Contacts of the helix formed by residues 108 - 122 (chain C) in PDB entry 3EGC
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 ASP 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C THR* 3.1 22.8 + - - +
106C ALA 4.1 3.8 - - - +
107C GLU* 1.3 76.3 - - - +
109C ILE* 1.3 62.5 + - - +
110C VAL* 3.3 21.9 + - - +
111C ARG* 3.2 34.6 + - - +
112C GLU* 3.0 22.3 + - - +
132C SER* 4.1 1.8 - - - -
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Residues in contact with ILE 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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133B GLU* 4.8 12.1 - - + +
107C GLU 3.8 3.8 + - - -
108C ASP* 1.3 72.6 + - - +
110C VAL* 1.3 71.2 + - + +
112C GLU* 3.6 18.8 - - - +
113C ARG* 3.0 37.7 + - - +
132C SER* 4.1 10.4 - - - +
133C GLU 3.8 14.1 + - - +
134C GLY* 4.2 11.4 - - - -
135C GLU 3.7 19.3 - - - +
136C HIS* 3.4 32.1 - - + +
138C TYR* 4.6 4.7 - - + -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 5.9 0.2 - - - +
193B SER* 5.6 2.9 - - - +
108C ASP* 3.2 17.1 + - - +
109C ILE* 1.3 83.8 - - + +
111C ARG* 1.3 64.7 + - + +
113C ARG* 3.6 28.2 + - - +
114C GLU* 3.2 39.8 + - + +
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Residues in contact with ARG 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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104C ASN* 2.8 29.5 + - - +
105C THR* 3.2 25.8 + - - +
106C ALA* 3.6 17.4 - - - +
108C ASP* 3.2 29.6 + - + +
110C VAL* 1.3 78.7 - - + +
112C GLU* 1.3 66.4 + - - +
114C GLU* 3.3 11.4 + - - +
115C ALA* 3.0 5.5 + - - +
90D GLU* 4.5 4.9 + - - -
91D SER* 5.5 8.7 + - - +
94D ARG* 2.5 48.5 + - - +
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Residues in contact with GLU 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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73C ILE* 4.2 6.1 - - + -
105C THR* 3.6 16.3 - - + +
108C ASP 3.0 11.9 + - - +
109C ILE* 3.2 15.9 + - - +
111C ARG* 1.3 75.1 - - - +
113C ARG* 1.3 59.1 + - - +
115C ALA* 3.1 4.5 + - - +
116C VAL* 2.9 33.6 + - + +
129C LEU* 3.5 24.9 - - + +
131C PRO* 3.3 10.9 - - - +
132C SER* 2.9 31.9 + - - +
136C HIS* 2.9 26.8 + - - -
138C TYR* 2.5 23.0 + - - +
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Residues in contact with ARG 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 3.7 15.8 + - - -
193B SER* 3.9 4.0 + - - -
194B ALA* 2.4 50.1 - - - +
195B GLY* 3.2 23.4 - - - +
109C ILE* 3.0 22.6 + - - +
110C VAL* 3.8 34.2 - - - +
112C GLU* 1.3 78.7 - - - +
114C GLU* 1.3 60.5 + - + +
116C VAL* 3.9 1.4 - - - +
117C GLY* 3.2 18.5 + - - -
138C TYR* 3.5 49.0 + - + -
142C GLU* 4.6 5.2 - - - +
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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 VAL* 3.2 31.1 + - + +
111C ARG* 4.1 15.1 - - - +
112C GLU 3.2 0.2 - - - -
113C ARG* 1.3 76.1 - - + +
115C ALA* 1.3 60.2 + - - +
117C GLY* 3.4 1.3 + - - -
118C GLN* 2.8 32.8 + - - +
94D ARG* 3.7 14.1 + - - +
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Residues in contact with ALA 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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73C ILE* 3.7 19.7 - - + -
103C ALA* 3.7 24.0 - - + -
105C THR* 5.3 0.2 - - + -
111C ARG 3.0 7.9 + - - +
112C GLU* 3.7 7.4 - - - +
114C GLU* 1.3 75.1 - - - +
116C VAL* 1.3 53.4 + - - +
118C GLN* 3.2 10.6 + - - +
119C PHE* 2.7 40.5 + - + +
