Contacts of the helix formed by residues 112 - 127 (chain B) 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 ARG 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A HIS* 3.5 31.5 + - - -
9B PHE* 3.6 46.9 - - + +
50B PRO* 5.1 7.9 - - - +
51B HIS* 3.5 32.6 + - + +
103B PHE* 6.3 0.4 - - + -
107B ALA* 5.2 2.0 - - - -
111B GLY* 1.3 72.5 - - - -
113B GLU* 1.3 72.5 + - + +
114B THR 3.1 1.1 - - - -
115B VAL* 2.4 40.2 + - - +
116B LEU* 2.9 19.1 + - + -
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLY* 6.0 0.4 - - - -
112B ARG* 1.3 89.6 - - + +
114B THR* 1.3 58.6 + - - +
115B VAL 3.0 5.9 + - - -
116B LEU* 4.1 20.1 - - - +
117B GLU* 3.1 28.9 + - - +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PHE* 2.6 39.9 + - + +
111B GLY* 4.9 1.6 - - - -
112B ARG 3.1 1.2 - - - +
113B GLU* 1.3 78.6 - - - +
115B VAL* 1.3 58.1 + - - +
117B GLU* 4.3 9.2 - - - +
118B TYR* 4.1 9.5 + - - +
140B LEU* 5.2 4.6 - - + +
141B SER 4.7 8.5 - - - +
142B THR* 5.5 0.4 - - - -
143B LEU* 3.7 45.8 - - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TRP* 5.3 8.3 - - + -
103B PHE* 5.4 9.0 - - + +
107B ALA* 3.6 29.6 - - + +
110B PHE* 3.5 11.7 - - + +
111B GLY 2.8 30.1 - - - +
112B ARG* 2.4 24.3 + - - +
114B THR* 1.3 65.0 - - - +
116B LEU* 1.3 65.3 + - + +
117B GLU 2.9 1.1 - - - -
118B TYR* 2.3 41.6 + - + +
119B LEU* 3.0 21.2 - - + +
140B LEU* 5.5 6.3 - - + -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE* 4.0 22.0 - - + +
10B GLY* 4.1 13.9 - - - +
11B ALA* 4.9 9.6 - - + -
103B PHE* 5.1 9.9 - - + -
112B ARG* 2.9 30.4 + - + +
113B GLU* 4.1 23.8 - - - +
115B VAL* 1.3 86.5 - - + +
117B GLU* 1.3 50.7 + - - +
118B TYR 2.7 6.9 + - - -
119B LEU* 3.2 13.9 + - + +
120B VAL* 2.7 38.4 + - + +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLU 3.1 17.8 + - - +
114B THR* 4.3 10.1 - - - +
115B VAL 2.9 0.6 - - - -
116B LEU* 1.3 77.6 - - - +
118B TYR* 1.3 60.1 + - - +
120B VAL* 3.8 17.2 - - + +
121B SER* 4.2 9.7 + - - -
143B LEU* 5.2 13.3 - - - +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 4.9 13.3 - + - -
102B TRP* 5.3 11.4 - + - -
114B THR 4.1 5.5 + - - +
115B VAL* 2.3 40.4 + - + +
117B GLU* 1.3 64.9 - - - +
119B LEU* 1.3 80.2 + - + +
120B VAL 2.8 2.5 + - - -
121B SER* 2.8 17.3 + - - -
122B PHE* 3.1 37.4 + + + -
138B PRO* 2.5 25.5 + - + -
139B ILE* 3.2 14.9 - - - +
140B LEU* 3.0 54.5 + - + +
132C TYR* 5.5 3.3 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 3.5 39.9 - - + -
16B LEU* 3.6 17.0 - - + -
19B LEU* 6.5 2.0 - - + -
102B TRP* 4.7 17.7 - - + -
103B PHE* 5.6 7.9 - - + -
115B VAL* 3.0 41.7 - - + +
116B LEU* 3.6 13.5 - - + +
118B TYR* 1.3 87.7 - - + +
120B VAL* 1.3 56.1 - - + +
122B PHE* 3.0 6.2 + - - -
123B GLY* 2.5 36.1 + - - -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 2.7 31.9 - - + +
117B GLU* 3.8 13.7 - - + +
118B TYR 2.8 1.4 + - - -
119B LEU* 1.3 81.3 - - + +
121B SER* 1.3 69.6 + - - +
123B GLY* 2.9 12.0 + - - -
124B VAL* 3.7 3.8 + - - +
127B ARG* 4.3 5.9 + - - -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU 4.2 8.1 + - - -
118B TYR* 2.8 10.9 + - - -
120B VAL* 1.3 80.5 - - - +
122B PHE* 1.3 65.2 + - - +
124B VAL* 2.8 25.6 + - - +
125B TRP* 3.4 3.4 + - - +
138B PRO* 5.3 8.3 - - - -
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 5.4 0.2 - - + -
19B LEU* 3.8 23.1 - - + -
20B PRO* 4.1 19.3 - - + -
23B PHE* 4.2 22.9 - + - -
118B TYR* 3.1 39.6 + + + +
119B LEU* 3.0 9.3 + - - +
121B SER* 1.3 77.4 - - - +
123B GLY* 1.3 71.8 + - - +
125B TRP* 2.7 26.3 + + + +
126B ILE* 3.4 27.3 + - + -
137B ALA* 5.1 4.5 - - + -
138B PRO* 4.0 31.8 - - + +
132C TYR* 4.4 17.0 - + - -
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 4.8 9.8 - - - -
119B LEU 2.5 18.4 + - - -
120B VAL 2.9 7.7 + - - -
122B PHE* 1.3 78.7 - - - +
124B VAL* 1.3 60.8 + - - +
126B ILE* 3.0 18.5 - - - +
127B ARG* 3.2 32.9 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B VAL 4.6 2.9 - - - +
121B SER* 2.8 13.3 + - - +
123B GLY* 1.3 73.9 - - - +
125B TRP* 1.3 70.8 + - - +
127B ARG* 2.9 39.9 + - + +
128B THR* 3.1 18.2 + - - +
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Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PRO* 6.5 0.7 - - + -
121B SER 3.4 3.4 + - - +
122B PHE* 2.7 34.9 + + + +
124B VAL* 1.3 77.4 - - - +
126B ILE* 1.3 81.3 + - + +
128B THR* 3.0 16.5 + - - -
133B ARG* 3.3 48.0 - - + +
134B PRO* 3.0 42.8 + - + +
135B PRO* 4.4 7.9 - - + -
136B ASN 3.8 3.2 + - - -
137B ALA* 3.5 33.5 - - + +
138B PRO* 3.6 18.6 - - + -
132C TYR* 5.6 8.3 - + - -
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 2.9 44.4 - - + +
20B PRO* 3.6 19.1 - - + -
122B PHE* 3.7 24.9 - - + +
123B GLY 3.0 16.2 - - - +
125B TRP* 1.3 85.2 - - + +
127B ARG* 1.3 62.6 + - - +
128B THR 2.6 16.5 + - - -
133B ARG* 3.2 20.1 + - - +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 3.4 48.4 - - + -
120B VAL 4.3 4.2 + - - -
123B GLY* 3.2 22.1 + - - +
124B VAL* 2.9 45.0 + - + +
126B ILE* 1.3 80.8 - - - +
128B THR* 1.3 57.3 + - - +
129B PRO* 3.5 9.1 - - - +
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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