Contacts of the helix formed by residues 133 - 148 (chain B) in PDB entry 3G33
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 SER 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B CYS* 4.2 0.7 - - - -
130B HIS 4.9 2.6 + - - -
131B ALA 4.0 2.2 + - - -
132B VAL* 1.3 77.8 - - - +
134B PRO* 1.3 76.7 - - - +
135B ARG* 3.9 11.9 + - - +
136B GLN* 3.0 43.3 + - - +
137B LEU* 3.3 8.5 + - - +
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Residues in contact with PRO 134 (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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121B ILE* 3.4 26.4 - - + +
122B GLU* 5.6 6.3 - - + -
125B CYS* 3.5 22.6 - - + -
133B SER* 1.3 87.8 - - - +
135B ARG* 1.3 66.0 + - + +
137B LEU* 3.3 5.3 + - + -
138B ARG* 3.2 44.8 + - - +
51C GLY* 5.5 1.6 - - - -
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Residues in contact with ARG 135 (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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133B SER* 4.1 10.8 - - - +
134B PRO* 1.3 83.5 - - + +
136B GLN* 1.3 64.6 + - + +
137B LEU 3.2 0.5 + - - -
138B ARG* 3.3 33.1 + - - +
139B ASP* 3.1 23.9 + - - +
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Residues in contact with GLN 136 (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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101B LEU* 4.0 28.0 - - + +
131B ALA 3.8 5.4 + - - +
132B VAL* 3.5 12.3 - - - +
133B SER* 3.0 36.8 + - - +
135B ARG* 1.3 80.3 - - + +
137B LEU* 1.3 58.0 + - - +
139B ASP* 3.5 5.1 + - - +
140B TRP* 3.0 40.4 + - + +
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Residues in contact with LEU 137 (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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101B LEU* 3.8 21.5 - - + -
104B ALA* 3.9 18.2 - - + -
105B VAL* 3.8 18.3 - - + +
108B LEU* 4.7 10.7 - - + +
121B ILE* 3.4 46.2 - - + +
124B LEU* 4.2 20.2 - - + -
125B CYS* 4.9 2.9 - - + +
132B VAL* 4.0 9.2 - - + -
133B SER 3.3 6.7 + - - +
134B PRO* 3.3 12.1 + - + +
135B ARG 3.2 0.6 - - - -
136B GLN* 1.3 78.2 - - - +
138B ARG* 1.3 65.1 + - - +
140B TRP 4.7 0.2 - - - +
141B GLU* 3.1 24.9 + - - +
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Residues in contact with ARG 138 (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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121B ILE* 3.8 2.0 - - + -
134B PRO* 3.2 37.4 + - - +
135B ARG* 3.7 23.7 - - - +
137B LEU* 1.3 78.9 - - - +
139B ASP* 1.3 65.7 + - - +
141B GLU* 3.4 20.4 + - - +
142B VAL* 3.5 13.3 + - - +
46C ASN* 4.0 25.7 - - - +
47C GLY* 4.9 4.8 - - - -
48C GLY 5.7 1.0 + - - -
51C GLY* 4.1 6.3 - - - -
52C GLY* 2.7 49.8 - - - +
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Residues in contact with ASP 139 (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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135B ARG* 3.1 22.7 + - - +
136B GLN* 3.9 5.8 - - - +
138B ARG* 1.3 78.8 - - - +
140B TRP* 1.3 63.2 + - + +
142B VAL* 3.1 12.8 + - - +
143B LEU* 3.0 23.8 + - - +
46C ASN* 5.0 9.2 + - - -
86C SER* 5.0 8.1 + - - -
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Residues in contact with TRP 140 (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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88B TYR* 3.7 23.3 - + - -
94B THR* 5.1 5.6 - - - -
98B GLN* 3.6 44.0 - - + -
101B LEU* 3.2 31.0 - - + +
102B LEU* 4.3 32.5 - - + -
105B VAL* 3.6 17.5 - - + -
136B GLN* 3.0 32.1 + - + +
139B ASP* 1.3 80.8 - - + +
141B GLU* 1.3 60.1 + - - +
142B VAL 3.2 0.2 - - - -
143B LEU* 3.5 27.4 - - + +
144B VAL* 2.9 40.7 + - + +
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Residues in contact with GLU 141 (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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105B VAL* 3.6 12.5 - - + +
