Contacts of the helix formed by residues 111 - 127 (chain A) in PDB entry 2G33
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 GLY 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ALA* 2.9 14.3 + - - +
110A PHE* 1.3 82.0 - - - +
112A ARG* 1.3 57.0 + - - -
113A GLU 3.3 1.6 - - - -
114A THR* 3.0 5.1 + - - -
115A VAL* 2.6 40.5 + - - +
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Residues in contact with ARG 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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8A GLU 4.0 7.5 + - - -
9A PHE* 4.3 30.5 - - + +
10A GLY* 5.1 1.1 - - - +
49A SER* 6.2 0.2 - - - -
50A PRO* 5.0 7.1 - - - +
51A HIS* 3.6 33.7 + - + +
103A PHE* 6.4 0.2 - - + -
107A ALA* 4.0 13.9 - - - +
111A GLY* 1.3 67.3 - - - -
113A GLU* 1.3 62.2 + - + +
115A VAL* 2.7 26.2 + - - +
116A LEU* 3.0 25.5 + - + +
47B HIS* 3.2 42.8 + - - -
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Residues in contact with GLU 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 GLY 3.3 0.4 - - - -
112A ARG* 1.3 84.7 - - + +
114A THR* 1.3 62.5 + - - +
116A LEU* 3.6 26.0 + - - +
117A GLU* 3.1 47.0 + - - +
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Residues in contact with THR 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 PHE* 3.2 48.9 + - + +
111A GLY* 3.0 6.3 + - - -
113A GLU* 1.3 77.1 - - - +
115A VAL* 1.3 58.7 + - - +
117A GLU* 3.8 18.1 + - - +
118A TYR* 3.8 6.9 + - - +
140A LEU* 5.3 6.1 - - + +
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Residues in contact with VAL 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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102A TRP* 5.3 9.0 - - + -
103A PHE* 4.9 21.5 - - + +
106A SER* 4.3 12.3 - - - -
107A ALA* 3.6 32.8 - - + +
110A PHE* 4.8 4.9 - - + -
111A GLY 2.6 28.9 + - - +
112A ARG* 2.7 10.6 + - - +
114A THR* 1.3 69.4 - - - +
116A LEU* 1.3 60.5 + - + +
117A GLU 2.9 1.1 - - - -
118A TYR* 2.3 35.7 + - + +
119A LEU* 2.6 25.0 - - + +
140A LEU* 5.7 5.8 - - + -
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Residues in contact with LEU 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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9A PHE 3.9 12.8 - - - +
10A GLY* 3.6 29.4 - - - +
11A ALA* 4.2 10.1 - - + -
15A LEU* 6.1 1.1 - - + -
103A PHE* 5.4 7.4 - - + -
112A ARG* 3.0 24.8 + - + +
113A GLU* 3.6 32.1 - - - +
115A VAL* 1.3 82.3 - - + +
117A GLU* 1.3 51.8 + - + +
118A TYR 2.7 4.7 + - - -
119A LEU* 3.3 17.7 - - + +
120A VAL* 2.5 33.4 - - - +
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Residues in contact with GLU 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 GLU* 3.1 34.4 + - - +
114A THR* 3.8 13.5 - - - +
115A VAL 2.9 0.2 - - - -
116A LEU* 1.3 77.0 - - + +
118A TYR* 1.3 56.1 + - - +
120A VAL* 3.9 7.0 - - - +
121A SER* 3.3 15.9 + - - -
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Residues in contact with TYR 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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19A LEU* 5.4 2.5 - - + -
23A PHE* 4.4 20.6 - + - -
102A TRP* 5.1 11.7 - + - -
114A THR 3.8 3.1 + - - +
115A VAL* 2.3 41.6 + - + +
117A GLU* 1.3 65.6 - - - +
119A LEU* 1.3 93.1 + - + +
120A VAL* 2.8 2.8 + - - +
121A SER* 2.8 24.8 + - - -
122A PHE* 3.8 28.4 - + + -
138A PRO* 2.6 27.7 + - + -
139A ILE* 3.6 22.7 - - - +
140A LEU* 3.0 45.4 - - + +
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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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11A ALA* 6.0 1.3 - - + -
15A LEU* 3.4 44.0 - - + -
