Contacts of the helix formed by residues 130 - 141 (chain J) in PDB entry 1XFB
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 GLY 130 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126I GLN* 3.3 17.1 + - - +
128J LEU 3.1 2.6 + - - -
129J ASP* 1.3 70.5 - - - +
131J LEU* 1.3 64.0 + - - +
132J SER 3.2 3.4 - - - -
133J GLU* 3.1 24.6 + - - +
134J ARG* 3.1 26.4 + - - +
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Residues in contact with LEU 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J VAL* 3.6 33.2 - - + -
127J GLY 3.7 7.0 - - - +
128J LEU* 3.1 21.3 + - + +
129J ASP 3.1 4.2 + - - -
130J GLY* 1.3 77.6 - - - +
132J SER* 1.3 58.5 + - - +
134J ARG* 3.2 21.7 + - + +
135J CYS* 2.8 44.1 + - - -
148J TRP* 4.4 4.3 - - + -
174J TYR* 4.0 28.9 - - + +
177J ILE* 4.0 30.3 - - + -
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Residues in contact with SER 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J LEU 4.9 0.2 + - - -
130J GLY 3.2 0.8 - - - -
131J LEU* 1.3 79.8 - - - +
133J GLU* 1.3 75.4 + - - +
135J CYS 3.3 0.9 + - - -
136J ALA* 3.0 20.1 + - - +
177J ILE* 3.5 20.7 - - - +
180J GLN* 3.5 14.2 + - - -
181J ASN* 2.9 30.1 + - - +
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Residues in contact with GLU 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I GLN* 5.5 1.6 + - - +
130J GLY* 3.1 27.9 + - - +
132J SER* 1.3 84.6 + - - +
134J ARG* 1.3 64.2 + - + +
136J ALA* 3.3 8.8 + - - +
137J GLN* 3.0 24.2 + - - +
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Residues in contact with ARG 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J LYS 4.5 1.6 + - - -
109J VAL* 3.0 41.3 + - - +
110J ASP 5.1 0.4 + - - -
111J LYS* 3.7 25.9 - - - +
127J GLY 3.4 20.0 + - - -
129J ASP 4.4 4.0 - - - -
130J GLY* 3.1 20.5 + - - +
131J LEU* 3.5 15.5 - - + +
133J GLU* 1.3 75.9 - - + +
135J CYS* 1.3 60.7 + - - +
137J GLN* 3.1 8.6 + - - +
138J TYR* 2.8 63.0 + - + +
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Residues in contact with CYS 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J VAL* 5.1 7.0 - - - -
131J LEU* 2.8 49.8 + - - +
132J SER 3.7 4.3 - - - +
134J ARG* 1.3 68.4 - - - +
136J ALA* 1.3 69.3 + - - +
137J GLN 3.0 0.3 + - - -
138J TYR* 3.0 5.7 + - - +
139J LYS* 2.8 26.2 + - - +
177J ILE* 4.8 0.4 - - - -
178J CYS* 4.0 29.6 - - - -
181J ASN* 3.7 20.4 - - + +
183J ILE* 3.6 16.3 - - + +
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Residues in contact with ALA 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J SER 3.0 9.0 + - - +
133J GLU* 3.4 13.0 - - - +
135J CYS* 1.3 77.6 - - - +
137J GLN* 1.3 56.9 + - - +
139J LYS* 3.6 6.6 - - - +
140J LYS* 3.1 36.9 + - - +
181J ASN* 3.5 21.0 + - - +
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Residues in contact with GLN 137 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85J TYR* 4.6 1.8 + - - +
133J GLU 3.0 14.5 + - - +
134J ARG* 3.3 10.8 - - - +
136J ALA* 1.3 74.3 - - - +
138J TYR* 1.3 71.3 + - + +
140J LYS* 2.9 37.3 + - - +
141J ASP* 2.9 51.6 + - - +
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Residues in contact with TYR 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J HIS* 2.6 45.5 + + - +
84J LEU* 3.7 15.0 - - + +
85J TYR* 3.6 15.7 - - - -
107J ILE* 3.8 37.4 - - + +
108J LYS 4.9 1.7 + - - -
109J VAL* 4.0 22.4 - - + -
134J ARG* 2.8 59.7 + - + +
135J CYS* 3.6 7.2 - - - +
137J GLN* 1.3 75.9 - - + +
139J LYS* 1.3 62.7 + - - +
141J ASP* 2.9 14.2 + - - +
142J GLY 3.2 0.9 + - - -
143J ALA* 3.0 21.8 + - + +
183J ILE* 4.5 1.8 - - + -
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Residues in contact with LYS 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J GLU* 2.9 28.4 + - - -
19J ILE* 3.7 5.5 - - - +
135J CYS 2.8 19.7 + - - +
136J ALA* 3.6 6.3 - - - +
138J TYR* 1.3 71.8 - - - +
140J LYS* 1.3 60.5 + - - +
142J GLY* 2.9 21.3 + - - -
143J ALA 3.2 20.5 + - - +
144J ASP* 2.9 23.5 + - - +
181J ASN 4.0 11.4 - - - +
182J GLY* 2.7 32.9 + - - +
183J ILE* 3.9 9.1 - - + +
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Residues in contact with LYS 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ALA* 3.1 17.6 + - - +
137J GLN* 2.9 37.7 + - - +
139J LYS* 1.3 79.5 - - - +
141J ASP* 1.3 62.8 + - - +
142J GLY 3.4 0.4 + - - -
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Residues in contact with ASP 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J LEU* 4.7 8.8 - - + +
85J TYR* 2.6 43.6 + - + +
95J VAL* 3.8 19.4 - - - +
99J GLN* 5.4 0.2 - - - +
137J GLN* 2.9 31.4 + - - +
138J TYR* 2.9 11.5 + - - +
140J LYS* 1.3 86.9 - - - +
142J GLY* 1.3 55.7 + - - +
143J ALA 3.7 0.4 - - - -
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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