Contacts of the helix formed by residues 104 - 116 (chain C) in PDB entry 5EG6
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 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C GLY* 3.3 14.3 - - - -
103C GLY* 1.3 71.4 - - - -
105C GLY* 1.3 61.0 + - - +
106C TRP 3.2 1.8 + - - -
107C LYS* 3.4 3.1 + - - +
108C LYS* 3.2 25.4 + - - +
505C EDO 2.9 28.7 + - - -
516C EDO 3.4 27.1 + - - -
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Residues in contact with GLY 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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70C GLY 3.0 22.4 + - - -
71C ASP 2.9 16.5 + - - -
72C GLN* 3.4 12.3 - - - +
104C SER* 1.3 80.5 + - - +
106C TRP* 1.3 55.9 + - - +
108C LYS* 3.8 3.6 - - - -
109C LYS* 2.9 30.0 + - - +
519C BU1 3.4 7.4 - - - +
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Residues in contact with TRP 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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72C GLN* 3.2 33.7 - - + -
73C THR 3.0 32.9 + - - +
74C VAL* 3.9 11.4 - - + -
101C LEU* 3.6 36.3 - - + -
102C MET 3.1 22.7 + - - -
103C GLY 3.6 5.4 - - - -
104C SER 3.2 1.2 - - - -
105C GLY* 1.3 74.1 - - - +
107C LYS* 1.3 60.2 + - - +
109C LYS* 3.3 3.7 + - + +
110C LYS* 2.9 29.2 + - - +
125C PRO* 4.0 31.6 - - + -
171C MET* 4.2 9.9 - - + -
173C TYR* 4.1 13.9 - + - -
179C ILE* 4.3 7.6 - - + -
366C PHE* 4.3 10.3 - + - -
516C EDO 3.4 7.2 - - - +
520C BU1 3.5 22.6 - - + +
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Residues in contact with LYS 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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104C SER 3.9 2.0 - - - +
106C TRP* 1.3 75.7 - - - +
108C LYS* 1.3 66.7 + - + +
110C LYS* 3.2 13.2 + - + +
111C GLU* 2.9 53.7 + - + +
516C EDO 2.9 37.1 + - - +
520C BU1 4.6 1.9 + - - +
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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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68C GLU* 5.5 6.7 - - - -
70C GLY* 5.7 3.1 - - - +
104C SER* 3.2 17.6 + - - +
105C GLY* 3.7 9.9 - - - +
107C LYS* 1.3 82.6 - - + +
109C LYS* 1.3 62.9 + - - +
111C GLU* 3.4 6.5 + - - +
112C GLN 3.1 7.3 + - - -
367C TYR* 6.1 1.1 - - + +
506C EDO 2.8 57.0 + - - +
519C BU1 3.6 19.9 + - + -
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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
----------------------------------------------------------
72C GLN* 4.0 13.2 - - - +
105C GLY 2.9 19.6 + - - +
106C TRP* 3.6 5.2 - - + +
107C LYS 3.3 0.2 - - - -
108C LYS* 1.3 75.7 - - - +
110C LYS* 1.3 63.5 + - - +
112C GLN* 2.9 26.8 + - - +
113C MET* 3.0 37.8 + - - +
173C TYR* 3.4 47.3 - - + +
177C ASP* 5.9 1.0 + - - -
368C GLU* 2.8 39.8 + - - +
372C PRO* 4.0 13.3 - - - +
519C BU1 3.5 10.1 - - - +
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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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106C TRP 2.9 17.4 + - - +
107C LYS* 3.5 12.1 - - + +
109C LYS* 1.3 78.4 - - - +
111C GLU* 1.3 66.0 + - + +
113C MET* 3.3 3.9 + - - +
114C GLU* 2.7 60.2 + - - +
120C GLU* 3.9 17.8 + - - +
123C SER* 4.1 23.4 + - - +
125C PRO* 6.3 1.1 - - + -
173C TYR* 6.4 0.2 - - - -
520C BU1 6.5 1.1 - - + -
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Residues in contact with GLU 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 LYS* 2.9 50.3 + - + +
108C LYS* 3.7 10.3 + - - +
109C LYS 3.3 0.2 - - - -
110C LYS* 1.3 81.3 - - + +
112C GLN* 1.3 58.5 + - - +
114C GLU* 3.5 5.8 + - - +
115C ARG* 2.9 38.2 + - - +
506C EDO 2.7 41.8 + - - -
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Residues in contact with GLN 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 3.1 9.1 + - - +
109C LYS* 2.9 40.9 + - - +
111C GLU* 1.3 76.7 - - - +
113C MET* 1.3 71.2 + - - +
115C ARG* 3.3 14.6 + - - +
116C ASP* 2.7 57.3 + - - +
368C GLU* 4.2 1.4 - - - +
371C GLY* 6.0 0.7 - - - -
372C PRO* 3.3 28.6 - - + +
506C EDO 3.3 13.8 + - - +
519C BU1 4.0 9.5 + - - +
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Residues in contact with MET 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 LYS* 3.0 40.8 + - - +
110C LYS* 3.8 4.5 - - - +
112C GLN* 1.3 94.7 - - - +
114C GLU* 1.3 61.3 + - - +
116C ASP* 3.3 9.7 + - - +
117C GLY 3.3 0.7 + - - -
118C CYS* 3.0 39.3 + - + +
122C GLU 3.6 22.4 - - - +
123C SER* 4.0 14.1 - - - +
173C TYR* 3.8 27.4 - - + -
175C ASN* 3.6 27.4 - - - +
177C ASP* 4.1 7.4 - - - +
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Residues in contact with GLU 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* 2.7 52.0 + - - +
111C GLU* 4.1 5.3 - - - +
113C MET* 1.3 76.1 - - - +
115C ARG* 1.3 65.0 + - - +
116C ASP 3.2 0.2 - - - -
117C GLY* 3.1 13.7 + - - -
118C CYS 3.3 21.6 + - - +
119C SER 4.2 1.3 - - - +
120C GLU* 3.6 15.9 - - - +
123C SER* 2.9 21.0 + - - +
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Residues in contact with ARG 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 GLU* 2.9 21.3 + - - +
112C GLN* 3.3 19.4 + - - +
114C GLU* 1.3 76.3 - - - +
116C ASP* 1.3 65.0 + - - +
117C GLY* 3.2 4.0 + - - -
506C EDO 2.5 50.9 + - - -
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Residues in contact with ASP 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 GLN* 2.7 43.5 + - - +
113C MET* 3.6 6.7 - - - +
114C GLU 3.2 0.4 - - - -
115C ARG* 1.3 84.4 + - - +
117C GLY* 1.3 55.8 + - - +
118C CYS* 3.7 3.1 - - - -
372C PRO* 4.8 2.8 - - - +
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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