Contacts of the helix formed by residues 103 - 117 (chain C) in PDB entry 2P4K
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 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C ILE* 4.0 6.5 - - - +
98C LYS* 4.0 12.2 - - - +
101C PHE* 3.4 2.0 + - - +
102C GLY* 1.3 78.2 - - - +
104C PHE* 1.3 58.9 + - - +
105C ASP* 3.5 6.7 + - - +
106C LYS* 2.9 45.4 + - - +
107C PHE* 2.9 28.6 + - - +
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Residues in contact with PHE 104 (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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87C GLY 3.7 18.6 - - - -
88C GLU* 3.7 36.1 - - + +
89C PRO* 3.4 29.8 - - + -
94C LEU* 4.3 11.2 - - + -
97C ILE* 3.9 16.4 - - + +
98C LYS* 4.7 6.4 - - - +
103C SER* 1.3 71.8 - - - +
105C ASP* 1.3 68.3 + - - +
107C PHE* 3.2 17.5 + + - +
108C LYS* 2.8 57.6 + - + +
181C TRP* 4.8 2.0 - + - -
186C TRP* 3.6 23.3 - + - -
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Residues in contact with ASP 105 (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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88C GLU* 5.1 2.0 - - - +
103C SER* 3.1 6.7 + - - +
104C PHE* 1.3 93.9 - - - +
106C LYS* 1.3 58.5 + - - +
108C LYS* 3.2 18.6 + - - +
109C GLU* 3.0 27.4 + - - +
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Residues in contact with LYS 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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101C PHE 3.1 24.5 - - - +
102C GLY* 4.1 6.5 + - - -
103C SER* 2.9 39.6 + - - +
105C ASP* 1.3 75.2 - - - +
107C PHE* 1.3 65.5 + - - +
109C GLU* 3.2 12.4 + - - +
110C LYS* 3.0 39.8 + - - +
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Residues in contact with PHE 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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97C ILE* 3.5 26.5 - - + -
101C PHE* 3.7 33.3 - + + +
103C SER 2.9 6.9 + - - +
104C PHE* 3.4 25.6 - + - +
106C LYS* 1.3 77.3 - - - +
108C LYS* 1.3 64.7 + - + +
110C LYS* 3.1 3.4 + - - +
111C LEU* 2.9 46.0 + - + +
126C LEU* 3.9 40.2 - - + -
137C ILE* 4.2 6.1 - - + -
156C LEU* 4.5 0.7 - - + -
181C TRP* 3.9 16.4 - + - -
186C TRP* 3.7 25.8 - + - -
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Residues in contact with LYS 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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104C PHE* 2.8 49.8 + - + +
105C ASP* 3.2 19.6 + - - +
107C PHE* 1.3 73.1 - - + +
109C GLU* 1.3 62.9 + - - +
112C THR* 2.8 32.1 + - - -
181C TRP* 3.5 63.0 - - + +
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Residues in contact with GLU 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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105C ASP 3.0 13.2 + - - +
106C LYS* 3.4 14.2 - - - +
108C LYS* 1.3 78.3 - - - +
110C LYS* 1.3 80.5 + - - +
112C THR* 3.6 5.3 - - - -
113C ALA* 2.8 37.2 + - + +
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Residues in contact with LYS 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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131A GLU* 4.0 45.0 + - - +
132A ARG* 6.1 0.8 - - - +
100C ASP 5.2 0.4 + - - -
101C PHE* 2.9 50.9 + - + +
106C LYS* 3.0 24.8 + - - +
107C PHE 3.1 1.3 + - - +
109C GLU* 1.3 95.3 - - - +
111C LEU* 1.3 60.1 + - - +
113C ALA* 3.4 3.9 + - - +
114C ALA* 2.9 27.9 + - - +
137C ILE* 3.6 19.5 - - + +
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Residues in contact with LEU 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 PHE* 2.9 30.1 + - + +
110C LYS* 1.3 73.4 - - - +
112C THR* 1.3 64.8 + - - +
114C ALA* 3.3 1.3 + - + -
115C SER* 2.8 36.5 + - - +
124C GLY* 3.9 6.3 - - - -
125C TRP 3.7 37.9 - - - +
126C LEU* 4.4 7.0 - - + +
137C ILE* 3.6 13.8 - - + +
156C LEU* 3.9 30.7 - - + +
158C ILE* 4.0 15.0 - - + -
177C LEU* 6.1 0.2 - - - -
181C TRP* 3.9 19.7 - - + -
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Residues in contact with THR 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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108C LYS* 2.8 24.5 + - - +
109C GLU* 3.6 5.6 - - - -
111C LEU* 1.3 77.5 - - - +
113C ALA* 1.3 54.6 + - - +
115C SER* 3.1 1.6 + - - -
116C VAL* 2.7 41.0 + - + +
174C PRO* 5.8 2.2 - - + +
177C LEU* 3.5 30.6 - - + +
181C TRP* 3.3 24.7 + - - -
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Residues in contact with ALA 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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109C GLU* 2.8 29.7 + - + +
110C LYS* 3.8 4.9 - - - +
112C THR* 1.3 79.9 - - - +
114C ALA* 1.3 62.0 + - - +
116C VAL* 3.9 6.0 - - - +
117C GLY* 2.9 22.0 + - - -
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Residues in contact with ALA 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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110C LYS 2.9 16.5 + - - +
111C LEU* 3.9 6.7 - - + +
112C THR 3.3 0.2 - - - -
113C ALA* 1.3 78.0 - - - +
115C SER* 1.3 61.1 + - - +
117C GLY* 3.5 7.4 + - - -
118C VAL* 3.6 17.0 + - - +
124C GLY* 5.1 1.8 - - - -
137C ILE* 3.8 22.9 - - + -
138C ALA 4.9 3.6 - - - +
139C ALA* 4.1 19.5 - - + +
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Residues in contact with SER 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 LEU* 2.8 23.4 + - - +
112C THR 3.6 3.6 - - - -
114C ALA* 1.3 76.1 - - - +
116C VAL* 1.3 62.3 + - - +
117C GLY 3.1 2.1 + - - -
118C VAL* 3.4 8.2 + - - -
124C GLY* 3.6 20.0 - - - -
158C ILE* 3.9 12.7 - - - +
160C VAL* 3.6 24.3 - - - +
173C ARG* 2.8 21.7 + - - -
177C LEU* 3.6 21.3 - - - +
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Residues in contact with VAL 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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112C THR* 2.7 25.1 + - + +
113C ALA* 3.9 6.1 - - - +
115C SER* 1.3 74.0 - - - +
117C GLY* 1.3 63.4 + - - +
118C VAL 3.8 1.7 - - - +
173C ARG* 3.3 20.2 + - + +
174C PRO* 4.1 30.3 - - + -
177C LEU* 3.3 23.6 - - + -
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Residues in contact with GLY 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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113C ALA 2.9 17.9 + - - -
114C ALA* 3.5 4.5 + - - -
115C SER 3.1 1.0 - - - -
116C VAL* 1.3 78.2 - - - +
118C VAL* 1.3 63.1 + - - +
119C GLN* 3.1 15.1 + - - +
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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