Contacts of the helix formed by residues 110 - 120 (chain W) in PDB entry 3J7Y
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 110 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104W TYR* 5.0 3.3 + - - -
106W PRO* 4.7 2.8 - - - +
107W HIS* 3.2 21.9 + - + +
108W PRO 4.1 0.7 - - - -
109W ARG* 1.3 74.8 - - - +
111W THR* 1.3 66.9 + - - +
112W GLU* 3.7 27.8 + - - +
113W ALA* 3.7 17.3 - - - +
114W VAL* 3.4 21.1 + - - +
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Residues in contact with THR 111 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108W PRO 5.0 1.6 - - - -
109W ARG 3.2 9.0 + - - -
110W ASN* 1.3 72.4 - - - +
112W GLU* 1.3 92.2 + - + +
114W VAL* 3.1 9.4 + - - +
115W ASP* 3.0 35.5 + - - +
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Residues in contact with GLU 112 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110W ASN* 3.6 16.1 + - - +
111W THR* 1.3 89.6 - - + +
113W ALA* 1.3 56.3 + - - +
115W ASP* 3.3 10.3 + - - +
116W LEU* 3.1 35.2 + - + +
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Residues in contact with ALA 113 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104W TYR* 4.3 11.7 - - + +
106W PRO* 3.2 32.1 - - + -
110W ASN* 3.7 18.7 - - - +
112W GLU* 1.3 76.2 + - - +
114W VAL* 1.3 60.9 + - - +
116W LEU* 3.2 15.1 + - - +
117W ILE* 2.9 31.4 + - - +
126W LEU* 5.4 0.9 - - - +
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Residues in contact with VAL 114 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546 PHE* 4.7 21.1 - - + -
150P TRP* 6.1 2.7 - - + -
106W PRO* 4.3 11.0 - - + -
107W HIS 3.6 9.6 - - - +
108W PRO* 3.5 24.0 - - + +
110W ASN 3.4 15.7 - - - +
111W THR* 3.1 10.6 + - - +
113W ALA* 1.3 78.1 - - - +
115W ASP* 1.3 63.0 + - - +
117W ILE* 3.2 6.5 + - - +
118W THR* 2.9 44.8 + - + +
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Residues in contact with ASP 115 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111W THR* 3.0 29.8 + - - +
112W GLU* 3.5 11.6 - - - +
113W ALA 3.2 0.2 - - - -
114W VAL* 1.3 80.4 - - - +
116W LEU* 1.3 56.6 + - + +
118W THR* 2.4 28.2 + - - +
119W ARG* 2.9 26.9 + - - +
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Residues in contact with LEU 116 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112W GLU* 3.1 20.2 + - + +
113W ALA* 3.3 15.3 - - - +
115W ASP* 1.3 77.9 - - + +
117W ILE* 1.3 63.2 + - + +
119W ARG* 3.2 15.9 + - - +
120W LEU* 3.2 14.1 + - - +
126W LEU* 5.6 7.9 - - + -
59f TYR* 4.7 26.0 - - + +
63f ILE* 3.4 37.4 - - + +
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Residues in contact with ILE 117 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506 LYS 4.0 2.6 - - - +
516 TYR* 4.1 5.4 - - + -
536 SER 4.7 2.7 - - - +
546 PHE* 4.1 15.5 - - + -
576 TYR* 3.4 51.6 - - + -
106W PRO* 2.5 46.2 - - + -
113W ALA 2.9 8.3 + - - +
114W VAL 3.4 9.9 - - - +
116W LEU* 1.3 75.3 - - - +
118W THR* 1.3 70.9 + - + +
120W LEU* 3.2 26.1 + - - +
126W LEU* 3.5 21.7 - - + +
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Residues in contact with THR 118 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506 LYS* 2.6 28.2 - - - +
516 TYR 3.1 14.2 - - - +
526 ARG* 3.6 24.4 - - - +
536 SER 4.2 11.2 - - - +
546 PHE* 5.0 0.4 - - - +
114W VAL* 2.9 28.7 + - + +
115W ASP* 2.4 31.7 + - - +
117W ILE* 1.3 79.1 - - + +
119W ARG* 1.3 58.6 + - - +
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Residues in contact with ARG 119 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506 LYS* 3.8 19.4 - - - +
115W ASP* 2.9 23.5 + - + +
116W LEU* 3.4 16.4 - - - +
118W THR* 1.3 80.5 + - - +
120W LEU* 1.3 62.1 + - - +
121W PRO* 3.7 1.0 - - - +
62f LEU 5.4 0.3 - - - +
63f ILE* 3.5 40.2 - - + +
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Residues in contact with LEU 120 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506 LYS* 2.6 31.4 - - - +
516 TYR* 3.9 3.0 - - + -
576 TYR* 3.7 20.6 - - + -
116W LEU 3.2 8.7 + - - +
117W ILE* 3.2 18.8 + - - +
119W ARG* 1.3 77.1 - - - +
121W PRO* 1.4 65.5 - - + +
124W ALA* 4.0 11.7 - - + +
126W LEU* 3.5 43.3 - - + +
59f TYR* 4.3 4.0 - - + +
62f LEU* 3.6 36.8 - - + -
63f ILE* 4.0 14.3 - - + +
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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