Contacts of the helix formed by residues 108 - 124 (chain A) in PDB entry 1CG4
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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107A LEU* 1.3 74.8 - - - +
109A TYR* 1.3 65.2 + - - +
111A VAL* 2.8 23.8 + - - +
112A ALA* 3.0 10.2 + - - +
181A VAL* 3.8 20.2 - - + +
185A LYS* 3.9 22.5 + - - +
186A VAL* 4.1 14.1 - - + +
189A ASP* 4.4 4.9 - - - +
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Residues in contact with TYR 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 LEU* 3.5 41.6 - - + +
108A ASP* 1.3 74.7 - - - +
110A HIS* 1.3 90.1 + + - +
112A ALA* 2.8 13.8 + - + +
113A LEU* 2.5 40.1 + - + +
139A ASP* 4.0 1.1 + - - -
146A LEU* 3.6 9.0 - - - +
164A VAL* 3.5 21.8 - - + +
165A MET* 3.7 35.2 - - + -
168A HIS* 3.4 45.5 - + + -
169A ASN* 5.9 1.1 - - - +
172A LEU* 4.8 3.6 - - + -
181A VAL* 3.8 15.7 - - + +
186A VAL* 4.5 1.6 - - + -
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Residues in contact with HIS 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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105A LEU 2.9 25.1 - - - -
106A ILE* 3.2 7.5 - - + -
107A LEU* 2.8 29.9 + - + +
108A ASP 3.0 0.8 + - - -
109A TYR* 1.3 110.4 - + - +
111A VAL* 1.3 57.4 + - - +
113A LEU* 3.3 5.5 + - + +
114A ASP* 2.7 29.1 + - - +
132A GLY* 3.8 21.1 - - - +
135A PRO* 3.5 26.3 - - + +
136A ALA* 3.8 15.4 - - - +
139A ASP* 3.4 19.4 + - + -
145A GLY* 6.2 0.4 - - - -
146A LEU 6.1 2.2 - - - -
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Residues in contact with VAL 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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37A HIS* 6.1 1.6 - - + +
106A ILE* 5.1 3.6 - - + -
107A LEU 4.5 6.7 - - - +
108A ASP* 2.8 19.2 + - - +
110A HIS* 1.3 69.8 - - - +
112A ALA* 1.3 67.5 + - - +
114A ASP* 3.6 5.3 - - - +
115A ASN* 2.8 44.5 + - - +
130A GLY 3.2 23.1 - - - +
131A ARG* 4.1 2.7 - - - -
132A GLY* 3.7 18.8 - - - +
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Residues in contact with ALA 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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108A ASP 3.0 5.0 + - - +
109A TYR* 2.8 13.7 + - - +
111A VAL* 1.3 78.0 - - - +
113A LEU* 1.3 55.0 + - - +
115A ASN* 3.2 7.3 + - - +
116A ALA* 2.9 27.2 + - - +
172A LEU* 3.7 17.2 - - + +
179A GLU 5.4 1.8 - - - +
181A VAL* 3.6 30.7 - - + -
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Residues in contact with LEU 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 TYR* 2.5 25.8 + - + +
110A HIS* 3.4 10.1 - - + +
112A ALA* 1.3 70.4 - - - +
114A ASP* 1.3 67.0 + - - +
116A ALA* 3.0 5.1 + - - -
117A ARG* 2.8 42.8 + - - +
135A PRO* 3.6 26.9 - - + -
139A ASP* 5.3 0.4 - - - +
168A HIS* 3.5 32.8 - - + +
171A GLN* 3.8 33.0 - - - +
172A LEU* 3.9 22.7 - - + -
176A TYR* 4.6 2.0 - - + -
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Residues in contact with ASP 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 HIS 2.7 20.4 + - - +
111A VAL* 3.2 6.5 + - - +
113A LEU* 1.3 71.9 - - - +
115A ASN* 1.3 64.5 + - - +
117A ARG* 4.1 5.0 - - - +
118A GLU* 3.1 23.6 + - - +
128A THR* 2.9 35.2 + - - +
130A GLY* 3.7 11.8 - - - -
131A ARG 2.8 27.9 - - - +
132A GLY* 4.1 2.5 - - - -
133A ILE 4.2 6.2 + - - -
134A GLY* 4.4 3.1 + - - -
135A PRO* 3.8 13.4 - - + +
440A IMO 4.7 1.9 + - - -
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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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111A VAL* 2.8 39.6 + - - +
