Contacts of the helix formed by residues 108 - 122 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A THR* 3.2 18.2 + - - +
106A ALA 4.4 2.9 - - - +
107A GLU* 1.3 77.6 - - - +
109A ILE* 1.3 66.6 + - - +
110A VAL* 3.2 19.6 + - - +
111A ARG* 3.2 35.6 + - - +
112A GLU* 3.0 17.5 + - - +
132A SER* 3.8 3.2 + - - -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU 3.9 3.6 + - - -
108A ASP* 1.3 74.4 + - - +
110A VAL* 1.3 68.5 + - + +
112A GLU* 3.5 19.4 - - - +
113A ARG* 3.0 38.9 + - - +
132A SER* 3.8 14.9 - - - +
133A GLU 4.0 13.6 + - - +
134A GLY* 4.0 12.6 - - - -
135A GLU 3.9 18.6 - - - +
136A HIS* 3.5 28.0 - - - +
138A TYR* 4.7 4.9 - - + -
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASP* 3.2 16.4 + - - +
109A ILE* 1.3 80.0 - - + +
111A ARG* 1.3 66.4 + - + +
113A ARG* 3.6 28.6 + - - +
114A GLU* 3.1 45.8 + - + +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASN* 2.8 29.7 + - - +
105A THR* 3.2 26.4 + - - +
106A ALA* 3.7 16.2 - - - +
108A ASP* 3.2 29.6 + - - +
110A VAL* 1.3 77.9 - - + +
112A GLU* 1.3 59.4 + - - +
114A GLU* 3.3 8.5 + - - +
115A ALA* 2.9 16.3 + - - +
90B GLU* 4.5 4.6 + - - -
91B SER* 5.7 5.3 - - - +
94B ARG* 2.7 48.9 + - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 4.3 4.3 - - + -
105A THR* 3.6 16.2 - - + +
108A ASP 3.0 13.0 + - - +
109A ILE* 3.2 17.0 + - - +
111A ARG* 1.3 75.4 - - - +
113A ARG* 1.3 57.3 + - - +
115A ALA* 3.2 4.2 + - - +
116A VAL* 2.9 34.6 + - + +
129A LEU* 3.8 24.6 - - + +
130A ALA 4.5 0.2 - - - +
131A PRO* 3.5 4.7 - - - +
132A SER* 2.9 33.3 + - - +
136A HIS* 2.9 29.2 + - - -
138A TYR* 2.6 21.2 + - - +
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ILE* 3.0 24.1 + - - +
110A VAL* 3.8 36.9 - - - +
111A ARG 3.3 0.2 - - - -
112A GLU* 1.3 76.8 - - - +
114A GLU* 1.3 63.0 + - + +
116A VAL* 3.4 1.8 + - - +
117A GLY* 3.2 19.8 + - - -
138A TYR* 3.5 53.5 - - + -
142A GLU* 4.5 7.6 - - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL* 3.1 32.4 + - + +
111A ARG* 3.7 15.7 - - - +
112A GLU 3.2 0.2 - - - -
113A ARG* 1.3 77.0 - - + +
115A ALA* 1.3 60.8 + - - +
117A GLY* 3.6 0.8 + - - -
118A GLN* 2.9 32.8 + - - +
94B ARG* 3.8 10.2 + - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 3.6 21.3 - - + -
103A ALA* 3.8 24.7 - - + -
105A THR* 5.2 0.7 - - + -
111A ARG 2.9 17.1 + - - +
112A GLU 3.6 4.7 - - - +
114A GLU* 1.3 75.0 - - - +
116A VAL* 1.3 55.6 + - - +
118A GLN* 3.1 10.6 + - - +
119A PHE* 2.7 39.8 + - + +
94B ARG* 3.6 9.6 - - - +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 3.7 19.1 - - + -
112A GLU* 2.9 25.2 + - + +
113A ARG 3.8 4.5 - - - +
114A GLU 3.3 0.2 - - - -
115A ALA* 1.3 76.1 - - - +
117A GLY* 1.3 54.3 + - - +
119A PHE* 3.2 2.1 + - - +
120A PHE* 2.8 33.7 + - + +
127A LEU* 3.9 18.8 - - + +
129A LEU* 5.1 4.7 - - + -
138A TYR* 3.6 24.2 - - + +
139A LEU* 4.0 10.8 - - + -
143A LEU* 3.7 35.7 - - + -
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG 3.2 11.3 + - - -
114A GLU* 4.0 2.0 - - - -
116A VAL* 1.3 78.6 - - - +
118A GLN* 1.3 60.5 + - - +
120A PHE* 3.8 6.4 - - - +
121A GLU* 2.8 31.7 + - - +
143A LEU* 6.1 0.4 - - - -
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 2.9 21.3 + - - +
115A ALA* 3.4 8.6 - - - +
117A GLY* 1.3 74.5 - - - +
119A PHE* 1.3 85.3 + - + +
121A GLU* 2.8 38.4 - - - +
122A ARG* 3.2 13.4 + - + +
94B ARG* 4.8 20.7 + - - +
98B TYR 4.7 7.8 + - - -
99B SER* 3.6 19.8 + - - +
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY* 3.7 14.8 - - - -
72A LEU 3.7 5.2 - - - -
73A ILE* 3.6 35.7 - - + -
101A LEU* 3.7 45.1 - - + -
102A LEU 3.7 15.0 - - - -
103A ALA* 3.6 19.5 - - + -
115A ALA* 2.7 17.9 + - + +
116A VAL 3.8 3.1 - - - +
118A GLN* 1.3 96.5 - - + +
120A PHE* 1.3 66.9 + - - +
122A ARG* 3.3 4.5 + - - +
123A ARG 3.2 4.5 + - - -
124A VAL* 3.2 33.9 + - + +
127A LEU* 3.8 14.8 - - + -
99B SER* 4.7 4.5 - - - -
100B VAL 5.8 0.4 - - - -
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A VAL 2.8 22.2 + - - +
117A GLY* 3.8 6.5 - - - +
119A PHE* 1.3 74.0 - - - +
121A GLU* 1.3 59.5 + - - +
123A ARG* 2.7 68.8 + - - -
124A VAL* 4.5 4.0 - - - +
127A LEU* 5.4 0.2 - - - +
142A GLU 5.0 4.5 - - - -
143A LEU* 3.6 24.2 - - + -
144A PRO* 3.4 40.4 - - + -
147A PHE* 3.9 32.5 - + + -
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLY 2.8 28.3 + - - +
118A GLN* 2.8 27.9 - - - +
120A PHE* 1.3 76.9 - - + +
122A ARG* 1.3 71.7 + - - +
123A ARG* 3.1 24.0 + - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 5.7 0.5 - - - -
101A LEU* 3.9 23.6 - - + -
118A GLN* 3.2 21.5 + - - +
119A PHE* 3.7 7.6 - - - +
120A PHE 3.2 1.0 - - - -
121A GLU* 1.3 85.1 + - - +
123A ARG* 1.3 68.7 + - - +
124A VAL* 3.4 1.9 + - + +
67B SER 3.2 22.8 + - - -
68B ASN* 3.3 24.5 + - - +
69B VAL* 3.7 17.8 - - - +
97B GLY 5.0 2.2 + - - -
99B SER* 2.9 25.6 + - - +
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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