Contacts of the helix formed by residues 110 - 120 (chain D) in PDB entry 6CET
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 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D TYR* 5.1 4.0 - - - -
109D ILE* 1.3 85.4 - - - +
111D ARG* 1.3 61.5 + - - -
112D GLY 3.1 3.1 - - - -
113D ASP* 2.9 31.0 + - - +
114D MET 3.2 6.6 + - - -
988D ARG* 3.9 8.1 - - - -
989D PHE* 5.7 3.1 - - - -
1395D ALA* 5.8 0.4 - - - +
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Residues in contact with ARG 111 (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 GLY* 1.3 68.4 - - - -
112D GLY* 1.3 59.0 + - - +
114D MET* 3.2 33.9 + - + +
115D TRP* 2.9 24.9 + - - +
360D ASN* 5.8 1.4 + - - -
752D CYS* 4.7 1.8 - - + -
753D LEU* 3.8 44.2 - - - +
754D PRO 3.1 30.1 + - - -
755D LEU* 3.9 21.0 - - + +
988D ARG* 3.0 47.2 - - - +
990D VAL 4.8 2.6 + - - -
991D GLU* 4.3 7.3 - - - +
992D GLY 3.8 25.5 + - - +
993D LEU* 5.5 0.8 - - - +
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Residues in contact with GLY 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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110D GLY 3.1 0.4 - - - -
111D ARG* 1.3 76.6 - - - +
113D ASP* 1.3 58.1 + - - +
115D TRP* 3.1 11.6 + - - +
116D ARG* 3.0 33.8 + - - +
985D GLY* 5.3 9.2 - - - -
988D ARG* 3.1 22.6 - - - +
989D PHE* 4.9 9.4 - - - -
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Residues in contact with ASP 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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109D ILE* 4.3 17.7 - - + +
110D GLY* 2.9 26.8 + - - +
112D GLY* 1.3 73.1 - - - +
114D MET* 1.3 59.4 + - - +
116D ARG* 3.3 26.2 + - + +
117D LEU* 2.9 33.6 + - - +
137D ILE* 5.1 12.3 - - + +
989D PHE* 5.8 1.5 - - - -
1394D THR* 3.9 29.0 - - - +
1395D ALA* 4.5 5.5 + - - +
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Residues in contact with MET 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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104D PHE* 4.7 2.5 - - + -
109D ILE* 3.6 28.5 - - + -
110D GLY 3.2 1.8 + - - -
111D ARG* 3.2 34.9 + - + +
113D ASP* 1.3 78.2 - - - +
115D TRP* 1.3 56.9 + - - +
117D LEU* 3.3 12.9 + - + +
118D LYS* 2.9 27.9 + - - +
164D PHE* 3.6 49.3 - - + -
752D CYS* 3.7 37.9 - - + -
755D LEU* 4.0 17.0 - - + +
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Residues in contact with TRP 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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111D ARG 2.9 12.9 + - - +
112D GLY* 3.1 14.1 + - - +
114D MET* 1.3 76.5 - - - +
116D ARG* 1.3 61.1 + - + +
118D LYS* 3.2 30.5 + - + +
119D LYS* 2.9 51.7 + - + +
755D LEU* 4.8 12.8 - - + -
756D THR* 4.5 22.7 - - + -
875D TYR* 4.7 19.5 - + - -
981D GLN* 3.0 44.3 + - + +
984D ASP* 5.0 6.8 + - - -
988D ARG* 6.4 1.3 - - + -
994D ASN* 4.5 16.2 - - - -
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Residues in contact with ARG 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 GLY* 3.0 15.5 + - - +
113D ASP* 3.3 36.9 + - + +
115D TRP* 1.3 78.2 - - + +
117D LEU* 1.3 59.9 + - - +
119D LYS* 3.7 12.0 - - + +
120D SER* 2.9 28.8 + - - -
134D PHE* 3.7 29.7 - - + -
135D ALA* 5.3 3.8 - - - -
981D GLN* 4.5 18.3 + - + +
982D LEU* 3.5 34.2 - - - +
985D GLY* 6.2 1.4 - - - -
1366D ARG* 3.5 38.8 - - - +
1393D VAL* 5.5 1.2 - - - +
1394D THR* 5.2 3.5 - - - +
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Residues in contact with LEU 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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102D LEU* 5.8 0.4 - - + -
104D PHE* 4.7 13.0 - - + -
109D ILE* 6.2 1.3 - - + -
113D ASP* 2.9 23.6 + - + +
114D MET* 3.3 17.2 + - + +
116D ARG* 1.3 76.1 - - - +
118D LYS* 1.3 51.6 + - - +
120D SER* 3.3 6.6 + - - +
121D LEU* 2.6 45.6 + - + +
132D VAL* 5.9 4.5 - - + -
133D GLU 5.5 0.4 - - - -
134D PHE* 3.7 31.2 - - + +
137D ILE* 3.7 28.7 - - + +
138D ARG 5.2 1.1 - - - +
139D ALA* 5.4 10.5 - - + -
164D PHE* 4.3 20.6 - - + -
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Residues in contact with LYS 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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114D MET 2.9 13.3 + - - +
115D TRP* 3.5 33.3 - - + +
117D LEU* 1.3 75.6 - - - +
119D LYS* 1.3 57.3 + - - +
121D LEU* 2.9 25.6 + - + +
122D VAL* 3.0 22.7 + - + +
158D GLU* 5.5 11.9 + - - +
160D THR* 4.1 21.8 + - - +
161D ARG* 4.9 2.6 - - - +
162D VAL* 4.2 36.6 - - + +
164D PHE* 5.4 2.2 - - + -
755D LEU* 6.2 2.7 - - + -
756D THR* 4.8 13.3 + - + +
996D ILE* 6.3 0.4 - - - +
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Residues in contact with LYS 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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115D TRP* 2.9 55.7 + - + +
116D ARG* 3.7 10.5 - - + +
117D LEU 3.2 0.4 - - - -
118D LYS* 1.3 78.9 - - - +
120D SER* 1.3 57.2 + - - +
121D LEU 3.2 0.2 - - - -
122D VAL* 3.3 23.4 - - + +
981D GLN* 3.6 18.6 - - + +
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Residues in contact with SER 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 ARG 2.9 13.9 + - - -
117D LEU* 3.3 10.6 + - - +
119D LYS* 1.3 76.1 - - - +
121D LEU* 1.3 58.7 + - - +
122D VAL 3.5 1.5 + - - -
124D THR* 5.0 4.9 - - - +
134D PHE* 3.3 45.0 - - - +
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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