112A ALA* 3.5 6.6 + - - +
114A ASP* 1.3 83.1 + - - +
116A ALA* 1.3 65.0 + - - +
118A GLU* 3.3 7.4 + - - +
119A LYS* 2.9 24.1 + - - +
130A GLY* 4.3 10.3 + - - -
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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 ALA 2.9 13.3 + - - +
113A LEU 3.0 6.5 + - - +
115A ASN* 1.3 74.7 - - - +
117A ARG* 1.3 65.2 + - - +
119A LYS* 2.9 10.9 + - - +
120A ALA* 2.8 20.6 + - - +
172A LEU* 4.2 9.2 - - + -
176A TYR* 3.5 41.4 - - + -
178A ALA* 5.1 4.9 - - + -
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Residues in contact with ARG 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 LEU* 2.8 44.0 + - - +
114A ASP* 4.1 5.4 - - - +
116A ALA* 1.3 70.2 - - - +
118A GLU* 1.3 68.2 + - - +
120A ALA* 2.8 17.6 + - - +
121A ARG* 3.0 20.1 + - + +
135A PRO* 4.4 9.7 - - + +
138A GLU* 2.5 47.3 + - - -
168A HIS* 5.8 1.6 + - - -
171A GLN* 2.8 33.0 + - - +
176A TYR* 2.9 26.0 + - - -
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Residues in contact with GLU 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 ASP* 3.1 19.2 + - - +
115A ASN* 3.5 7.2 - - - +
117A ARG* 1.3 80.4 - - - +
119A LYS* 1.3 64.5 + - - +
121A ARG* 3.4 17.9 + - - +
122A GLY* 3.6 6.2 + - - -
125A ALA* 4.0 13.5 - - + +
126A ILE* 3.6 19.6 + - - +
127A GLY* 2.5 34.5 + - - -
128A THR* 3.0 26.1 + - - +
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Residues in contact with LYS 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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115A ASN 2.9 14.4 + - - +
116A ALA* 2.9 13.2 + - - +
118A GLU* 1.3 75.9 - - - +
120A ALA* 1.3 55.0 + - - +
122A GLY* 2.7 30.2 + - - -
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Residues in contact with ALA 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 2.8 10.5 + - - +
117A ARG* 2.8 17.2 + - - +
119A LYS* 1.3 74.1 - - - +
121A ARG* 1.3 60.3 + - + +
122A GLY* 3.1 1.4 + - - -
175A TYR* 5.7 4.7 - - + -
176A TYR* 4.4 15.7 - - + -
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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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117A ARG* 3.0 19.2 + - + +
118A GLU* 3.7 13.7 - - - +
119A LYS 3.0 0.4 + - - -
120A ALA* 1.3 76.3 - - + +
122A GLY* 1.3 65.4 + - - +
123A ALA 3.0 3.3 + - - -
124A LYS* 2.7 74.9 + - + +
125A ALA* 4.0 4.7 - - - -
126A ILE* 3.6 39.4 - - - +
236A PRO* 3.9 25.7 - - - +
237A TYR* 3.7 12.7 + - - -
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Residues in contact with GLY 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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118A GLU 3.6 3.0 + - - +
119A LYS 2.7 23.4 + - - -
120A ALA 3.1 1.7 - - - -
121A ARG* 1.3 68.7 - - - +
123A ALA* 1.3 62.3 + - - +
125A ALA* 3.1 19.8 - - - +
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Residues in contact with ALA 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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121A ARG 3.0 1.8 + - - -
122A GLY* 1.3 67.7 - - - +
124A LYS* 1.3 54.4 + - - +
125A ALA* 2.7 20.1 + - - +
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Residues in contact with LYS 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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121A ARG* 2.7 73.2 + - - +
123A ALA* 1.3 76.3 - - - +
125A ALA* 1.3 51.5 + - - +
237A TYR* 3.0 18.6 + - - +
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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