Contacts of the helix formed by residues 111 - 125 (chain A) in PDB entry 3DFG
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.4 4.4 - - - -
110A GLY* 1.3 73.0 - - - +
112A TRP* 1.3 63.6 + - - +
113A THR* 2.8 25.3 + - - -
114A GLU* 3.1 31.7 + - + +
115A ASN* 3.1 25.4 + - - +
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Residues in contact with TRP 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A VAL* 4.5 3.8 - - + -
78A ALA* 3.8 25.6 - - + -
82A TYR 3.5 22.7 - - - -
83A GLY* 4.3 0.7 - - - -
84A PRO* 3.7 41.1 - - + -
87A ILE* 3.3 25.6 - - + -
105A MET* 3.7 28.7 + - + +
108A PHE* 3.3 42.9 - + + +
111A ASP* 1.3 73.2 + - - +
113A THR* 1.3 63.1 + - - +
115A ASN* 3.2 7.8 + - - +
116A ALA 3.1 17.0 + - - -
147A PHE* 3.3 15.9 - + + -
148A ASP* 5.1 4.7 - - - +
151A SER* 4.4 1.6 - - - -
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Residues in contact with THR 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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111A ASP* 2.8 11.2 + - - -
112A TRP* 1.3 77.8 - - - +
114A GLU* 1.3 64.7 + - + +
116A ALA* 3.1 4.0 + - - +
117A LEU* 3.0 26.8 + - + +
148A ASP* 4.9 0.3 + - - -
150A ASN* 4.4 12.2 + - - +
151A SER* 3.1 31.5 + - - +
154A LEU* 3.5 32.3 - - + -
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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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111A ASP* 3.1 35.9 + - + +
113A THR* 1.3 77.0 - - - +
115A ASN* 1.3 60.8 + - - +
117A LEU* 3.3 23.8 + - - +
118A ASP* 2.9 30.0 + - - +
121A ARG* 3.7 22.4 + - - -
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Residues in contact with ASN 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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78A ALA 3.5 22.9 - - - +
81A GLY* 5.6 4.1 - - - -
82A TYR 5.6 0.4 - - - +
108A PHE* 3.8 22.6 - - - -
110A GLY* 5.9 0.4 - - - -
111A ASP 3.1 16.5 + - - +
112A TRP* 3.5 15.4 - - + +
113A THR 3.2 0.2 - - - -
114A GLU* 1.3 82.3 - - - +
116A ALA* 1.3 60.3 + - - +
118A ASP* 3.4 8.1 + - - +
119A LEU* 3.0 22.9 + - - +
122A ARG* 5.2 0.7 + - - -
147A PHE* 4.2 13.6 - - + -
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Residues in contact with ALA 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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112A TRP 3.1 7.3 + - - +
113A THR 3.1 8.7 + - - +
115A ASN* 1.3 78.5 - - - +
117A LEU* 1.3 62.2 + - + +
119A LEU* 3.3 4.1 + - - +
120A ILE* 3.1 28.2 + - - +
142A LEU* 4.1 16.9 - - + +
147A PHE* 3.6 33.8 - - + -
151A SER* 4.2 18.4 - - - +
155A ALA* 4.7 1.6 - - + -
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Residues in contact with LEU 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 THR* 3.0 20.8 + - + +
114A GLU* 3.3 26.9 + - - +
116A ALA* 1.3 78.3 - - + +
118A ASP* 1.3 56.6 + - - +
120A ILE* 3.3 6.4 + - - +
121A ARG* 2.9 50.7 + - + +
151A SER 5.8 0.2 - - - +
154A LEU* 4.0 28.7 - - + +
155A ALA* 3.7 32.3 - - + +
157A ARG* 4.9 9.0 - - - +
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Residues in contact with ASP 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 18.2 + - - +
115A ASN* 3.6 9.8 - - - +
117A LEU* 1.3 74.1 - - - +
119A LEU* 1.3 59.7 + - - +
121A ARG* 3.2 24.3 + - - +
122A ARG* 2.8 66.0 + - - +
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Residues in contact with LEU 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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81A GLY* 4.0 10.8 - - - +
115A ASN 3.0 13.9 + - - +
116A ALA* 3.3 8.7 + - - +
118A ASP* 1.3 76.7 - - - +
120A ILE* 1.3 63.8 + - - +
122A ARG* 3.3 35.2 + - + +
123A ARG* 3.2 22.3 + - + +
141A LEU* 4.0 28.5 - - + -
142A LEU* 3.8 22.2 - - + -
145A ARG* 3.9 33.0 - - + +
147A PHE* 4.6 2.2 - - + -
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Residues in contact with ILE 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 ALA 3.1 14.3 + - - +
117A LEU* 3.7 8.5 - - - +
118A ASP 3.2 0.2 - - - -
119A LEU* 1.3 77.2 - - - +
121A ARG* 1.3 60.0 + - + +
123A ARG* 3.3 0.6 + - - -
124A PHE* 2.8 42.1 + - + +
128A GLY* 4.2 4.0 - - - -
129A PRO* 3.6 31.0 - - + -
138A ALA* 3.8 26.9 - - + +
141A LEU* 4.5 9.9 - - + -
142A LEU* 3.8 31.2 - - + -
155A ALA* 3.9 15.9 - - + +
157A ARG* 4.2 6.5 - - - +
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Residues in contact with ARG 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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114A GLU* 3.7 22.4 + - - -
117A LEU* 2.9 38.1 + - - +
118A ASP* 3.6 35.5 + - - +
120A ILE* 1.3 77.3 - - + +
122A ARG* 1.3 59.4 + - + +
125A GLY* 2.8 44.2 + - - +
126A GLU* 3.3 37.4 + - - +
157A ARG* 5.8 4.3 - - - +
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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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79A SER 5.8 0.6 + - - -
80A SER 5.1 2.0 + - - -
81A GLY* 4.3 17.6 - - - +
115A ASN 5.2 0.8 + - - -
118A ASP* 2.8 46.0 + - - +
119A LEU* 3.5 40.1 - - + +
121A ARG* 1.3 77.0 - - + +
123A ARG* 1.3 60.4 + - - +
145A ARG* 5.5 0.4 - - - +
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Residues in contact with ARG 123 (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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119A LEU* 3.2 17.2 + - + +
120A ILE* 3.9 2.2 - - - +
121A ARG 3.2 0.4 - - - -
122A ARG* 1.3 80.4 - - - +
124A PHE* 1.3 95.4 + - + +
137A LYS* 3.5 36.6 - - - +
141A LEU* 3.8 33.3 - - + +
144A ARG* 5.3 2.8 - - - +
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Residues in contact with PHE 124 (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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120A ILE* 2.8 37.1 + - + +
123A ARG* 1.3 109.6 - - + +
125A GLY* 1.3 57.7 + - - +
127A ASP* 5.0 1.7 + - - +
128A GLY 3.6 25.5 + - - +
129A PRO* 4.1 5.8 - - + -
134A GLN* 3.6 58.9 + - + +
137A LYS* 4.2 12.3 - - + -
138A ALA* 3.7 22.4 - - + -
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Residues in contact with GLY 125 (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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121A ARG* 2.8 39.1 + - - +
123A ARG 3.6 0.8 - - - -
124A PHE* 1.3 73.9 - - - +
126A GLU* 1.3 60.1 + - - -
127A ASP 3.2 3.4 - - - -
128A GLY* 2.9 19.1 + - - -
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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