Contacts of the helix formed by residues 108 - 122 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D THR* 3.0 17.6 + - - +
106D ALA 3.2 3.3 + - - +
107D GLU* 1.3 75.6 - - - +
109D ILE* 1.3 62.6 + - - +
110D VAL* 3.2 19.8 + - - +
111D ARG* 3.2 37.3 + - - +
112D GLU* 3.0 23.4 + - - +
132D SER* 3.7 2.4 + - - -
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU 3.8 4.2 + - - -
108D ASP* 1.3 71.3 + - - +
110D VAL* 1.3 68.0 + - + +
112D GLU* 3.4 32.4 - - - +
113D ARG* 3.0 41.0 + - - +
132D SER* 4.0 12.9 - - - +
133D GLU 3.8 14.1 + - - +
134D GLY* 4.2 11.0 - - - -
135D GLU 3.9 18.4 - - - +
136D HIS* 3.4 18.4 - - + +
138D TYR* 4.6 4.0 - - + -
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ASP* 3.2 16.1 + - - +
109D ILE* 1.3 80.9 - - + +
111D ARG* 1.3 63.4 + - + +
113D ARG* 3.6 27.5 + - - +
114D GLU* 3.1 43.1 + - + +
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Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 4.6 4.0 + - - -
91C SER* 5.5 6.2 + - - +
94C ARG* 3.0 35.6 + - - +
104D ASN* 3.0 29.1 + - - +
105D THR* 3.4 20.7 + - - +
106D ALA* 3.8 18.0 - - - +
108D ASP* 3.2 32.9 + - + +
110D VAL* 1.3 78.7 - - + +
112D GLU* 1.3 64.4 + - - +
114D GLU* 3.3 12.9 + - - +
115D ALA* 2.9 20.1 + - - +
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ILE* 4.4 3.7 - - + +
105D THR* 3.5 19.3 - - + +
108D ASP 3.0 10.7 + - - +
109D ILE* 3.4 16.9 - - - +
111D ARG* 1.3 75.7 - - - +
113D ARG* 1.3 57.1 + - - +
115D ALA* 3.0 4.4 + - - +
116D VAL* 2.9 34.1 + - + +
129D LEU* 3.8 23.6 - - + +
130D ALA 4.3 0.5 - - - +
131D PRO* 3.4 9.2 - - - +
132D SER* 2.9 32.1 + - - +
136D HIS* 2.9 26.8 + - - -
138D TYR* 2.7 22.1 + - - +
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Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ILE* 3.0 25.6 + - - +
110D VAL* 3.9 37.4 - - - +
112D GLU* 1.3 76.0 - - - +
114D GLU* 1.3 63.1 + - + +
116D VAL* 3.5 2.6 + - - +
117D GLY* 3.2 19.2 + - - -
138D TYR* 3.7 52.9 - - + -
142D GLU* 4.5 7.4 - - - +
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ARG* 4.0 9.3 + - - +
110D VAL* 3.1 34.6 + - + +
111D ARG* 3.7 19.3 - - - +
112D GLU 3.3 0.2 - - - -
113D ARG* 1.3 77.2 - - + +
115D ALA* 1.3 57.5 + - - +
117D GLY* 4.1 0.6 - - - -
118D GLN* 3.0 30.7 + - - +
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ARG* 3.9 10.3 - - - +
73D ILE* 3.8 18.6 - - + -
103D ALA* 3.8 24.0 - - + -
105D THR* 5.0 0.9 - - + -
111D ARG 2.9 16.0 + - - +
112D GLU* 3.0 6.3 + - - +
114D GLU* 1.3 74.0 - - - +
116D VAL* 1.3 58.4 + - - +
118D GLN* 3.2 9.6 + - - +
119D PHE* 2.7 40.3 + - + +
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ILE* 3.5 18.8 - - + +
112D GLU* 2.9 24.4 + - + +
113D ARG 3.7 5.6 - - - +
115D ALA* 1.3 77.5 - - - +
117D GLY* 1.3 56.1 + - - +
119D PHE* 3.8 1.6 - - - +
120D PHE* 2.8 28.3 + - + +
127D LEU* 3.9 17.8 - - + +
129D LEU* 5.2 4.5 - - + -
138D TYR* 3.5 25.6 - - + +
139D LEU* 4.0 9.9 - - + -
143D LEU* 3.7 34.8 - - + -
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ARG 3.2 12.2 + - - -
114D GLU* 4.1 1.1 - - - -
116D VAL* 1.3 77.7 - - - +
118D GLN* 1.3 54.4 + - - +
120D PHE* 3.4 6.4 + - - +
121D GLU* 2.8 39.0 + - - +
143D LEU* 6.0 0.9 - - - -
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Residues in contact with GLN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ARG* 4.2 23.9 + - - +
98C TYR 4.9 4.8 + - - -
99C SER* 3.8 23.0 + - - +
114D GLU* 3.0 20.6 + - - +
115D ALA* 3.4 8.3 - - - +
117D GLY* 1.3 75.7 - - - +
119D PHE* 1.3 87.9 + - + +
121D GLU* 2.9 36.7 - - - +
122D ARG* 3.1 13.8 + - + +
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Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C SER* 4.9 3.6 - - - -
100C VAL 5.8 0.4 - - - -
71D GLY* 3.6 17.7 - - - -
72D LEU 3.7 20.6 - - - -
73D ILE* 3.7 24.5 - - + -
101D LEU* 3.8 36.6 - - + -
102D LEU 3.7 14.6 - - - -
103D ALA* 3.6 20.2 - - + -
115D ALA 2.7 18.7 + - - +
116D VAL 3.9 2.7 - - - +
118D GLN* 1.3 96.8 - - + +
120D PHE* 1.3 65.2 + - - +
122D ARG* 3.2 15.5 + - - +
123D ARG 3.2 7.6 + - - -
124D VAL* 3.4 19.6 + - + +
127D LEU* 4.0 14.8 - - + -
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Residues in contact with PHE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL 2.8 23.3 + - - +
117D GLY* 3.7 6.1 - - - +
119D PHE* 1.3 73.2 - - - +
121D GLU* 1.3 60.0 + - + +
123D ARG* 2.7 70.5 + - - +
124D VAL* 4.3 4.9 - - - +
142D GLU 5.1 4.3 - - - -
143D LEU* 3.7 23.1 - - + -
144D PRO* 3.5 39.0 - - + -
147D PHE* 3.9 32.6 - + + -
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLY 2.8 29.6 + - - +
118D GLN* 2.9 29.7 - - - +
120D PHE* 1.3 76.5 - - + +
122D ARG* 1.3 72.2 + - - +
123D ARG* 2.9 22.4 + - - +
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Residues in contact with ARG 122 (chain D).
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 3.2 23.8 + - - -
68C ASN* 3.4 21.6 + - - +
69C VAL* 3.6 18.1 - - - +
97C GLY 5.2 2.4 + - - -
99C SER* 2.8 24.5 + - - -
67D SER* 5.7 0.3 - - - -
101D LEU* 3.9 23.8 - - + -
118D GLN* 3.1 21.8 + - - +
119D PHE* 3.5 12.6 - - - +
120D PHE 3.1 0.4 - - - -
121D GLU* 1.3 86.0 + - - +
123D ARG* 1.3 68.5 + - - +
124D VAL* 3.3 2.1 + - + +
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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