Contacts of the helix formed by residues 127 - 143 (chain A) in PDB entry 2OKC
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 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A MSE 2.8 13.2 + - - -
126A ASP* 1.3 68.8 - - - +
128A ASP* 1.3 61.3 - - - -
129A VAL* 3.1 4.6 - - - +
130A LYS* 3.8 23.2 + - - +
131A GLY* 3.4 7.1 + - - -
229A LEU 3.4 21.1 - - - +
230A HIS* 5.2 1.7 - - - -
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASP* 2.7 17.2 + - + +
127A GLY* 1.3 71.6 - - - -
129A VAL* 1.3 57.6 + - + +
131A GLY* 3.3 3.9 + - - -
132A ALA* 2.9 30.4 + - - +
230A HIS* 5.6 1.5 - - - -
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 5.6 14.8 - - + +
125A MSE 3.8 32.8 - - + -
126A ASP* 3.8 36.1 - - + +
127A GLY 3.1 0.8 - - - +
128A ASP* 1.3 78.1 - - + +
130A LYS* 1.3 66.5 + - - +
132A ALA* 3.3 5.0 + - - +
133A ILE* 3.0 37.1 + - + +
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 6.5 0.4 - - + -
44A MSE 4.4 10.2 - - - +
122A TRP* 3.2 46.6 + - + +
123A LEU* 4.3 21.4 - - - +
124A ILE 5.2 0.4 - - - +
125A MSE 4.2 18.6 + - + -
127A GLY* 3.8 30.6 + - - +
128A ASP 3.4 0.4 - - - -
129A VAL* 1.3 80.3 - - - +
131A GLY* 1.3 63.7 + - - +
133A ILE* 3.8 6.5 - - - +
134A TYR* 3.1 25.1 + - - +
229A LEU* 4.1 33.3 + - + +
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Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY 3.4 6.4 + - - -
128A ASP 3.3 7.7 + - - -
130A LYS* 1.3 78.9 - - - +
132A ALA* 1.3 55.8 + - - +
134A TYR* 3.3 0.9 + - - +
135A GLU* 2.9 29.6 + - - +
229A LEU* 3.7 11.8 + - - -
230A HIS* 3.4 36.2 + - - -
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP 2.9 18.5 + - - +
129A VAL* 3.3 5.4 + - - +
131A GLY* 1.3 70.5 - - - +
133A ILE* 1.3 61.0 + - - +
135A GLU* 3.9 6.3 - - - +
136A SER* 3.0 29.3 + - - -
230A HIS* 5.1 0.9 - - - -
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLN* 4.3 12.8 - - + +
11A LEU* 4.0 33.0 - - + -
12A THR* 4.0 26.2 - - + +
15A VAL* 5.2 4.7 - - + -
122A TRP* 5.0 11.7 - - + -
125A MSE 4.4 5.4 - - - -
129A VAL* 3.0 39.2 + - + +
130A LYS* 3.8 5.2 - - - +
132A ALA* 1.3 75.2 - - + +
134A TYR* 1.3 58.8 + - - +
136A SER* 3.1 7.2 + - - -
137A ILE* 2.8 50.4 + - + +
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 5.4 5.2 - - + -
36A LEU* 6.1 3.4 - - + -
37A THR* 2.7 31.1 + - - +
40A LEU* 5.0 8.1 - - + -
130A LYS 3.1 16.9 + - - +
131A GLY* 3.6 4.3 - - - +
133A ILE* 1.3 77.2 - - - +
135A GLU* 1.3 58.0 + - - +
137A ILE* 3.1 20.3 + - + +
138A LEU* 2.8 50.2 + - + +
222A LEU* 3.4 33.1 - - + +
225A MSE 3.3 26.9 - - + +
226A ASN* 3.5 33.4 - - + +
229A LEU* 3.6 18.8 - - + -
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLY 2.9 14.5 + - - +
132A ALA* 4.0 7.4 - - - +
134A TYR* 1.3 72.0 - - - +
136A SER* 1.3 57.7 + - - +
138A LEU* 3.9 8.3 - - - +
139A GLU* 3.1 28.9 + - - +
153A PHE* 5.2 2.0 - - - -
156A ARG* 3.0 53.4 + - - +
