Contacts of the helix formed by residues 105 - 119 (chain D) in PDB entry 2CX9
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 SER 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D ALA 3.8 0.4 + - - -
104D GLY* 1.3 76.9 - - - -
106D GLU* 1.3 66.8 + - - +
107D ALA* 3.3 15.3 + - - +
108D GLN* 2.8 28.7 + - - +
109D LYS* 2.9 22.6 + - - +
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Residues in contact with GLU 106 (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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61D TYR* 2.7 28.4 + - - -
105D SER* 1.3 74.5 - - - +
107D ALA* 1.3 57.7 - - - +
109D LYS* 3.0 26.3 + - - +
110D GLU* 3.0 31.2 + - - +
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Residues in contact with ALA 107 (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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105D SER* 3.1 9.5 + - - +
106D GLU* 1.3 80.9 - - - +
108D GLN* 1.3 58.3 + - + +
110D GLU* 3.8 4.4 - - - +
111D ALA* 2.9 31.0 + - - +
228D GLU* 6.5 0.4 - - + -
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Residues in contact with GLN 108 (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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100D ILE* 4.6 3.6 - - + -
103D ALA 4.1 2.1 - - - +
104D GLY* 3.2 13.0 - - - -
105D SER* 2.8 40.3 + - - +
107D ALA* 1.3 77.7 - - + +
109D LYS* 1.3 57.3 + - - +
111D ALA* 3.0 6.0 + - - -
112D PHE* 2.8 48.1 + - + -
191D ALA* 5.6 2.4 - - - +
228D GLU* 3.1 29.9 + - + +
229D ALA 4.2 2.0 + - - -
230D LEU 2.8 31.5 + - - +
231D LEU* 3.8 12.2 - - + +
232D GLY 4.8 0.9 + - - -
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Residues in contact with LYS 109 (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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61D TYR* 3.0 41.8 + - + +
100D ILE* 3.6 20.0 - - + +
101D LEU* 3.8 28.0 + - + +
104D GLY* 3.8 13.2 + - - +
105D SER 2.9 20.8 + - - +
106D GLU* 3.0 20.8 + - - +
108D GLN* 1.3 75.4 - - - +
110D GLU* 1.3 59.8 + - - +
113D LEU* 2.8 57.4 + - + +
114D PRO* 3.3 0.7 - - - +
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Residues in contact with GLU 110 (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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61D TYR* 4.2 13.8 - - + -
106D GLU 3.0 19.9 + - - +
107D ALA* 3.8 5.2 - - - +
109D LYS* 1.3 77.4 - - - +
111D ALA* 1.3 58.3 + - - +
114D PRO* 3.2 29.8 - - - +
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Residues in contact with ALA 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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107D ALA 2.9 18.8 + - - +
108D GLN* 3.0 8.9 + - - +
110D GLU* 1.3 81.0 - - - +
112D PHE* 1.3 70.1 + - + +
114D PRO* 4.5 2.1 - - - +
115D LYS* 5.1 7.6 - - - +
193D PHE* 3.6 20.4 - - + -
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Residues in contact with PHE 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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100D ILE* 3.6 29.2 - - + -
108D GLN* 2.8 44.4 + - + +
111D ALA* 1.3 80.5 - - + +
113D LEU* 1.3 65.4 + - - +
114D PRO* 3.2 3.8 - - - -
115D LYS* 3.3 6.1 + - - +
116D LEU* 3.1 27.2 + - + +
167D VAL* 3.7 18.5 - - + +
191D ALA* 3.6 34.8 - - + -
192D PHE* 3.8 15.9 - - - -
193D PHE* 3.3 43.5 - + - -
228D GLU 5.1 4.5 - - - -
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Residues in contact with LEU 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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57D VAL* 4.3 10.5 - - + -
61D TYR* 3.8 29.4 - - + +
97D THR* 3.9 33.2 - - + +
100D ILE* 4.0 17.3 - - + -
101D LEU* 3.9 21.3 - - + +
109D LYS* 2.8 53.1 + - + +
112D PHE* 1.3 72.2 - - - +
114D PRO* 1.3 53.9 - - + +
116D LEU* 4.3 5.6 - - + -
117D ALA* 2.7 37.6 + - - +
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Residues in contact with PRO 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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61D TYR* 3.5 20.2 - - + +
62D GLY* 5.2 4.1 - - - +
109D LYS 3.3 6.3 - - - +
110D GLU* 3.2 40.8 - - - +
111D ALA 4.3 2.0 - - - +
112D PHE 3.4 4.5 - - - +
113D LEU* 1.3 90.7 - - + +
115D LYS* 1.3 64.3 + - + +
117D ALA* 3.9 2.2 - - + +
118D SER* 3.1 24.8 + - - -
120D GLU* 5.1 1.1 - - - -
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Residues in contact with LYS 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 ALA 5.1 5.4 + - - +
112D PHE 3.3 7.8 + - - +
114D PRO* 1.3 79.1 - - + +
116D LEU* 1.3 66.4 + - - +
118D SER* 3.0 13.3 + - - -
119D GLY 3.1 7.4 + - - -
120D GLU* 3.2 48.5 + - + +
121D ALA* 3.2 18.0 + - + -
167D VAL* 5.7 0.2 - - + -
193D PHE* 4.1 31.9 - - + -
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Residues in contact with LEU 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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53D PHE 3.1 1.8 - - - +
92D HIS* 3.0 33.8 + - + -
96D ALA* 4.8 0.9 - - + +
97D THR* 3.8 29.8 - - + +
100D ILE* 3.7 29.8 - - + -
112D PHE* 3.1 26.2 + - + +
113D LEU* 3.7 9.6 - - + +
115D LYS* 1.3 76.7 - - - +
117D ALA* 1.3 62.2 + - - +
119D GLY* 3.1 11.3 + - - -
121D ALA 3.4 17.7 - - - +
123D GLY* 3.8 15.5 - - - +
167D VAL* 3.9 23.8 - - + -
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Residues in contact with ALA 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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48D ALA 5.2 1.7 - - - +
51D GLY* 4.7 6.4 - - - +
53D PHE* 3.5 14.1 + - - +
54D GLY* 3.4 28.1 + - - -
57D VAL* 4.1 10.7 - - + +
62D GLY 3.7 26.0 - - - +
63D GLY* 3.9 8.0 - - - +
113D LEU 2.7 22.4 + - - +
114D PRO 3.9 2.7 - - - +
116D LEU* 1.3 73.4 - - - +
118D SER* 1.3 58.2 + - - +
119D GLY 3.4 0.2 - - - -
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Residues in contact with SER 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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48D ALA* 3.3 23.7 - - - +
53D PHE* 4.7 0.2 - - - -
62D GLY 5.0 2.4 + - - -
114D PRO 3.1 13.3 + - - -
115D LYS 3.0 12.8 + - - -
117D ALA* 1.3 76.6 - - - +
119D GLY* 1.3 59.1 + - - +
120D GLU* 3.2 26.5 + - - +
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Residues in contact with GLY 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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41D TRP* 5.4 4.0 - - - -
44D VAL* 4.7 7.2 - - - +
48D ALA* 4.5 3.8 - - - -
53D PHE* 4.0 18.6 - - - +
115D LYS 3.1 1.0 + - - -
116D LEU 3.1 16.5 + - - -
117D ALA 3.4 0.4 - - - -
118D SER* 1.3 78.4 - - - +
120D GLU* 1.3 59.5 + - - +
121D ALA* 2.9 10.7 + - - -
122D LEU* 3.8 18.1 + - - +
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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