - - +
150D SER* 4.8 2.0 - - - -
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Residues in contact with GLU 144 (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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140D ARG* 3.3 13.4 + - - +
141D LEU* 3.2 17.3 + - - +
142D LEU 3.2 1.0 - - - -
143D CYS* 1.3 75.7 - - + +
145D HIS* 1.3 64.5 + - + +
310D ALA* 4.1 10.2 - - - +
311D PRO* 3.5 37.6 - - - +
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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