108B LEU* 3.7 16.3 - - + +
109B LEU* 3.7 20.8 - - + +
112B LYS* 2.6 36.6 + - - +
137B LEU 3.1 19.2 + - - +
138B ARG* 3.5 10.6 - - - +
139B ASP 3.2 0.2 - - - -
140B TRP* 1.3 75.7 - - - +
142B VAL* 1.3 61.8 + - - +
144B VAL* 4.1 1.7 - - - +
145B LEU* 3.2 29.4 + - - +
53C GLY* 4.3 2.6 - - - -
54C LEU* 2.2 50.7 + - + +
59C VAL* 4.9 0.2 - - - +
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Residues in contact with VAL 142 (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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138B ARG 3.5 15.5 - - - +
139B ASP* 3.1 8.6 + - - +
141B GLU* 1.3 74.1 - - - +
143B LEU* 1.3 65.2 + - - +
145B LEU* 3.8 7.3 - - + +
146B GLY* 3.2 19.2 + - - -
150B TRP* 5.6 2.5 - - + -
46C ASN* 4.7 7.0 - - - +
54C LEU* 4.7 16.4 - - + -
84C ALA* 3.4 29.2 - - + +
85C THR* 5.7 0.2 - - - -
86C SER 5.8 0.2 - - - +
92C ILE* 3.2 38.6 - - + -
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Residues in contact with LEU 143 (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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88B TYR* 3.8 23.3 - - + +
139B ASP 3.0 12.9 + - - +
140B TRP* 3.5 40.6 - - + +
142B VAL* 1.3 79.1 - - - +
144B VAL* 1.3 62.4 + - - +
146B GLY* 3.4 1.0 + - - -
147B LYS* 3.2 36.8 + - + +
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Residues in contact with VAL 144 (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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88B TYR* 4.1 20.9 - - + -
102B LEU* 3.8 25.1 - - + -
105B VAL* 3.6 19.1 - - + -
106B CYS* 4.8 11.7 - - - -
109B LEU* 3.9 15.5 - - + -
140B TRP* 2.9 27.7 + - + +
141B GLU 4.1 0.9 - - - +
143B LEU* 1.3 73.2 - - - +
145B LEU* 1.3 67.3 + - - +
147B LYS* 3.3 1.9 + - - +
148B LEU* 2.9 45.5 + - + +
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Residues in contact with LEU 145 (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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109B LEU* 4.0 9.6 - - + -
141B GLU 3.2 21.0 + - - +
142B VAL* 3.8 6.7 - - + +
144B VAL* 1.3 78.7 - - - +
146B GLY* 1.3 57.3 + - - +
148B LEU* 3.2 3.7 + - - -
149B LYS 2.8 8.3 + - - -
150B TRP* 2.6 77.9 + - + +
152B LEU* 3.2 38.1 - - + -
54C LEU* 3.6 27.6 - - + -
59C VAL* 4.1 13.5 - - + -
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Residues in contact with GLY 146 (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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142B VAL 3.2 13.0 + - - -
143B LEU 3.9 2.7 - - - -
145B LEU* 1.3 78.2 - - - +
147B LYS* 1.3 58.8 + - - +
149B LYS* 3.1 22.2 + - - +
150B TRP* 4.0 12.6 - - - +
81C ASP* 5.1 0.3 - - - +
82C VAL 4.3 10.3 - - - +
84C ALA* 5.8 4.7 - - - -
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Residues in contact with LYS 147 (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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88B TYR* 3.8 22.4 - - + +
91B CYS* 4.4 15.2 - - - -
92B VAL* 3.6 32.6 - - + +
143B LEU* 3.2 29.6 + - + +
144B VAL 3.3 4.5 + - - +
146B GLY* 1.3 75.8 - - - +
148B LEU* 1.3 63.0 + - + +
149B LYS* 3.2 4.9 + - - +
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Residues in contact with LEU 148 (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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84B TYR* 3.9 26.0 - - + +
87B ARG* 3.6 45.1 + - + +
88B TYR* 3.8 15.7 - - + +
91B CYS* 5.7 0.2 - - - -
144B VAL* 2.9 37.2 + - + +
145B LEU 4.0 2.0 - - - +
147B LYS* 1.3 80.8 - - - +
149B LYS* 1.3 69.7 + - - +
150B TRP 3.1 1.1 - - - -
151B ASP* 2.9 19.1 + - - +
152B LEU* 3.7 30.3 - - + -
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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