Contacts of the helix formed by residues 139 - 145 (chain T) in PDB entry 3J0S
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 CYS 139 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328I LYS* 5.7 5.2 - - - -
77T ASP* 5.1 6.7 - - - -
104T TRP* 3.4 18.4 - - - -
137T ALA* 3.4 2.8 - - - +
138T ASN* 1.3 89.1 - - - +
140T TYR* 1.3 77.8 + - - +
141T GLU* 3.3 21.2 + - + +
142T GLU* 3.5 10.3 + - + +
143T VAL* 3.4 13.9 + - - +
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Residues in contact with TYR 140 (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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72T VAL* 3.2 40.8 - - + +
73T LYS* 4.6 7.1 + - + -
75T LEU 4.1 3.6 - - - -
76T PRO* 2.9 31.5 - - + +
77T ASP* 3.6 35.2 - - + -
78T LYS* 5.3 3.4 - - + +
104T TRP* 4.4 4.9 - + - -
139T CYS* 1.3 80.0 - - - +
141T GLU* 1.3 55.2 + - + +
143T VAL* 3.3 4.9 + - + +
144T LYS* 2.7 46.2 + - + +
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Residues in contact with GLU 141 (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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139T CYS* 3.3 14.6 - - + -
140T TYR* 1.3 77.5 - - + +
142T GLU* 1.3 64.1 + - + +
144T LYS* 4.2 10.5 - - + -
145T ASP* 3.0 38.8 + - - +
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Residues in contact with GLU 142 (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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147I ARG* 5.0 2.4 + - - -
295I ALA* 4.8 6.0 - - - +
326I LYS* 4.7 16.1 - - - +
328I LYS* 3.2 35.2 + - - +
68T TYR* 4.4 0.7 + - - -
136T GLN 4.1 5.0 - - - +
137T ALA* 3.4 32.5 - - + +
138T ASN* 4.1 8.1 + - - +
139T CYS* 3.5 9.3 + - + +
140T TYR 3.3 0.4 - - - -
141T GLU* 1.3 81.2 - - + +
143T VAL* 1.3 62.2 + - - +
145T ASP* 3.7 7.5 + - - +
148T THR* 3.2 36.5 + - + +
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Residues in contact with VAL 143 (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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68T TYR* 2.8 32.7 + - + +
71T PHE* 4.0 26.7 - - + -
72T VAL* 3.6 25.0 - - + +
75T LEU* 5.0 5.6 - - + +
102T ILE* 5.7 5.4 - - + -
103T PHE 5.9 0.2 - - - +
104T TRP* 3.3 40.4 - - + -
137T ALA* 3.5 13.5 - - + -
139T CYS 3.4 2.1 + - - +
140T TYR* 3.3 8.6 + - + +
142T GLU* 1.3 76.1 - - - +
144T LYS* 1.3 60.0 + - - +
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Residues in contact with LYS 144 (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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68T TYR* 4.0 9.7 - - - +
72T VAL* 3.7 26.9 - - + +
73T LYS* 4.7 14.6 - - - +
140T TYR* 2.7 29.5 + - - +
141T GLU* 3.7 10.8 - - + +
143T VAL* 1.3 76.2 - - - +
145T ASP* 1.3 68.2 + - - +
146T ARG* 3.5 10.7 + - - -
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Residues in contact with ASP 145 (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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68T TYR* 3.6 18.2 + - - -
141T GLU* 3.0 28.5 + - - +
142T GLU* 3.7 9.3 + - - +
143T VAL 3.4 1.2 - - - -
144T LYS* 1.3 84.1 - - - +
146T ARG* 1.3 65.2 + - - +
147T CYS* 3.2 10.0 + - + +
148T THR* 3.5 15.6 + - - +
149T LEU 4.1 0.3 + - - -
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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