94D ARG* 3.1 18.8 - - - +
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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
----------------------------------------------------------
73C ILE* 3.7 18.8 - - + -
112C GLU* 2.9 24.9 + - + +
113C ARG 3.9 4.5 - - - +
115C ALA* 1.3 74.4 - - - +
117C GLY* 1.3 55.6 + - - +
119C PHE* 3.3 1.5 + - - +
120C PHE* 2.8 36.9 + - - +
127C LEU* 4.0 17.0 - - + +
129C LEU* 5.1 4.3 - - + -
138C TYR* 3.5 25.1 - - + +
139C LEU* 3.9 11.7 - - + -
143C LEU* 3.7 34.8 - - + -
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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 ARG 3.2 11.9 + - - -
114C GLU 3.7 2.2 - - - -
116C VAL* 1.3 79.5 - - - +
118C GLN* 1.3 56.2 + - - +
120C PHE* 3.8 6.0 - - - +
121C GLU* 2.7 39.5 + - - +
143C LEU* 6.1 0.7 - - - -
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Residues in contact with GLN 118 (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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103C ALA* 5.4 2.4 - - - +
114C GLU* 2.8 22.9 + - - +
115C ALA* 3.3 10.7 - - - +
117C GLY* 1.3 73.0 - - - +
119C PHE* 1.3 87.6 + - + +
121C GLU* 2.9 32.3 - - - +
122C ARG* 3.1 15.4 + - + +
94D ARG* 4.5 25.1 + - - +
97D GLY* 6.0 3.2 - - - -
98D TYR 4.7 5.4 + - - +
99D SER* 3.6 23.4 + - - +
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Residues in contact with PHE 119 (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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71C GLY* 3.5 18.4 - - - -
72C LEU 3.7 5.4 - - - -
73C ILE* 3.7 32.8 - - + -
101C LEU* 3.6 44.0 - - + -
102C LEU 3.7 14.4 - - - -
103C ALA* 3.6 19.1 - - + -
115C ALA 2.7 18.8 + - - +
116C VAL 4.0 2.0 - - - +
118C GLN* 1.3 98.4 - - + +
120C PHE* 1.3 67.3 + - - +
122C ARG* 3.0 15.6 + - - +
123C ARG 3.2 7.6 + - - -
124C VAL* 3.3 26.9 + - + +
127C LEU* 4.0 6.3 - - + -
99D SER* 4.5 4.9 - - - -
100D VAL 5.6 0.7 - - - -
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Residues in contact with PHE 120 (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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116C VAL 2.8 23.6 + - - +
117C GLY* 3.8 5.6 - - - +
119C PHE* 1.3 72.1 - - - +
121C GLU* 1.3 55.3 + - + +
123C ARG* 2.6 73.9 + - - +
124C VAL* 4.3 5.9 - - - +
127C LEU* 5.3 0.2 - - - +
142C GLU 5.0 5.2 - - - -
143C LEU* 3.5 23.8 - - + -
144C PRO* 3.2 42.2 - - + -
147C PHE* 3.8 31.3 - + + -
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Residues in contact with GLU 121 (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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117C GLY 2.7 34.0 + - - +
118C GLN* 2.9 24.6 - - - +
120C PHE* 1.3 76.9 - - + +
122C ARG* 1.3 72.2 + - - +
123C ARG* 2.9 24.0 + - - +
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Residues in contact with ARG 122 (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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67C SER* 5.8 0.2 - - - -
69C VAL* 6.2 0.3 - - - +
101C LEU* 3.9 22.4 - - + -
118C GLN* 3.1 19.4 + - + +
119C PHE* 3.0 13.8 + - - +
121C GLU* 1.3 85.4 + - - +
123C ARG* 1.3 70.4 + - - +
124C VAL* 3.4 1.8 + - - +
67D SER 3.0 23.8 + - - -
68D ASN* 3.2 23.0 + - - +
69D VAL* 3.4 22.0 - - - +
97D GLY 5.1 1.8 + - - -
99D SER* 3.0 25.1 + - - +
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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