Contacts of the helix formed by residues 130 - 141 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128K LEU 3.1 2.6 + - - -
129K ASP* 1.3 70.3 - - - +
131K LEU* 1.3 64.6 + - - +
132K SER 3.2 3.1 - - - -
133K GLU* 3.1 23.5 + - - +
134K ARG* 3.1 27.0 + - - +
126L GLN* 3.2 18.4 + - - +
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Residues in contact with LEU 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K VAL* 3.6 33.0 - - + +
127K GLY 3.7 7.4 - - - +
128K LEU* 3.1 21.7 + - + +
129K ASP 3.1 4.4 + - - -
130K GLY* 1.3 76.1 - - - +
132K SER* 1.3 58.8 + - - +
134K ARG* 3.5 20.9 - - + +
135K CYS* 2.8 44.1 + - - -
148K TRP* 4.4 3.6 - - + -
174K TYR* 4.0 30.1 - - + +
177K ILE* 4.0 30.1 - - + -
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Residues in contact with SER 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K GLY 3.2 0.8 - - - -
131K LEU* 1.3 78.8 - - - +
133K GLU* 1.3 74.5 + - - +
135K CYS 3.3 0.7 + - - -
136K ALA* 3.0 20.3 + - - +
177K ILE* 3.5 20.7 - - - +
180K GLN* 3.5 14.9 + - - -
181K ASN* 2.9 30.0 + - - +
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Residues in contact with GLU 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K GLY* 3.3 27.4 - - - +
132K SER* 1.3 84.9 + - - +
134K ARG* 1.3 64.4 + - + +
136K ALA* 3.3 9.2 + - - +
137K GLN* 3.0 24.1 + - - +
126L GLN* 5.2 3.5 + - - +
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Residues in contact with ARG 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K LYS 4.5 1.6 + - - -
109K VAL* 3.0 41.5 + - - +
110K ASP 5.1 0.4 + - - -
111K LYS* 3.7 24.7 - - - +
127K GLY 3.4 20.2 + - - -
129K ASP 4.4 4.0 - - - -
130K GLY 3.1 18.8 + - - +
131K LEU* 3.5 15.9 - - + +
133K GLU* 1.3 76.2 - - + +
135K CYS* 1.3 61.1 + - - +
137K GLN* 3.1 9.4 + - - +
138K TYR* 2.8 62.3 + - + +
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Residues in contact with CYS 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K VAL* 5.1 7.4 - - - -
131K LEU* 2.8 49.4 + - - +
132K SER 3.7 3.8 - - - +
134K ARG* 1.3 69.8 - - - +
136K ALA* 1.3 68.8 + - - +
137K GLN 3.0 0.2 + - - -
138K TYR* 3.0 5.5 + - - +
139K LYS* 2.8 26.0 + - - +
177K ILE* 4.8 0.4 - - - -
178K CYS* 4.0 29.6 - - - -
181K ASN* 3.7 20.9 - - + +
183K ILE* 3.6 17.5 - - + +
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Residues in contact with ALA 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K SER 3.0 10.2 + - - +
133K GLU* 3.4 12.6 - - - +
135K CYS* 1.3 76.4 - - - +
137K GLN* 1.3 56.0 + - - +
139K LYS* 3.6 6.8 + - - +
140K LYS* 3.1 37.0 + - - +
181K ASN* 3.5 20.3 + - - +
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Residues in contact with GLN 137 (chain K).
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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85K TYR* 4.6 1.7 + - - +
133K GLU 3.0 13.2 + - - +
134K ARG* 3.3 11.2 - - - +
135K CYS 3.0 0.2 - - - -
136K ALA* 1.3 74.0 - - - +
138K TYR* 1.3 71.0 + - + +
140K LYS* 2.9 37.1 + - - +
141K ASP* 2.9 50.8 + - - +
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Residues in contact with TYR 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K HIS* 2.6 44.8 + + - +
84K LEU* 3.7 14.7 - - + +
85K TYR* 3.6 16.8 - - - -
107K ILE* 3.8 35.4 - - + +
108K LYS 4.9 1.5 + - - -
109K VAL* 4.0 22.7 - - + -
134K ARG* 2.8 58.4 + - + +
135K CYS* 3.6 7.4 - - - +
137K GLN* 1.3 75.0 - - + +
139K LYS* 1.3 63.4 + - - +
141K ASP* 2.9 14.5 + - - +
142K GLY 3.2 0.5 + - - -
143K ALA* 3.0 22.4 + - + +
183K ILE* 4.5 1.6 - - + -
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Residues in contact with LYS 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K GLU* 2.9 28.6 + - - -
19K ILE* 3.7 5.7 - - - +
135K CYS 2.8 20.3 + - - +
136K ALA* 3.6 7.0 - - - +
138K TYR* 1.3 72.4 - - - +
140K LYS* 1.3 59.3 + - - +
142K GLY* 2.9 21.5 + - - -
143K ALA 3.2 20.6 + - - +
144K ASP* 2.9 22.4 + - - +
181K ASN 4.0 9.9 - - - +
182K GLY* 2.7 32.4 + - - +
183K ILE* 3.9 9.8 - - + +
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Residues in contact with LYS 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K ALA* 3.1 17.8 + - - +
137K GLN* 2.9 37.0 + - - +
139K LYS* 1.3 79.8 - - - +
141K ASP* 1.3 63.2 + - - +
142K GLY 3.4 0.6 + - - -
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Residues in contact with ASP 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K LEU* 4.7 8.6 - - + +
85K TYR* 2.6 43.9 + - + +
95K VAL* 3.8 19.8 - - - +
99K GLN* 5.4 0.2 - - - +
137K GLN* 2.9 32.1 + - - +
138K TYR* 2.9 11.5 + - - +
140K LYS* 1.3 86.7 - - - +
142K GLY* 1.3 55.8 + - - +
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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