Contacts of the helix formed by residues 105 - 117 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C ALA 3.7 1.4 + - - -
104C GLY* 1.3 76.0 - - - -
106C GLU* 1.3 61.0 + - - +
107C ALA* 3.1 10.7 + - - +
108C GLN* 2.8 37.9 + - - +
109C LYS* 2.8 27.6 + - - +
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TYR* 3.4 18.5 + - - -
104C GLY 5.1 0.2 - - - +
105C SER* 1.3 74.0 - - - +
107C ALA* 1.3 57.6 + - - +
109C LYS* 3.2 30.6 + - - +
110C GLU* 3.1 30.8 + - - +
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C SER* 3.0 9.3 + - - +
106C GLU* 1.3 77.0 - - - +
108C GLN* 1.3 66.5 + - + +
110C GLU* 3.4 6.1 + - - +
111C ALA* 3.0 24.2 + - - +
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ILE* 4.6 3.4 - - + -
103C ALA 3.9 1.9 - - - +
104C GLY* 3.2 12.3 - - - -
105C SER* 2.8 39.3 + - - +
107C ALA* 1.3 75.7 - - + +
109C LYS* 1.3 64.6 + - - +
111C ALA* 3.1 3.6 + - - -
112C PHE* 3.0 43.0 + - + -
191C ALA* 5.6 3.0 - - - +
228C GLU* 3.5 25.4 + - + +
229C ALA 3.9 3.0 + - - -
230C LEU 2.8 31.8 + - - +
231C LEU* 3.4 16.3 - - + +
232C GLY 4.7 1.0 + - - -
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TYR* 3.4 37.8 + - + +
100C ILE* 4.1 12.1 - - - +
101C LEU* 3.8 24.5 + - + +
102C LEU 5.7 0.4 - - - -
104C GLY 2.9 26.6 + - - +
105C SER 2.8 22.2 + - - +
106C GLU* 3.2 24.5 + - - +
108C GLN* 1.3 76.6 - - - +
110C GLU* 1.3 62.7 + - - +
113C LEU* 2.9 47.4 + - + +
114C PRO* 3.3 0.2 - - - +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ALA 5.6 2.3 - - - +
61C TYR* 4.3 15.2 - - + -
106C GLU 3.1 16.3 + - - +
107C ALA* 3.7 6.1 - - - +
109C LYS* 1.3 78.9 - - - +
111C ALA* 1.3 57.5 + - - +
114C PRO* 3.0 34.3 - - - +
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ALA 3.0 17.3 + - - +
108C GLN* 3.5 6.1 - - - +
109C LYS 3.1 0.2 - - - -
110C GLU* 1.3 79.7 - - - +
112C PHE* 1.3 72.9 + - + +
114C PRO* 4.5 3.3 - - - +
115C LYS* 4.8 5.7 - - - +
193C PHE* 3.4 23.2 - - + -
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Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ILE* 3.7 28.5 - - + -
108C GLN* 3.0 41.3 + - + +
111C ALA* 1.3 85.4 - - + +
113C LEU* 1.3 69.2 + - - +
114C PRO* 3.2 3.5 - - - +
115C LYS* 2.9 19.8 + - - +
116C LEU* 3.2 15.9 + - + +
167C VAL* 3.5 18.2 - - + -
191C ALA* 3.9 17.7 - - + -
192C PHE* 3.7 31.6 - - - -
193C PHE* 3.4 39.7 - + - -
228C GLU 5.4 4.9 - - - -
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C VAL* 4.3 8.7 - - + -
61C TYR* 3.5 36.6 - - + -
97C THR* 3.9 26.7 - - + +
100C ILE* 3.7 19.1 - - + -
101C LEU* 3.8 36.3 - - + +
109C LYS* 2.9 35.4 + - + +
112C PHE* 1.3 72.9 - - - +
114C PRO* 1.3 65.3 - - + +
116C LEU* 4.4 6.1 - - + -
117C ALA* 2.8 28.9 + - - +
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Residues in contact with PRO 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TYR* 3.1 24.3 - - + +
62C GLY* 5.1 3.7 - - - -
109C LYS 3.3 5.8 - - - +
110C GLU* 3.0 36.6 - - - +
111C ALA 4.4 3.6 - - - +
112C PHE 3.2 4.7 - - - +
113C LEU* 1.3 92.4 - - + +
115C LYS* 1.3 65.0 + - + +
117C ALA* 4.0 2.3 - - - +
118C SER* 3.2 19.6 + - - -
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ALA 4.8 4.5 - - - +
112C PHE 2.9 14.0 + - - +
114C PRO* 1.3 76.2 - - + +
116C LEU* 1.3 57.7 + - + +
118C SER* 2.7 27.7 + - - -
119C GLY* 2.9 11.4 + - - -
120C GLU* 3.7 10.9 + - + -
121C ALA* 4.0 19.7 - - + +
167C VAL* 5.6 0.7 - - + -
193C PHE* 3.8 37.8 - - + -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PHE* 3.3 1.3 - - - +
92C HIS* 3.0 30.8 + - + -
96C ALA* 4.8 1.1 - - + -
97C THR* 3.5 30.5 - - + +
100C ILE* 3.5 31.9 - - + -
112C PHE* 3.2 18.5 + - + +
113C LEU* 3.8 10.1 - - + +
115C LYS* 1.3 76.8 - - - +
117C ALA* 1.3 59.8 + - - +
118C SER 2.9 6.1 + - - -
119C GLY* 3.0 11.3 + - - -
121C ALA 3.5 18.4 + - - +
123C GLY* 4.1 9.9 - - - +
167C VAL* 3.6 30.3 - - + -
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Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ALA 4.9 5.2 - - - +
51C GLY* 4.6 4.3 - - - +
53C PHE* 3.4 16.3 + - - +
54C GLY* 3.5 26.3 + - - -
57C VAL* 4.0 11.6 - - + +
62C GLY 4.3 5.9 - - - +
63C GLY* 3.7 25.5 - - - +
97C THR* 5.7 0.2 - - - -
113C LEU 2.8 21.0 + - - +
114C PRO 4.0 4.0 - - - +
116C LEU* 1.3 73.1 - - - +
118C SER* 1.3 58.3 + - - +
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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