Contacts of the helix formed by residues 135 - 143 (chain a) in PDB entry 5GJQ
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 ILE 135 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2a THR* 4.0 23.1 - - + -
4a MET* 4.9 0.2 - - - -
127a ILE* 4.2 21.1 - - + -
131a GLY 4.0 0.9 - - - +
132a SER* 2.9 18.6 + - - +
134a TYR* 1.3 85.6 - - + +
136a TYR* 1.3 66.2 - - - +
137a GLY 3.2 1.8 - - - +
138a TYR* 3.6 7.2 + - + +
139a VAL* 3.1 28.1 + - + +
159a ALA* 3.7 33.7 - - + +
160a LEU* 4.9 2.9 - - + -
162a LEU* 4.0 10.5 - - + -
163a ALA* 3.6 32.8 - - + +
166a ARG* 6.4 0.2 - - + -
137o GLY* 4.8 3.1 - - - -
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Residues in contact with TYR 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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127a ILE* 3.5 26.4 + - + +
132a SER* 3.2 31.8 + - - -
133a SER* 3.6 21.1 - - - +
134a TYR 3.6 0.8 - - - -
135a ILE* 1.3 79.0 - - - +
137a GLY* 1.3 64.0 + - - +
139a VAL* 3.2 5.5 - - + +
140a ASP* 2.9 29.2 + - - -
33g LEU* 3.6 28.5 - - + +
35g ARG* 3.6 32.1 + - + +
134o TYR* 3.9 11.2 + + + +
166o ARG* 3.4 58.1 - - + +
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Residues in contact with GLY 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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135a ILE 3.2 0.2 - - - -
136a TYR* 1.3 78.4 - - - +
138a TYR* 1.3 62.5 + - - +
140a ASP* 3.0 18.3 + - - +
141a ALA* 3.0 15.6 + - - +
134o TYR* 3.1 17.8 + - - +
135o ILE* 4.8 2.9 - - - -
138o TYR* 4.1 12.8 - - - -
162o LEU* 4.0 19.3 - - - +
166o ARG* 5.6 1.3 - - - +
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Residues in contact with TYR 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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135a ILE* 3.6 7.7 + - + +
136a TYR 3.5 0.4 - - - -
137a GLY* 1.3 73.0 - - - +
139a VAL* 1.3 62.0 + - - +
141a ALA 2.9 3.5 + - - -
142a THR* 2.5 66.2 + - + +
155a PHE* 4.2 10.3 + + - -
158a ASN* 3.3 31.5 + - + +
159a ALA* 3.9 30.7 - - + -
162a LEU* 3.6 23.1 - - + -
197a PHE* 5.4 0.6 - + - -
137o GLY* 4.2 2.7 - - - -
138o TYR* 3.8 31.3 - + - +
141o ALA* 3.9 26.0 - - + -
142o THR* 5.9 0.4 - - - -
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Residues in contact with VAL 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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4a MET* 3.5 23.1 - - + -
125a PHE* 3.5 33.6 - - + -
127a ILE* 4.5 13.5 - - + -
135a ILE* 3.1 15.2 + - + +
136a TYR* 3.2 19.1 - - + +
138a TYR* 1.3 86.0 - - + +
140a ASP* 1.3 65.1 + - - +
142a THR 4.1 0.2 - - - -
143a TYR* 3.3 26.0 + - - +
155a PHE* 3.4 25.4 - - + -
159a ALA* 5.1 2.7 - - + -
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Residues in contact with ASP 140 (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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125a PHE* 3.8 14.2 - - - -
136a TYR 2.9 25.6 + - - +
137a GLY* 3.0 7.2 + - - +
139a VAL* 1.3 78.6 - - - +
141a ALA* 1.3 60.4 + - - +
142a THR 3.4 0.2 - - - -
143a TYR* 4.4 8.1 + - - +
37g ARG* 4.6 12.5 + - - +
162o LEU* 4.0 15.0 - - + +
165o GLU* 5.8 0.9 - - - +
166o ARG* 2.9 50.5 + - - +
197o PHE* 3.6 21.6 - - + +
198o ALA 5.5 1.4 - - - +
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Residues in contact with ALA 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 GLY 3.0 12.4 + - - +
138a TYR 2.9 4.2 + - - +
140a ASP* 1.3 77.8 - - - +
142a THR* 1.3 63.8 + - - +
143a TYR 3.6 2.3 - - - +
138o TYR* 3.9 26.5 - - + -
162o LEU* 4.2 2.2 - - + -
197o PHE* 3.4 32.7 - - + -
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Residues in contact with THR 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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138a TYR* 2.5 55.8 + - + +
141a ALA* 1.3 81.1 - - - +
143a TYR* 1.3 66.0 + - - +
144a ARG* 4.1 5.0 + - - +
147a MET* 3.3 12.9 - - + +
155a PHE* 3.5 28.3 - - + -
138o TYR* 6.1 0.2 - - - -
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Residues in contact with TYR 143 (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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6a VAL* 4.5 13.0 - - + -
7a GLN* 4.8 8.7 + - - +
124a SER* 3.5 26.1 + - - -
125a PHE* 3.8 32.8 - + + -
139a VAL 3.3 21.0 + - - +
140a ASP* 4.4 6.8 - - - +
141a ALA 3.6 3.7 - - - +
142a THR* 1.3 84.1 + - - +
144a ARG* 1.3 88.2 + - - +
145a GLU* 4.1 23.9 + - + +
146a GLY 5.1 1.2 + - - -
147a MET* 3.6 14.8 - - + -
155a PHE* 3.9 19.5 - + + -
198o ALA 5.5 6.5 - - - -
200o ALA* 4.6 10.8 - - + -
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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