Contacts of the helix formed by residues 132 - 144 (chain B) in PDB entry 5JKC
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B LEU* 1.3 75.4 - - - +
133B GLN* 1.3 66.5 + - - +
134B GLU* 3.2 12.8 - - - +
135B ASP* 3.1 27.2 + - - +
136B CYS* 3.2 9.5 + - - -
199B GLU 3.6 2.5 - - - +
201B ARG* 3.9 21.1 - - + +
202B ASN 5.1 0.9 - - - -
206B CYS* 2.1 62.7 - - - +
207B LEU 2.9 17.0 + - - -
208B GLN* 4.4 1.6 - - - -
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU 3.6 1.0 + - - -
132B CYS* 1.3 71.3 - - - +
134B GLU* 1.3 53.0 + - - +
136B CYS* 3.2 6.7 + - - +
137B GLU* 2.7 64.4 + - + +
196B ALA* 6.3 0.4 - - - +
197B SER 3.6 14.2 + - - +
198B PRO* 3.5 26.1 + - - +
199B GLU 3.0 13.8 + - - +
200B ARG* 2.8 37.0 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B CYS* 3.2 0.9 - - - +
133B GLN* 1.3 75.4 + - - +
135B ASP* 1.3 59.7 + - - +
137B GLU* 4.3 5.8 - - - -
138B GLU* 2.8 50.5 + - - +
200B ARG* 3.4 43.9 + - - +
201B ARG* 2.9 63.3 + - - +
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Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B HIS* 4.9 1.3 + - - -
131B LEU* 4.7 8.3 - - + -
132B CYS* 3.1 18.4 + - - +
134B GLU* 1.3 74.1 - - - +
136B CYS* 1.3 64.0 + - - +
138B GLU* 4.3 2.9 - - - +
139B TRP* 3.2 27.0 + - - +
186B CYS* 4.9 0.7 - - - -
201B ARG* 2.9 43.4 + - - +
207B LEU 4.4 1.3 - - - -
208B GLN* 3.3 17.9 - - - +
209B LYS* 2.9 43.4 + - + +
210B TRP* 3.8 2.4 + - - +
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Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.9 20.0 - - - -
132B CYS 3.2 7.0 + - - +
133B GLN* 3.8 7.6 - - - +
135B ASP* 1.3 79.2 - - - +
137B GLU* 1.3 56.7 + - - +
139B TRP* 3.5 2.5 + - - +
140B TRP* 3.0 30.7 + - - +
182B PRO* 3.6 18.6 - - + +
185B LEU* 5.2 0.7 - - - +
186B CYS* 2.0 52.5 - - + -
196B ALA* 4.0 18.4 - - + -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLN* 2.7 48.5 + - + +
134B GLU* 3.8 4.6 - - - +
136B CYS* 1.3 68.8 - - - +
138B GLU* 1.3 56.8 + - + +
140B TRP* 3.2 5.5 + - - +
141B GLU* 2.8 36.0 + - - +
182B PRO* 4.1 23.1 - - + +
200B ARG* 3.1 21.8 + - - -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B HIS* 3.6 16.1 - - + +
134B GLU* 2.8 37.4 + - - +
135B ASP* 4.3 2.5 - - - +
137B GLU* 1.3 69.9 - - + +
139B TRP* 1.3 65.8 + - - +
141B GLU* 3.2 6.7 + - - +
142B ASP* 2.9 33.2 + - - +
201B ARG* 4.4 20.4 + - - -
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Residues in contact with TRP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B HIS* 3.4 36.6 - - + +
90B PHE* 3.6 47.5 - + - -
93B ALA* 3.8 21.3 - - + -
131B LEU* 4.4 9.2 - - + -
135B ASP 3.2 19.1 + - - +
136B CYS 3.6 4.3 - - - +
138B GLU* 1.3 78.2 - - - +
140B TRP* 1.3 63.7 + - - +
142B ASP* 3.3 1.4 + - - +
143B CYS* 3.1 28.3 + - - +
185B LEU* 3.7 16.6 - - + +
186B CYS* 3.8 32.1 - - - -
189B THR* 4.1 15.7 - - - -
190B TRP* 4.3 6.5 - + - -
194B PHE* 4.5 5.6 - + - -
209B LYS* 3.5 26.2 - - + -
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Residues in contact with TRP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B CYS 3.0 18.7 + - - +
137B GLU 3.4 5.2 - - - +
139B TRP* 1.3 78.4 - - - +
141B GLU* 1.3 78.4 + - + +
143B CYS* 3.3 2.1 + - - +
144B ARG* 3.2 49.5 + - + +
175B PHE* 5.8 2.4 - - + +
176B SER* 3.8 25.0 - - - +
179B PHE* 2.8 23.6 + - + +
180B PRO 3.6 17.9 - - - -
181B THR 3.6 8.2 - - - -
182B PRO* 3.5 39.0 - - + -
185B LEU* 3.4 23.1 - - + +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLU 2.8 21.3 + - - +
138B GLU* 3.2 9.4 + - - +
140B TRP* 1.3 88.1 - - + +
142B ASP* 1.3 70.0 + - - +
143B CYS 3.3 0.5 + - - -
144B ARG* 2.4 60.7 + - - +
145B MET* 5.7 1.7 - - - +
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MET* 4.9 6.1 - - - +
85B GLY* 4.3 12.5 - - - +
86B CYS* 3.7 13.0 + - - +
89B HIS* 2.6 37.4 + - + -
138B GLU* 2.9 19.9 + - - +
141B GLU* 1.3 85.9 - - - +
143B CYS* 1.3 61.0 + - - +
144B ARG 3.5 0.2 - - - -
145B MET* 4.8 4.7 + - - +
146B SER* 4.3 2.4 + - - -
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Residues in contact with CYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B CYS* 2.0 52.5 - - - -
89B HIS* 4.8 0.4 - - - -
90B PHE* 3.7 8.5 - - - -
139B TRP* 3.1 36.2 + - - +
140B TRP 3.3 3.6 + - - +
141B GLU 3.2 0.4 - - - -
142B ASP* 1.3 78.3 - - - +
144B ARG* 1.3 64.4 + - - +
145B MET 3.2 2.9 - - - -
146B SER* 3.0 12.7 + - - -
175B PHE* 3.1 31.8 - - + +
185B LEU* 4.4 3.4 - - + -
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TRP* 3.2 55.0 + - + +
141B GLU* 2.4 57.1 + - - +
143B CYS* 1.3 77.0 - - - +
145B MET* 1.3 86.8 + - + +
146B SER 3.5 6.4 - - - +
174B PRO* 3.6 19.9 - - - +
175B PHE* 3.8 6.5 + - - -
176B SER* 4.1 15.6 + - - +
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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