Contacts of the helix formed by residues 133 - 142 (chain A) in PDB entry 2G3T
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 ASN 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A VAL* 4.4 4.0 - - + +
130A ALA* 2.9 18.5 + - + +
132A TRP* 1.3 104.6 - - + +
134A GLU* 1.3 55.3 + - - +
135A PRO* 3.5 10.6 - - - +
136A SER* 3.2 30.6 + - - -
137A ILE* 2.9 31.1 + - - +
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Residues in contact with GLU 134 (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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131A GLU 4.6 5.9 - - - +
132A TRP 3.0 12.1 + - - +
133A ASN* 1.3 71.8 - - - +
135A PRO* 1.3 70.7 - - + +
137A ILE* 3.2 23.0 + - - +
138A ASN* 2.9 47.5 + - - +
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Residues in contact with PRO 135 (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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132A TRP 4.8 0.9 - - - +
133A ASN* 3.4 13.7 - - - +
134A GLU* 1.3 94.7 - - + +
136A SER* 1.3 55.5 + - - +
138A ASN* 3.5 6.4 + - + +
139A PHE* 3.0 27.5 + - - +
142A ARG* 5.0 2.4 + - - -
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Residues in contact with SER 136 (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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129A VAL* 3.9 10.1 - - - +
133A ASN* 3.2 32.6 + - - -
135A PRO* 1.3 77.8 - - - +
137A ILE* 1.3 66.2 + - - +
139A PHE* 3.3 6.6 + - - +
140A TYR* 3.1 51.8 + - - -
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Residues in contact with ILE 137 (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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129A VAL* 3.7 20.4 - - + -
130A ALA 3.9 5.6 - - - +
131A GLU* 3.3 30.3 - - - +
133A ASN 2.9 18.3 + - - +
134A GLU* 3.5 26.9 - - - +
136A SER* 1.3 78.4 - - - +
138A ASN* 1.3 60.0 + - - +
140A TYR* 3.5 3.8 + - - +
141A LYS* 3.0 61.9 + - + +
147A ASP* 5.7 4.7 - - - +
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Residues in contact with ASN 138 (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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134A GLU* 2.9 42.0 + - - +
135A PRO* 4.0 5.5 - - + +
137A ILE* 1.3 77.4 - - - +
139A PHE* 1.3 61.1 + - - +
141A LYS* 3.7 10.9 - - - +
142A ARG* 2.8 54.6 + - + +
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Residues in contact with PHE 139 (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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94A PHE* 6.2 2.7 - + - -
106A GLY 5.7 2.7 - - - -
107A SER* 4.9 14.1 - - - -
110A LEU* 4.9 11.9 - - + -
135A PRO 3.0 18.8 + - - +
136A SER* 3.3 8.7 + - - +
138A ASN* 1.3 77.4 - - - +
140A TYR* 1.3 93.3 + + - +
142A ARG* 3.6 26.4 + - - +
143A ARG* 3.0 65.2 + - - +
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Residues in contact with TYR 140 (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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91A LEU* 4.3 12.5 - - + +
94A PHE* 4.9 9.2 - - - +
110A LEU* 4.2 25.5 - - + +
125A MET* 5.5 1.1 - - + -
127A PHE* 3.5 41.0 - + + -
129A VAL* 4.1 10.1 - - + -
136A SER* 3.1 44.4 + - - +
137A ILE* 4.0 3.6 - - - +
139A PHE* 1.3 99.5 - + - +
141A LYS* 1.3 64.8 + - + +
142A ARG 3.1 2.0 - - - -
143A ARG* 3.0 20.1 + - + +
144A GLY 3.4 0.3 + - - -
145A ALA* 3.0 31.7 + - + +
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Residues in contact with LYS 141 (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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137A ILE* 3.0 46.2 + - + +
138A ASN* 3.2 12.7 + - - +
140A TYR* 1.3 76.8 - - - +
142A ARG* 1.3 61.3 + - + +
143A ARG 3.0 1.6 + - - -
144A GLY* 3.1 12.6 + - - -
145A ALA* 4.0 21.3 + - + +
146A SER* 5.5 0.4 - - - +
147A ASP* 4.0 30.1 + - - +
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Residues in contact with ARG 142 (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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135A PRO 5.0 1.8 + - - -
138A ASN* 2.8 45.2 + - + +
139A PHE* 3.7 36.3 + - - +
140A TYR 3.1 0.2 - - - -
141A LYS* 1.3 76.0 - - + +
143A ARG* 1.3 68.6 + - + +
144A GLY 3.4 0.6 + - - -
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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