Contacts of the helix formed by residues 132 - 138 (chain T) in PDB entry 3EXG
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 PHE 132 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138R HIS* 6.1 0.4 - - - -
83T PHE* 3.8 13.0 - - + -
84T ASN* 3.7 32.8 - - - -
86T SER* 5.3 0.4 - - - -
87T MET* 3.9 25.6 - - + -
90T ILE* 5.9 0.2 - - + -
118T ASN* 2.8 25.9 - - - +
130T GLN* 3.3 50.7 - - + -
131T CYS* 1.3 75.3 - - - +
133T ALA* 1.3 67.4 + - - +
134T ALA* 3.3 3.1 - - - -
135T TRP* 2.8 41.6 + + + +
136T TYR* 3.1 38.7 + + + -
170T LEU* 4.3 4.5 - - + -
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Residues in contact with ALA 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T CYS* 3.4 17.4 - - - -
132T PHE* 1.3 75.0 - - - +
134T ALA* 1.3 64.3 + - - +
137T GLY* 2.8 25.1 + - - -
144T VAL* 4.8 0.7 - - - -
170T LEU* 3.6 25.0 - - + +
212T HIS* 4.0 10.1 - - + -
241T ILE* 3.7 22.5 - - + +
271T VAL* 3.9 18.2 - - + -
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Residues in contact with ALA 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138R HIS* 4.1 15.5 - - + +
269R PHE* 4.1 16.9 - - + +
131T CYS* 5.2 0.8 - - - -
132T PHE 3.3 0.4 - - - -
133T ALA* 1.3 79.5 - - - +
135T TRP* 1.3 69.7 + - + +
137T GLY 3.8 1.0 - - - -
138T HIS* 3.3 19.2 + - - +
269T PHE 3.3 26.7 - - - +
270T GLY* 3.8 17.7 - - - -
271T VAL* 4.0 5.0 - - + +
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Residues in contact with TRP 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90R ILE* 4.1 25.4 - - + -
94R ILE* 4.1 17.5 - - + -
134R ALA 4.9 0.4 - - - -
135R TRP* 3.0 83.3 + + + +
136R TYR* 5.9 0.2 - + - -
138R HIS* 3.6 27.4 + + + -
139R CYS* 3.9 17.3 - - - -
87T MET* 4.3 15.5 - - + -
90T ILE* 4.0 21.1 - - + -
130T GLN* 4.4 6.5 - - - -
131T CYS 5.8 0.4 - - - -
132T PHE* 2.8 49.0 + + + +
134T ALA* 1.3 80.4 - - + +
136T TYR* 1.3 63.6 + - + +
138T HIS* 3.2 8.5 - - - +
139T CYS* 4.0 1.2 - - - -
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Residues in contact with TYR 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R TRP* 5.6 0.4 - + - -
80T PHE* 5.5 0.2 - - - -
83T PHE* 3.8 21.3 - + - -
86T SER* 2.8 27.8 + - - -
87T MET* 6.0 0.2 - - - +
90T ILE* 3.4 39.9 - - + +
93T VAL* 4.4 18.1 - - + +
94T ILE* 4.6 6.7 - - + -
132T PHE* 3.1 40.2 + + + +
135T TRP* 1.3 75.3 - - + +
137T GLY* 1.3 59.9 + - - +
138T HIS 2.8 11.8 + - - -
139T CYS* 3.1 20.2 + - - +
142T LEU* 3.9 21.4 - - + +
144T VAL* 3.6 27.4 - - + +
168T VAL* 4.3 17.3 - - + -
170T LEU* 4.7 2.7 - - + -
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Residues in contact with GLY 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269R PHE* 2.8 28.8 - - - -
133T ALA 2.8 23.8 + - - -
136T TYR* 1.3 70.1 - - - +
138T HIS* 1.3 50.6 + - - +
139T CYS 3.3 0.9 - - - -
144T VAL* 3.6 15.7 - - - +
241T ILE* 4.1 8.3 - - - -
242T ARG* 2.8 31.7 + - - +
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Residues in contact with HIS 138 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130R GLN* 5.1 1.3 - - - -
131R CYS 4.7 8.9 + - - -
134R ALA* 3.7 25.2 - - + +
135R TRP* 3.7 22.2 - + + +
263R GLU* 5.8 0.4 - - - -
265R GLY* 5.8 1.1 - - - -
266R TRP* 3.5 61.6 + + + +
268R GLN* 2.7 26.3 + - - +
269R PHE* 3.4 13.8 + - + -
270R GLY* 4.2 1.8 - - - -
299R ASP* 4.8 0.5 - - - +
134T ALA 3.3 10.0 + - - +
135T TRP* 3.2 15.0 + - - +
136T TYR 2.8 3.0 + - - -
137T GLY* 1.3 73.2 - - - +
139T CYS* 1.3 57.0 + - - +
140T PRO* 3.6 4.2 - - - +
242T ARG* 3.4 9.7 + - - +
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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