16A LEU* 3.7 15.5 - - + -
18A PHE* 4.8 5.4 - - + -
19A LEU* 5.4 9.9 - - + -
102A TRP* 5.4 9.2 - - + -
103A PHE* 5.9 5.8 - - + -
115A VAL* 2.6 49.8 - - + +
116A LEU* 3.3 17.0 - - + +
118A TYR* 1.3 89.5 - - + +
120A VAL* 1.3 71.7 + - + +
122A PHE* 2.6 19.4 + - - +
123A GLY* 2.8 8.6 + - - -
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Residues in contact with VAL 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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18A PHE* 4.5 10.5 - - - -
116A LEU* 2.5 30.5 - - + +
117A GLU* 3.9 7.0 - - - +
118A TYR 3.4 3.6 - - - +
119A LEU* 1.3 78.0 - - + +
121A SER* 1.3 60.9 + - - +
123A GLY* 2.6 30.5 + - - -
124A VAL* 3.2 8.5 + - + +
127A ARG* 4.3 4.8 + - - +
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Residues in contact with SER 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 GLU 3.3 14.4 + - - -
118A TYR* 2.8 14.1 + - - -
120A VAL* 1.3 79.3 - - - +
122A PHE* 1.3 55.2 + - - -
124A VAL* 2.6 41.1 + - - +
125A TRP* 3.2 4.4 + - - +
138A PRO* 5.2 8.1 - - - -
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Residues in contact with PHE 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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18A PHE* 5.3 1.3 - + + -
19A LEU* 3.7 30.3 - - + -
20A PRO* 4.0 26.2 - - + -
23A PHE* 4.1 16.4 - + - -
118A TYR* 3.6 30.9 + + + -
119A LEU 2.6 15.3 + - - +
121A SER* 1.3 76.2 - - - +
123A GLY* 1.3 66.2 + - - -
125A TRP* 2.9 29.4 + + - +
126A ILE* 3.0 24.7 + - + -
137A ALA* 5.3 3.1 - - + -
138A PRO* 3.6 38.0 - - + +
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Residues in contact with GLY 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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18A PHE* 3.7 25.4 - - - -
119A LEU 2.8 6.1 + - - -
120A VAL 2.6 19.4 + - - -
122A PHE* 1.3 73.0 - - - +
124A VAL* 1.3 52.4 + - - -
126A ILE* 2.8 17.1 - - - +
127A ARG* 2.6 37.2 + - - +
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Residues in contact with VAL 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 VAL* 4.0 6.1 - - + +
121A SER* 2.6 22.3 + - - +
123A GLY* 1.3 69.0 - - - -
125A TRP* 1.3 68.7 + - - +
126A ILE 3.0 1.4 + - - -
127A ARG* 3.0 35.3 + - - +
128A THR* 2.7 28.0 + - - +
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Residues in contact with TRP 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 SER 3.2 2.9 + - - +
122A PHE* 2.9 31.8 + + - +
124A VAL* 1.3 80.9 - - - +
126A ILE* 1.3 87.4 + - + +
128A THR* 3.4 9.1 - - - -
133A ARG* 3.4 47.2 - - + +
134A PRO* 3.0 46.5 + - + +
135A PRO* 4.4 6.5 - - + -
136A ASN 3.6 4.1 + - - -
137A ALA* 3.4 29.2 - - + +
138A PRO* 3.7 22.4 - - + -
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Residues in contact with ILE 126 (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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18A PHE* 4.0 25.4 - - + +
20A PRO* 4.0 26.0 - - + -
122A PHE* 3.0 22.1 + - + +
123A GLY* 2.8 33.0 - - - +
125A TRP* 1.3 89.4 - - + +
127A ARG* 1.3 58.6 + - + +
128A THR 2.7 13.0 + - - -
133A ARG* 3.1 31.9 + - - +
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Residues in contact with ARG 127 (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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18A PHE* 4.8 20.0 - - - -
120A VAL* 4.3 5.7 + - - +
123A GLY* 2.6 30.8 + - - +
124A VAL* 3.2 34.0 - - - +
126A ILE* 1.3 76.4 - - + +
128A THR* 1.3 59.8 + - - +
129A PRO* 4.3 4.3 - - - +
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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