Contacts of the helix formed by residues 109 - 122 (chain C) in PDB entry 5NJ8
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 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C ARG 4.4 0.4 - - - +
108C GLU* 1.3 78.9 - - - +
110C LEU* 1.3 66.6 + - - +
111C ASN* 3.6 1.1 - - - -
112C LEU* 3.5 17.5 + - - +
113C GLN* 3.0 27.2 + - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG* 3.8 26.2 - - - +
108C GLU 3.6 0.6 - - - +
109C GLY* 1.3 82.0 - - - +
111C ASN* 1.3 60.0 + - - +
112C LEU 2.9 4.7 - - - -
113C GLN* 4.2 1.1 - - + +
114C GLU* 2.9 31.9 + - - +
117C PHE* 3.4 34.4 - - + -
188D TYR* 5.1 17.3 - - + +
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Residues in contact with ASN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG 5.3 0.5 - - - +
108C GLU* 2.7 29.1 + - - +
110C LEU* 1.3 72.8 - - - +
112C LEU* 1.3 75.3 + - - +
114C GLU* 3.5 24.0 - - - +
161D ASP* 4.6 6.8 - - - +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B ASP* 5.4 11.3 - - + -
326B ASP* 3.4 11.0 + - - +
327B PRO* 5.7 11.0 - - + -
328B GLU 5.8 3.1 - - - +
108C GLU 4.0 9.9 - - - +
109C GLY* 3.5 13.5 - - - +
110C LEU 2.9 0.4 - - - -
111C ASN* 1.3 109.1 + - - +
113C GLN* 1.3 56.8 + - - +
114C GLU 3.3 4.5 - - - -
116C GLU* 4.1 2.9 - - - +
161D ASP* 2.6 30.0 - - - +
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Residues in contact with GLN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B ASP 5.6 3.4 - - - +
325B ASP* 6.1 1.3 - - - +
109C GLY 3.0 16.1 + - - +
110C LEU* 3.5 0.8 + - + -
112C LEU* 1.3 73.9 - - - +
114C GLU* 1.3 65.7 + - - +
115C GLY 3.2 2.7 - - - -
116C GLU* 3.2 16.7 + - + +
117C PHE* 2.9 47.8 + - + -
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Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LEU 2.9 17.2 + - - +
111C ASN* 3.5 23.3 - - - +
112C LEU 3.3 1.6 - - - -
113C GLN* 1.3 75.7 - - - +
115C GLY* 1.3 69.2 + - - +
117C PHE* 2.7 22.6 + - - +
118C LEU* 2.7 25.8 + - + +
161D ASP* 4.7 13.3 - - + +
162D GLN* 5.8 0.5 - - - -
165D LYS* 3.8 23.6 - - + +
176D LEU* 3.6 23.5 - - + +
190D SER* 4.3 12.1 - - - -
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Residues in contact with GLY 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLN 3.2 1.4 + - - -
114C GLU* 1.3 85.6 - - - +
116C GLU* 1.3 66.4 + - - +
118C LEU* 3.0 12.2 + - - +
119C LEU* 2.9 25.7 + - - +
161D ASP* 3.8 21.9 + - - -
164D LEU* 4.7 12.3 - - - +
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Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B ASP* 2.7 33.7 - - + +
325B ASP* 4.2 10.2 - - - -
326B ASP* 4.4 2.8 + - - +
112C LEU 4.1 0.9 - - - +
113C GLN* 3.2 20.7 + - + +
115C GLY* 1.3 72.9 + - - +
117C PHE* 1.3 61.5 + - + +
119C LEU* 2.6 40.4 + - + +
120C GLN* 3.0 12.5 + - - +
155D LYS* 5.4 2.4 - - - +
157D SER* 5.3 9.4 - - - -
161D ASP* 3.9 10.3 - - - +
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LEU* 3.4 29.8 - - + -
113C GLN* 2.9 48.7 + - + -
114C GLU* 2.7 19.8 + - - +
116C GLU* 1.3 73.1 - - + +
118C LEU* 1.3 50.7 + - + +
120C GLN* 3.9 0.8 - - - +
121C ALA* 2.7 41.9 + - + +
176D LEU* 6.3 0.4 - - + -
338D VAL* 5.6 13.0 - - + -
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLU* 2.7 46.3 + - + +
115C GLY* 3.3 9.4 - - - +
116C GLU 3.0 0.2 - - - -
117C PHE* 1.3 75.8 - - + +
119C LEU* 1.3 69.1 + - + +
120C GLN 3.1 1.3 + - - -
121C ALA* 3.3 10.7 + - + +
122C LEU* 3.4 18.3 + - + +
164D LEU* 5.0 6.3 - - + +
165D LYS* 5.7 2.5 - - - -
168D ILE* 4.4 24.2 - - + -
175D PHE 5.3 0.2 - - - +
176D LEU* 3.4 39.5 - - + -
340D ILE* 4.3 17.9 - - + -
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C GLY 2.9 16.6 + - - +
116C GLU* 2.6 34.5 + - + +
118C LEU* 1.3 74.7 - - + +
120C GLN* 1.3 55.4 + - + +
122C LEU 4.8 4.2 - - - +
124C GLY 4.9 2.1 - - - +
126C VAL* 6.4 0.9 - - + -
137C TYR* 4.9 6.5 - - - +
139C SER* 4.1 26.7 - - - -
140C SER* 3.9 18.8 - - - +
141C THR* 2.8 33.1 - - + +
157D SER* 5.9 6.5 - - - -
164D LEU* 5.6 9.0 - - + -
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Residues in contact with GLN 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLY* 3.0 32.5 + - - +
116C GLU 3.0 10.4 + - - +
117C PHE* 3.9 1.1 - - - +
119C LEU* 1.3 76.1 - - - +
121C ALA* 1.3 62.3 + - - +
122C LEU 3.6 6.7 - - - +
141C THR* 5.1 1.1 - - + -
144C ASP* 3.4 25.3 + - - +
145C TYR* 5.4 4.3 + - - +
310D GLY 5.6 0.5 - - - -
311D TYR* 5.1 8.2 - - - +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PHE* 2.7 24.8 + - + +
118C LEU* 3.3 3.6 + - - +
120C GLN* 1.3 78.2 - - - +
122C LEU* 1.3 66.7 + - - +
123C ASN 3.4 0.2 + - - -
309D THR* 3.0 37.9 - - - +
310D GLY* 3.7 14.5 + - - +
311D TYR* 5.2 3.4 - - + +
338D VAL 4.9 3.8 - - - +
340D ILE* 4.8 13.2 - - + +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 3.4 14.3 + - + +
119C LEU 4.8 2.8 - - - +
120C GLN 4.3 6.1 - - - +
121C ALA* 1.3 80.0 - - - +
123C ASN* 1.3 63.8 + - - +
124C GLY 3.0 23.8 + - - +
125C PHE* 5.7 1.3 - - - +
126C VAL* 6.4 1.6 - - + -
145C TYR* 3.1 10.4 + - - -
309D THR* 4.2 4.3 - - - -
340D ILE* 5.9 1.7 - - - +
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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