Contacts of the helix formed by residues 103 - 113 (chain D) in PDB entry 2E9X
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 PHE 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D PRO 3.9 16.6 - - - -
42D GLU* 5.3 2.2 - - - -
43D LEU 5.6 1.3 - - - -
99D LYS* 3.0 41.6 + - + +
100D ILE 3.6 2.7 - - - -
102D LYS* 1.3 109.9 - - + +
104D PHE* 1.3 64.9 + - - +
105D PRO* 3.3 6.5 - - - -
106D HIS* 3.0 13.4 + - + -
107D VAL* 2.9 28.7 + - + +
163D PRO* 3.4 22.2 - - + -
164D LYS 3.9 5.2 - - - -
165D PRO* 3.6 45.1 - - + -
166D ASP 5.2 0.7 - - - -
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Residues in contact with PHE 104 (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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81A TYR* 3.7 24.0 - + - -
100D ILE* 2.9 20.3 + - + +
101D GLU 3.2 19.1 - - - +
102D LYS 4.8 1.3 - - - -
103D PHE* 1.3 75.1 - - - +
105D PRO* 1.3 96.9 - - + +
107D VAL* 3.4 4.2 + - - +
108D LEU* 3.1 29.9 + - + +
130D ALA* 4.6 11.4 - - + +
133D PHE* 3.6 24.7 - + + -
134D MET* 3.5 43.7 - - + -
137D THR* 4.4 13.9 - - + -
158D LEU* 3.9 19.1 - - + -
162D VAL* 4.2 9.0 - - + -
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Residues in contact with PRO 105 (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 PHE 3.4 4.7 - - - -
104D PHE* 1.3 120.9 - - + +
106D HIS* 1.3 59.4 + - + +
108D LEU* 3.9 1.7 - - - +
109D GLU* 3.0 29.1 + - - +
134D MET* 4.0 18.1 - - + +
158D LEU* 3.6 20.0 - - + +
159D PHE* 3.8 30.9 - - + +
162D VAL* 3.9 15.0 - - + -
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Residues in contact with HIS 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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103D PHE* 3.0 16.7 + - + +
105D PRO* 1.3 77.3 - - + +
107D VAL* 1.3 65.4 + - - +
109D GLU* 4.0 0.5 - - - +
110D LYS* 3.1 26.5 + - - +
159D PHE* 2.9 56.0 + + + -
162D VAL* 2.6 26.5 + - - +
163D PRO 3.2 19.2 + - - -
164D LYS* 3.3 32.3 - - + +
165D PRO* 4.4 13.7 - - + -
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Residues in contact with VAL 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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43D LEU* 3.9 24.9 - - + -
99D LYS 4.4 8.3 - - - +
100D ILE* 4.5 7.4 - - + +
103D PHE* 2.9 33.2 + - + +
104D PHE* 3.9 5.8 - - - +
106D HIS* 1.3 76.7 - - + +
108D LEU* 1.3 61.1 + - - +
110D LYS* 4.0 4.7 - - - +
111D GLU* 3.3 22.0 + - - +
121D SER* 6.1 0.4 - - - -
122D LEU* 3.3 40.0 - - + +
130D ALA* 5.0 6.1 - - + -
165D PRO* 6.1 1.6 - - + -
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Residues in contact with LEU 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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104D PHE 3.1 19.1 + - - +
105D PRO 3.9 3.1 - - - +
107D VAL* 1.3 76.3 - - - +
109D GLU* 1.3 64.0 + - - +
111D GLU* 3.4 4.4 + - - +
112D LYS* 3.0 24.1 + - - +
122D LEU* 4.7 1.3 - - + -
127D LEU* 3.8 16.1 - - + +
130D ALA* 3.7 33.2 - - + +
131D ARG* 3.8 25.1 - - + +
134D MET* 3.4 46.7 - - + -
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Residues in contact with GLU 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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105D PRO 3.0 19.0 + - - +
106D HIS 4.0 2.0 - - - +
108D LEU* 1.3 76.9 - - - +
110D LYS* 1.3 63.4 + - - +
112D LYS* 3.3 26.5 + - - +
113D THR* 3.1 49.1 + - + +
159D PHE* 3.7 31.2 - - + -
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Residues in contact with LYS 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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42D GLU* 3.8 22.0 + - - -
43D LEU 4.9 4.4 + - - -
106D HIS 3.1 18.9 + - - +
107D VAL* 4.0 5.6 - - - +
108D LEU 3.3 0.2 - - - -
109D GLU* 1.3 79.4 - - - +
111D GLU* 1.3 56.7 + - - +
113D THR* 3.3 7.4 + - - -
114D ARG* 3.1 27.1 + - + +
118D GLU* 5.1 11.2 - - - -
121D SER* 4.3 23.5 + - - +
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Residues in contact with GLU 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 VAL 3.3 15.8 + - - +
108D LEU* 3.8 4.3 - - - +
109D GLU 3.3 0.2 - - - -
110D LYS* 1.3 76.9 - - - +
112D LYS* 1.3 65.3 + - - +
114D ARG* 2.8 50.9 + - - +
120D SER* 2.7 25.2 + - - -
121D SER 4.3 2.9 + - - -
122D LEU* 3.9 15.2 + - + -
127D LEU* 4.2 31.5 - - + +
131D ARG* 6.0 0.4 - - - +
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Residues in contact with LYS 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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108D LEU 3.0 18.1 + - - +
109D GLU* 3.7 32.4 + - - +
111D GLU* 1.3 80.3 - - - +
113D THR* 1.3 62.4 + - + +
114D ARG 3.7 2.9 + - - +
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Residues in contact with THR 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 GLU* 3.1 38.6 + - + +
110D LYS* 3.3 9.4 + - - -
112D LYS* 1.3 83.2 - - + +
114D ARG* 1.3 66.4 + - - +
115D PRO* 3.3 10.4 - - - +
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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
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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