Contacts of the helix formed by residues 111 - 122 (chain D) in PDB entry 5E6J
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 ASN 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D TRP* 3.7 33.3 - - + -
105D ILE* 3.1 22.5 - - + +
106D LYS 3.0 21.0 + - - +
107D TRP* 3.6 9.7 - - - -
108D ALA* 2.8 34.4 + - - +
109D ASP 4.5 0.2 - - - +
110D ASN* 1.3 72.9 - - - +
112D CYS* 1.3 58.1 + - - +
113D TYR* 3.2 4.3 - - - -
114D LEU* 3.2 13.7 + - + +
115D SER* 2.8 33.6 + - - -
76E AYE 3.8 0.8 - - - +
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Residues in contact with CYS 112 (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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107D TRP* 4.4 4.0 - - + -
111D ASN* 1.3 81.5 + - - +
113D TYR* 1.3 59.5 + - - +
115D SER* 3.3 9.0 + - - -
116D SER* 2.8 31.2 + - - -
273D HIS* 4.3 9.0 - - + -
274D TYR* 3.6 38.0 - - - +
287D ASP* 5.4 0.9 - - - +
288D GLY* 6.1 3.1 - - - +
75E GLY 4.2 0.2 - - - -
76E AYE 1.7 63.2 - - + +
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Residues in contact with TYR 113 (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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110D ASN 3.5 22.2 - - - -
111D ASN 4.6 0.2 - - - -
112D CYS* 1.3 76.1 - - - +
114D LEU* 1.3 97.1 + - + +
116D SER* 3.1 3.5 + - - -
117D VAL* 2.8 32.3 + - + +
153D LEU* 3.6 21.8 - - - +
158D LYS* 3.3 26.3 - - + +
159D THR 5.0 0.7 + - - -
162D GLU 3.5 15.1 + - - -
164D GLY* 3.6 18.4 - - - +
165D ASP 4.5 2.5 - - - -
166D VAL* 3.5 14.3 - - + +
169D THR* 3.8 22.7 - - - -
274D TYR* 3.5 27.8 - - + -
75E GLY 3.5 16.8 - - - +
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Residues in contact with LEU 114 (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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94D TRP* 4.0 26.5 - - + -
105D ILE* 4.2 11.2 - - + -
111D ASN* 3.2 10.9 + - + +
113D TYR* 1.3 114.5 - - + +
115D SER* 1.3 57.6 + - - +
117D VAL* 3.1 6.8 + - - +
118D LEU* 2.8 30.0 + - - +
149D CYS* 4.7 8.9 - - + +
152D ILE* 3.5 38.2 - - + +
153D LEU* 3.8 31.0 - - + -
158D LYS* 6.1 0.2 - - + -
169D THR* 4.6 1.6 - - + -
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Residues in contact with SER 115 (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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104D SER* 3.2 23.9 + - - -
105D ILE* 3.6 31.6 + - - +
111D ASN* 2.8 21.0 + - - -
112D CYS* 3.4 11.4 - - - -
114D LEU* 1.3 74.5 - - - +
116D SER* 1.3 56.4 + - - +
118D LEU* 3.2 3.0 + - - +
119D LEU* 2.9 41.6 + - - +
288D GLY* 4.6 7.2 + - - -
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Residues in contact with SER 116 (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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112D CYS 2.8 17.2 + - - -
113D TYR 3.4 7.9 - - - -
115D SER* 1.3 76.8 - - - +
117D VAL* 1.3 56.8 + - - +
119D LEU* 4.0 1.1 - - - +
120D ALA* 2.8 33.0 + - - +
166D VAL* 4.0 6.1 - - - -
263D ASN* 3.4 27.0 + - - -
274D TYR* 3.7 16.3 - - - +
275D THR* 4.3 1.4 - - - -
276D HIS* 4.0 27.6 + - - +
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Residues in contact with VAL 117 (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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113D TYR 2.8 20.5 + - - +
114D LEU* 3.3 10.1 - - - +
116D SER* 1.3 76.2 - - - +
118D LEU* 1.3 57.2 + - - +
120D ALA* 3.6 4.5 - - - +
121D LEU* 2.8 51.1 + - + +
152D ILE* 3.8 19.5 - - + -
166D VAL* 3.8 24.5 - - + +
169D THR* 4.0 25.6 - - + -
170D MET* 4.0 11.0 - - + -
173D LEU* 3.9 7.6 - - + -
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Residues in contact with LEU 118 (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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103D THR* 3.6 12.1 - - + +
104D SER 4.6 1.6 - - - +
105D ILE* 3.8 28.3 - - + -
114D LEU 2.8 15.5 + - - +
115D SER* 3.2 8.9 + - - +
117D VAL* 1.3 74.2 - - - +
119D LEU* 1.3 57.4 + - - +
121D LEU* 3.2 8.0 + - + +
122D GLN* 2.9 63.4 + - + +
137D TYR* 6.1 1.1 - - + -
140D ALA* 4.4 15.5 - - + -
145D ALA* 3.8 25.1 - - + -
148D PHE* 4.6 16.4 - - + -
149D CYS* 4.2 7.0 - - - -
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Residues in contact with LEU 119 (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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99D VAL 4.8 1.1 - - - +
102D LEU* 3.8 25.9 - - + +
103D THR 3.4 21.8 - - - +
104D SER* 3.8 13.0 - - - +
115D SER* 2.9 37.3 + - - +
116D SER 4.0 0.2 - - - +
118D LEU* 1.3 72.6 - - - +
120D ALA* 1.3 63.7 + - - +
122D GLN* 3.5 10.3 + - - +
123D GLN* 3.2 22.5 + - - +
276D HIS* 3.5 31.0 - - + -
286D ILE* 3.5 39.9 - - + +
288D GLY 5.9 0.2 - - - +
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Residues in contact with ALA 120 (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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116D SER 2.8 21.0 + - - +
117D VAL* 3.6 6.5 - - - +
119D LEU* 1.3 76.2 - - - +
121D LEU* 1.3 64.1 + - - +
123D GLN* 3.0 17.2 + - - +
124D LEU* 3.5 14.7 + - + +
166D VAL* 6.0 0.2 - - + -
170D MET* 5.2 3.8 - - + -
261D CYS* 4.3 4.6 - - - -
263D ASN* 4.9 1.6 - - - +
276D HIS* 3.8 14.0 - - + +
305D PHE* 3.9 35.2 - - + -
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Residues in contact with LEU 121 (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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117D VAL* 2.8 31.6 + - + +
118D LEU* 3.7 3.1 - - + +
120D ALA* 1.3 74.1 - - - +
122D GLN* 1.3 57.5 - - - +
123D GLN 2.8 6.9 + - - -
124D LEU* 2.9 20.9 + - + +
126D VAL* 4.3 21.5 - - + +
128D PHE* 4.3 11.0 - - + -
137D TYR* 2.9 28.4 + - + -
148D PHE* 3.8 23.6 - - + -
170D MET* 4.0 25.6 - - + -
173D LEU* 3.5 30.3 - - + -
174D LEU* 5.2 5.8 - - + -
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Residues in contact with GLN 122 (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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102D LEU* 3.8 23.8 - - + +
103D THR* 2.6 60.0 + - - +
118D LEU* 2.9 35.4 + - + +
119D LEU* 3.7 14.9 - - - +
120D ALA 3.2 0.6 - - - -
121D LEU* 1.3 75.0 - - - +
123D GLN* 1.3 57.7 + - - +
137D TYR* 4.0 9.0 - - + -
141D ARG* 3.2 51.9 + - + +
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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