Contacts of the helix formed by residues 108 - 122 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105F THR* 3.0 22.5 + - - +
106F ALA 3.2 2.8 - - - +
107F GLU* 1.3 76.1 - - - +
109F ILE* 1.3 61.6 + - - +
110F VAL* 3.3 19.3 + - - +
111F ARG* 3.4 34.2 + - - +
112F GLU* 2.9 24.3 + - - +
132F SER* 4.0 2.5 - - - -
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Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU 3.8 4.9 + - - -
108F ASP* 1.3 74.7 + - - +
110F VAL* 1.3 70.0 + - + +
112F GLU* 3.6 18.3 - - - +
113F ARG* 3.0 36.1 + - - +
132F SER* 4.0 6.8 - - - +
133F GLU 3.9 13.4 + - - +
134F GLY* 3.9 14.1 - - - -
135F GLU 3.8 15.7 - - - +
136F HIS* 3.3 38.1 - - + +
138F TYR* 4.8 4.3 - - + -
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Residues in contact with VAL 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F ASP* 3.2 16.0 + - - +
109F ILE* 1.3 81.7 - - + +
111F ARG* 1.3 66.5 + - + +
113F ARG* 3.3 32.1 + - - +
114F GLU* 3.0 39.8 + - + +
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Residues in contact with ARG 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E GLU* 4.9 3.0 + - - -
91E SER* 6.2 1.8 - - - -
94E ARG* 2.8 44.5 + - - +
104F ASN* 2.7 30.5 + - - +
105F THR* 3.1 20.0 + - - +
106F ALA* 3.6 19.2 - - - +
108F ASP* 3.3 31.9 + - + +
110F VAL* 1.3 80.8 - - + +
112F GLU* 1.3 56.8 + - - +
114F GLU* 3.2 12.7 + - - +
115F ALA* 2.8 16.8 + - - +
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Residues in contact with GLU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ILE* 4.3 3.6 - - + -
105F THR* 3.5 17.6 - - + +
108F ASP 2.9 13.9 + - - +
109F ILE* 3.3 15.3 + - - +
111F ARG* 1.3 74.1 - - - +
113F ARG* 1.3 56.8 + - - +
115F ALA* 3.2 4.7 + - - +
116F VAL* 2.9 35.4 + - + +
129F LEU* 4.0 26.2 - - + +
130F ALA 4.6 0.3 - - - +
131F PRO* 3.6 4.0 - - - +
132F SER* 2.9 33.3 + - - +
136F HIS* 2.9 29.8 + - - -
138F TYR* 2.7 20.8 + - - +
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Residues in contact with ARG 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ILE* 3.0 22.6 + - - +
110F VAL* 3.6 41.5 - - - +
112F GLU* 1.3 77.1 - - - +
114F GLU* 1.3 62.9 + - + +
116F VAL* 3.4 2.4 + - - +
117F GLY* 3.1 18.9 + - - -
138F TYR* 3.5 52.9 + - + +
142F GLU* 4.6 7.4 - - - +
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Residues in contact with GLU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ARG* 4.1 9.5 + - - +
110F VAL* 3.0 31.3 + - + +
111F ARG* 3.2 19.8 + - - +
113F ARG* 1.3 71.3 - - + +
115F ALA* 1.3 68.0 + - - +
117F GLY* 3.2 2.6 + - - -
118F GLN* 2.9 27.4 + - - +
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ARG* 3.7 10.7 - - - +
73F ILE* 3.7 22.0 - - + -
103F ALA* 3.8 23.8 - - + -
105F THR* 5.2 0.9 - - + -
111F ARG 2.8 17.6 + - - +
112F GLU* 3.7 7.0 - - - +
114F GLU* 1.3 71.3 - - - +
116F VAL* 1.3 57.6 + - - +
118F GLN* 3.2 11.1 + - - +
119F PHE* 2.8 36.0 + - + +
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Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ILE* 3.7 17.5 - - + +
112F GLU* 2.9 25.5 + - + +
113F ARG 3.7 5.6 - - - +
115F ALA* 1.3 76.0 - - - +
117F GLY* 1.3 58.2 + - - +
119F PHE* 3.4 1.8 + - - +
120F PHE* 2.9 28.5 + - + +
127F LEU* 3.8 17.2 - - + +
129F LEU* 5.2 3.6 - - + -
138F TYR* 3.4 25.6 - - + +
139F LEU* 4.0 10.8 - - + -
143F LEU* 3.6 35.7 - - + -
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Residues in contact with GLY 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ARG 3.1 11.9 + - - -
114F GLU* 3.7 2.5 - - - -
116F VAL* 1.3 79.4 - - - +
118F GLN* 1.3 50.6 + - - +
120F PHE* 3.3 6.8 + - - +
121F GLU* 2.8 40.0 + - - +
143F LEU* 6.1 0.7 - - - -
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Residues in contact with GLN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ARG* 4.9 23.2 + - - +
97E GLY* 6.2 0.3 - - - -
98E TYR 5.1 3.7 + - - -
99E SER* 3.7 21.2 + - - +
102F LEU 5.8 0.2 + - - -
114F GLU* 2.9 20.1 + - - +
115F ALA* 3.4 8.3 - - - +
117F GLY* 1.3 77.0 - - - +
119F PHE* 1.3 82.6 + - + +
121F GLU* 2.9 36.3 - - - +
122F ARG* 3.1 17.4 - - + +
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Residues in contact with PHE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E SER* 4.5 6.1 - - - -
100E VAL 5.9 0.2 - - - -
71F GLY* 3.7 15.3 - - - -
72F LEU 3.8 8.5 - - - -
73F ILE* 3.6 27.1 - - + -
101F LEU* 3.8 35.0 - - + -
102F LEU 3.7 15.3 - - - -
103F ALA* 3.4 33.9 - - + -
115F ALA* 2.8 18.7 + - + +
116F VAL* 3.9 2.0 - - - +
118F GLN* 1.3 96.4 - - + +
120F PHE* 1.3 65.5 + - - +
122F ARG* 3.3 10.1 + - - +
124F VAL* 3.1 32.7 + - + +
127F LEU* 3.9 16.2 - - + -
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Residues in contact with PHE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F VAL 2.9 19.0 + - - +
117F GLY* 3.7 6.5 - - - +
119F PHE* 1.3 78.0 - - - +
121F GLU* 1.3 59.1 + - - +
123F ARG* 2.7 66.8 + - - -
124F VAL* 4.6 4.0 - - - -
142F GLU 4.9 4.0 - - - -
143F LEU* 3.5 22.0 - - + -
144F PRO* 3.3 37.9 - - + -
147F PHE* 3.5 39.4 - + + -
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Residues in contact with GLU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F GLY 2.8 21.5 + - - +
118F GLN* 2.9 29.2 - - - +
120F PHE* 1.3 75.8 - - + +
122F ARG* 1.3 71.5 + - - +
123F ARG* 2.9 23.3 + - - +
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Residues in contact with ARG 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E SER 3.3 22.0 + - - -
68E ASN* 3.3 23.6 + - - +
69E VAL* 3.6 21.6 - - - +
97E GLY 5.0 2.0 + - - -
99E SER* 3.1 23.3 + - - +
69F VAL* 6.0 0.5 - - - +
101F LEU* 4.1 21.3 - - + -
118F GLN* 3.1 27.3 + - + +
119F PHE* 3.6 8.1 - - - +
120F PHE 3.1 1.6 - - - -
121F GLU* 1.3 86.0 + - - +
123F ARG* 1.3 70.0 + - - +
124F VAL* 3.2 1.9 + - - +
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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