Contacts of the helix formed by residues 105 - 118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ALA 3.7 1.0 + - - -
104A GLY* 1.3 78.5 - - - +
106A GLU* 1.3 65.5 + - - +
107A ALA* 3.5 7.8 + - - +
108A GLN* 3.0 37.7 + - - +
109A LYS* 3.0 20.2 + - - +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 2.5 38.2 + - - +
104A GLY 4.8 0.7 - - - +
105A SER* 1.3 74.7 - - - +
107A ALA* 1.3 57.7 + - - +
109A LYS* 2.9 26.9 + - - +
110A GLU* 3.0 28.4 + - - +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A SER* 3.2 8.0 + - - +
106A GLU* 1.3 77.5 - - - +
108A GLN* 1.3 60.1 + - + +
110A GLU* 3.3 6.6 + - - +
111A ALA* 3.0 28.6 + - - +
228A GLU* 6.4 1.8 - - + -
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 4.8 1.6 - - + -
103A ALA 4.3 1.6 - - - +
104A GLY* 3.5 11.1 - - - -
105A SER* 3.0 37.8 + - - +
107A ALA* 1.3 75.1 - - + +
109A LYS* 1.3 60.8 + - - +
111A ALA* 3.1 3.8 + - - -
112A PHE* 2.8 53.5 + - + +
191A ALA* 5.7 0.4 - - - +
228A GLU* 3.0 32.4 + - + +
229A ALA 4.1 2.4 + - - -
230A LEU 2.8 30.9 + - - +
231A LEU* 3.6 13.3 - - + +
232A GLY 5.0 0.5 + - - -
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 3.7 21.6 - - + -
100A ILE* 3.8 18.2 - - - +
101A LEU* 3.8 27.8 + - + +
104A GLY 3.5 18.2 + - - +
105A SER 3.0 13.3 + - - +
106A GLU* 2.9 38.0 + - - +
107A ALA 3.3 0.2 - - - -
108A GLN* 1.3 75.6 - - - +
110A GLU* 1.3 59.0 + - - +
113A LEU* 2.9 62.7 + - + +
114A PRO* 3.4 1.2 - - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA 5.5 1.2 - - - +
61A TYR* 3.5 22.1 - - + -
106A GLU 3.0 18.1 + - - +
107A ALA* 3.7 7.2 - - - +
108A GLN 3.2 0.4 - - - -
109A LYS* 1.3 76.3 - - - +
111A ALA* 1.3 60.6 + - - +
114A PRO* 3.3 22.7 - - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA 3.0 17.6 + - - +
108A GLN* 3.1 8.0 + - - +
110A GLU* 1.3 80.0 - - - +
112A PHE* 1.3 68.1 + - + +
114A PRO* 4.6 1.1 - - - +
115A LYS* 5.4 5.0 + - - +
193A PHE* 3.2 27.9 - - + -
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 3.6 31.0 - - + -
108A GLN* 2.8 48.7 + - + +
111A ALA* 1.3 80.2 - - + +
113A LEU* 1.3 64.2 + - - +
114A PRO* 3.5 2.4 - - - -
115A LYS* 3.6 6.5 + - - +
116A LEU* 3.2 26.2 + - + +
167A VAL* 4.0 18.3 - - + +
191A ALA* 3.4 34.5 - - + -
192A PHE* 4.0 15.3 - - - -
193A PHE* 3.3 40.8 - + - -
228A GLU 4.8 6.1 - - - -
231A LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL* 4.2 11.4 - - + -
61A TYR* 3.9 26.9 - - + +
97A THR* 4.0 32.5 - - + +
100A ILE* 3.9 18.4 - - + -
101A LEU* 4.1 18.6 - - + +
109A LYS* 2.9 56.2 + - + +
112A PHE* 1.3 69.6 - - - +
114A PRO* 1.3 58.3 - - + +
116A LEU* 3.1 4.4 + - + -
117A ALA* 2.6 37.4 + - - +
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Residues in contact with PRO 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 3.5 22.0 - - + +
62A GLY* 5.0 4.9 - - - +
109A LYS 3.4 5.8 - - - +
110A GLU* 3.3 40.6 - - - +
111A ALA 4.6 0.9 - - - +
112A PHE 3.6 2.5 - - - -
113A LEU* 1.3 90.2 - - + +
115A LYS* 1.3 59.6 + - + +
117A ALA* 3.9 2.2 - - + +
118A SER* 3.1 30.0 + - - -
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA 5.4 3.6 + - - +
112A PHE 3.6 7.2 + - - +
113A LEU 3.3 0.2 - - - -
114A PRO* 1.3 80.8 - - + +
116A LEU* 1.3 65.1 + - + +
118A SER* 3.1 7.6 + - - -
119A GLY 3.1 0.2 + - - -
120A GLU* 3.0 38.4 + - + -
121A ALA* 3.2 21.8 + - + -
167A VAL* 5.8 0.2 - - + -
193A PHE* 4.2 29.0 - - + -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE 3.1 2.9 - - - +
92A HIS* 2.8 28.9 + - + -
96A ALA* 4.9 0.9 - - + -
97A THR* 3.7 29.4 - - + +
100A ILE* 3.7 29.8 - - + -
112A PHE* 3.2 25.5 + - + +
113A LEU* 3.1 9.3 + - + +
115A LYS* 1.3 76.5 - - - +
117A ALA* 1.3 61.3 + - - +
119A GLY* 3.2 8.8 + - - -
121A ALA 3.4 17.5 - - - +
123A GLY* 3.7 28.3 - - - +
167A VAL* 3.8 22.2 - - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA 5.2 1.0 - - - +
51A GLY* 4.8 7.1 - - - +
53A PHE* 3.5 4.7 + - - +
54A GLY* 3.4 30.5 + - - -
57A VAL* 4.2 9.8 - - + +
62A GLY 3.4 32.0 - - - +
63A GLY* 3.9 9.4 - - - +
97A THR* 5.8 0.2 - - - -
113A LEU 2.6 23.8 + - - +
114A PRO 3.9 2.2 - - - +
116A LEU* 1.3 76.0 - - - +
118A SER* 1.3 58.4 + - - +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.3 23.7 - - - +
62A GLY 4.7 3.3 + - - -
114A PRO 3.1 15.4 + - - -
115A LYS* 3.1 9.2 + - - -
117A ALA* 1.3 77.2 - - - +
119A GLY* 1.3 59.4 + - - +
120A GLU* 2.9 33.6 + - - +
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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