Contacts of the helix formed by residues 132 - 144 (chain D) in PDB entry 5JKE
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 CYS 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D PRO 3.6 0.6 + - - -
131D LEU* 1.3 76.4 - - - +
133D GLN* 1.3 66.2 + - - +
134D GLU* 3.3 3.1 - - - +
135D ASP* 3.1 26.3 + - - +
136D CYS* 3.3 9.2 + - - +
199D GLU 3.5 2.2 - - - +
201D ARG* 3.8 28.5 - - + +
202D ASN 5.2 0.7 - - - -
206D CYS* 2.1 61.9 - - - -
207D LEU 2.9 17.8 + - - -
208D GLN* 4.3 2.5 - - - -
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Residues in contact with GLN 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 LEU 4.5 0.2 - - - -
132D CYS* 1.3 71.5 - - - +
134D GLU* 1.3 59.0 + - - +
136D CYS* 3.4 6.2 + - - +
137D GLU* 2.8 54.7 + - + +
197D SER 3.6 10.6 + - - +
198D PRO* 3.6 29.7 + - - +
199D GLU 3.0 18.5 + - - +
200D ARG* 2.9 34.6 + - - +
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Residues in contact with GLU 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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133D GLN* 1.3 72.0 + - - +
135D ASP* 1.3 61.3 + - - +
137D GLU* 4.4 5.6 - - - -
138D GLU* 2.8 53.3 + - - +
200D ARG* 3.4 45.4 + - - +
201D ARG* 3.0 60.8 + - - +
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Residues in contact with ASP 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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89D HIS* 5.0 0.3 + - - -
131D LEU* 4.5 10.3 - - + -
132D CYS* 3.1 21.9 + - - +
134D GLU* 1.3 75.5 - - - +
136D CYS* 1.3 64.5 + - - +
138D GLU* 4.2 2.7 - - - +
139D TRP* 3.1 25.6 + - - +
186D CYS* 5.1 0.4 - - - -
201D ARG* 3.0 42.8 + - - +
207D LEU 4.3 1.6 - - - -
208D GLN* 3.2 13.7 - - - +
209D LYS* 2.9 45.3 + - + +
210D TRP* 4.0 1.9 + - - +
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Residues in contact with CYS 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 LEU* 3.9 21.1 - - - -
132D CYS 3.3 7.8 + - - +
133D GLN* 3.9 7.2 - - - +
135D ASP* 1.3 80.5 - - - +
137D GLU* 1.3 56.3 + - - +
139D TRP* 3.5 3.0 + - - +
140D TRP* 3.0 28.9 + - - +
182D PRO* 3.6 18.4 - - + +
185D LEU* 5.0 0.3 - - - +
186D CYS* 2.0 52.3 - - - -
196D ALA* 4.0 18.8 - - + -
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Residues in contact with GLU 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 GLN* 2.8 46.6 + - + +
134D GLU* 3.2 4.4 + - - +
136D CYS* 1.3 71.3 - - - +
138D GLU* 1.3 57.3 + - + +
140D TRP* 3.1 6.3 + - + +
141D GLU* 2.7 36.5 + - - +
182D PRO* 4.0 22.2 - - + -
200D ARG* 3.1 20.8 + - - -
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Residues in contact with GLU 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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89D HIS* 3.8 15.5 - - + +
134D GLU* 2.8 37.4 + - - +
135D ASP* 4.2 2.3 - - - +
137D GLU* 1.3 74.5 - - + +
139D TRP* 1.3 63.2 + - - +
141D GLU* 3.9 7.9 - - + -
142D ASP* 2.9 33.4 + - - +
201D ARG* 4.9 14.0 + - - -
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Residues in contact with TRP 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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89D HIS* 3.3 38.2 - - + +
90D PHE* 3.6 49.0 - + - -
93D ALA* 3.9 20.6 - - + -
131D LEU* 4.3 9.4 - - + -
135D ASP 3.1 20.4 + - - +
136D CYS 3.6 3.8 - - - +
138D GLU* 1.3 77.1 - - - +
140D TRP* 1.3 63.0 + - - +
142D ASP* 3.9 1.2 - - - +
143D CYS* 3.1 25.6 + - - +
185D LEU* 3.6 19.3 - - + +
186D CYS* 3.9 32.3 - - - -
189D THR* 4.1 14.4 - - - -
190D TRP* 4.2 7.6 - + - -
194D PHE* 4.7 5.2 - + - -
209D LYS* 3.4 27.1 - - + -
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Residues in contact with TRP 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 CYS 3.0 18.6 + - - +
137D GLU* 3.1 5.6 + - + +
139D TRP* 1.3 75.8 - - - +
141D GLU* 1.3 79.8 + - - +
143D CYS* 3.4 2.6 + - - +
144D ARG* 3.2 48.4 + - + +
175D PHE* 5.4 3.8 - - + +
176D SER* 3.9 24.3 - - - +
179D PHE* 2.7 23.4 + - + -
180D PRO 3.7 17.3 - - - -
181D THR 3.6 8.8 - - - -
182D PRO* 3.5 37.5 - - + -
185D LEU* 3.4 22.1 - - + +
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Residues in contact with GLU 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 GLU 2.7 19.9 + - - +
138D GLU* 3.4 11.7 - - - +
140D TRP* 1.3 89.0 - - - +
142D ASP* 1.3 69.3 + - - +
143D CYS 3.3 0.3 + - - -
144D ARG* 2.5 59.1 + - - +
145D MET* 5.9 0.7 - - - +
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Residues in contact with ASP 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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83D MET* 5.0 5.9 - - - +
85D GLY* 4.2 12.7 - - - +
86D CYS* 3.7 13.7 + - - +
89D HIS* 2.6 36.5 + - + -
138D GLU* 2.9 19.8 + - - +
141D GLU* 1.3 84.7 - - - +
143D CYS* 1.3 59.4 + - - +
144D ARG 3.5 0.4 - - - -
145D MET* 4.9 3.3 + - - +
146D SER* 4.4 2.3 + - - -
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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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86D CYS* 2.0 52.9 - - - -
89D HIS* 4.8 0.4 - - - -
90D PHE* 3.8 7.4 - - - -
139D TRP* 3.1 37.1 + - - +
140D TRP 3.4 3.1 + - - +
141D GLU 3.2 0.4 - - - -
142D ASP* 1.3 76.6 - - - +
144D ARG* 1.3 62.9 + - - +
145D MET 3.3 3.4 - - - -
146D SER* 3.0 13.2 + - - -
175D PHE* 3.3 32.5 - - + +
185D LEU* 4.6 3.6 - - + -
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Residues in contact with ARG 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 TRP* 3.2 52.6 + - + +
141D GLU* 2.5 55.1 + - - +
142D ASP 3.5 0.2 - - - -
143D CYS* 1.3 77.5 - - - +
145D MET* 1.3 83.2 + - + +
146D SER 3.5 6.1 - - - +
174D PRO* 3.8 18.5 - - - +
175D PHE* 3.8 8.0 + - - -
176D SER* 4.3 16.6 + - - +
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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