Contacts of the helix formed by residues 102 - 107 (chain D) in PDB entry 3BT9
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 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D TYR* 3.5 34.5 - + + +
47D GLU* 3.9 31.0 - - + -
50D PHE* 3.4 39.3 - + + -
51D LEU* 4.1 5.4 - - + -
54D LEU* 5.2 0.7 - - + -
98D ALA 2.8 20.0 + - - +
99D ILE* 4.3 3.8 - - - +
101D GLU* 1.3 73.4 - - - +
103D TYR* 1.3 60.2 + - - +
105D GLU* 4.1 2.2 - - - -
106D TYR* 3.5 35.3 + + - +
112D ILE* 3.8 24.0 - - + -
116D MET* 3.7 37.9 - - + +
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Residues in contact with TYR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ILE* 3.4 14.2 + - + +
100D ILE* 2.8 12.8 + - - +
102D PHE* 1.3 77.0 - - - +
104D THR* 1.3 55.9 + - + +
105D GLU 2.7 16.4 + - - -
107D TYR* 3.0 54.5 + + + +
113D ASN* 3.8 13.9 + - - -
116D MET* 3.9 42.1 - - + +
117D ASN* 5.3 3.5 + - - -
120D GLU* 4.1 11.3 + - - -
164E HIS* 4.9 13.2 - - + -
165E GLU* 3.4 41.9 - - + +
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Residues in contact with THR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ILE* 3.1 25.7 + - + +
101D GLU* 3.2 10.8 + - - -
103D TYR* 1.3 77.6 - - + +
105D GLU* 1.3 55.9 + - - +
107D TYR* 3.8 22.1 - - - -
108D LYS* 5.5 0.9 + - - -
16E ILE 4.8 6.3 + - - +
17E LYS* 3.6 28.9 + - - +
164E HIS* 5.4 14.4 - - + -
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D TYR* 3.5 11.1 - - - -
21D ASN* 3.4 21.0 - - - +
101D GLU 3.5 10.7 + - - +
102D PHE* 4.8 0.2 - - - -
103D TYR 2.7 7.9 + - - -
104D THR* 1.3 78.2 - - - +
106D TYR* 1.3 91.7 + - + +
107D TYR* 3.6 4.0 - - - -
108D LYS* 4.2 14.4 - - - +
109D THR* 5.8 0.9 - - - +
999D SO4 3.5 20.7 + - - -
17E LYS* 6.0 1.6 - - - +
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Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D TYR* 3.9 14.4 - + - -
47D GLU* 3.9 24.0 - - + +
102D PHE* 3.5 33.2 + + + +
103D TYR 3.3 2.2 + - - -
105D GLU* 1.3 107.4 + - - +
107D TYR* 1.3 58.9 + - - +
108D LYS 2.7 11.1 + - - +
109D THR* 3.4 40.3 + - + +
112D ILE* 4.0 27.8 - - + -
113D ASN* 4.0 7.2 + - - -
116D MET* 6.2 1.3 - - + -
999D SO4 2.9 21.0 + - - -
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 3.0 53.4 + + + +
104D THR* 3.8 24.9 - - - -
106D TYR* 1.3 76.8 - - - +
108D LYS* 1.3 99.7 + - + +
113D ASN* 3.4 34.5 + - - +
116D MET* 6.1 0.2 - - - -
164E HIS* 5.0 11.4 - - + -
165E GLU* 6.5 0.2 - - - -
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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