186A LEU* 3.6 12.0 - - + +
226A ASN* 3.1 18.9 + - - +
230A HIS* 3.7 26.0 - - + +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 4.3 14.9 - - - +
132A ALA 3.0 20.2 + - - -
133A ILE* 3.3 7.9 - - - -
135A GLU* 1.3 74.3 - - - +
137A ILE* 1.3 64.5 + - - +
139A GLU* 3.5 7.3 + - - +
140A LYS* 3.1 25.6 + - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 5.1 5.8 - - + -
15A VAL* 3.9 31.4 - - + -
29A PHE* 4.4 6.2 - - + -
33A ILE* 3.2 39.4 - - + +
36A LEU* 4.6 9.6 - - + -
133A ILE* 2.8 43.0 + - + +
134A TYR* 3.5 21.1 - - + +
136A SER* 1.3 71.5 - - - +
138A LEU* 1.3 66.1 + - + +
139A GLU 3.3 0.2 + - - -
140A LYS* 3.4 4.9 + - - +
141A ASN* 3.2 22.0 + - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.7 8.1 - - + -
134A TYR* 2.8 41.4 + - + +
135A GLU* 3.9 9.6 - - - +
137A ILE* 1.3 73.2 - - + +
139A GLU* 1.3 58.1 + - - +
142A GLY* 2.9 15.1 + - - -
153A PHE* 4.1 7.9 - - + -
156A ARG* 5.1 0.2 - - - +
181A THR* 3.8 28.0 - - + +
222A LEU* 3.9 36.1 - - + +
226A ASN* 3.7 36.3 - - + +
502A IPA 2.5 28.1 + - - +
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 3.1 19.3 + - - +
136A SER* 3.8 7.4 + - - +
137A ILE 3.2 0.2 - - - -
138A LEU* 1.3 74.8 - - - +
140A LYS* 1.3 61.2 + - - +
142A GLY* 3.0 1.0 + - - -
143A GLN* 2.8 67.9 + - - +
153A PHE* 3.6 30.5 - - + -
156A ARG* 6.0 0.9 - - - -
379A LYS* 3.4 17.7 + - - -
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 4.9 12.6 - - + -
136A SER 3.1 17.5 + - - +
137A ILE* 4.0 4.9 - - - +
139A GLU* 1.3 78.7 + - - +
141A ASN* 1.3 65.0 + - - +
143A GLN* 3.8 8.7 - - - +
144A ASP* 3.6 14.6 - - - +
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Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.4 39.6 - - + +
30A THR* 3.0 24.4 + - - -
33A ILE* 4.0 5.3 - - + +
137A ILE 3.2 11.7 + - - +
140A LYS* 1.3 77.5 - - - +
142A GLY* 1.3 59.2 - - - +
144A ASP* 3.0 20.5 + - - +
147A SER* 3.1 24.5 + - - -
149A ALA* 3.2 13.3 + - - +
502A IPA 3.1 28.2 - - - +
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU 2.9 17.7 + - - -
139A GLU 3.0 4.2 + - - -
141A ASN* 1.3 76.8 - - - +
143A GLN* 1.3 61.3 + - - +
144A ASP 3.6 1.0 + - - -
150A GLY* 3.0 31.0 + - - -
153A PHE* 4.2 10.8 - - - +
342A TYR* 3.4 8.7 - - - +
502A IPA 3.6 17.0 + - - -
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Residues in contact with GLN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLU* 2.8 43.9 + - - +
140A LYS* 3.8 10.0 - - - +
142A GLY* 1.3 74.8 - - - +
144A ASP* 1.3 57.6 + - - +
145A LYS* 4.0 2.2 + - - -
153A PHE* 3.8 20.7 - - + -
155A PRO* 4.7 16.0 - - - +
340A ILE 4.7 5.0 + - - +
342A TYR* 4.6 11.7 - - - +
375A LEU* 3.4 40.1 - - + +
379A LYS* 4.2 15.4 + - - +
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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
------------------------------------------------------------
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