Contacts of the helix formed by residues 130 - 141 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I LEU 3.1 2.4 + - - -
129I ASP* 1.3 70.5 - - - +
131I LEU* 1.3 64.3 + - - +
132I SER 3.2 3.4 - - - -
133I GLU* 3.1 23.0 + - - +
134I ARG* 3.1 27.6 + - - +
126J GLN* 3.1 18.6 + - - +
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Residues in contact with LEU 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I VAL* 3.6 33.4 - - + +
127I GLY 3.7 7.4 - - - +
128I LEU* 3.1 21.5 + - + +
129I ASP 3.1 4.0 + - - -
130I GLY* 1.3 77.4 - - - +
132I SER* 1.3 57.2 + - - +
134I ARG* 3.2 22.0 + - + +
135I CYS* 2.8 43.2 + - - -
148I TRP* 4.4 4.0 - - + -
174I TYR* 4.0 29.6 - - + +
177I ILE* 4.0 29.6 - - + -
178I CYS* 4.8 0.2 - - - -
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Residues in contact with SER 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I LEU 4.9 0.2 + - - -
130I GLY 3.1 1.4 + - - -
131I LEU* 1.3 78.8 - - - +
133I GLU* 1.3 74.5 + - - +
135I CYS 3.3 0.7 + - - -
136I ALA* 3.0 20.0 + - - +
177I ILE* 3.5 20.2 - - - +
180I GLN* 3.5 14.0 + - - -
181I ASN* 2.9 30.8 + - - +
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Residues in contact with GLU 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I GLY* 3.3 27.6 - - - +
132I SER* 1.3 86.3 + - - +
134I ARG* 1.3 64.1 + - + +
136I ALA* 3.3 8.8 + - - +
137I GLN* 3.0 23.8 + - - +
126J GLN* 5.3 1.9 + - - +
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Residues in contact with ARG 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I LYS 4.5 1.8 + - - -
109I VAL* 3.0 41.9 + - - +
110I ASP 5.1 0.4 + - - -
111I LYS* 3.7 24.3 - - - +
127I GLY 3.4 20.0 + - - -
129I ASP 4.4 4.3 - - - -
130I GLY* 3.1 20.1 + - - +
131I LEU* 3.5 15.3 - - + +
133I GLU* 1.3 75.6 - - + +
135I CYS* 1.3 60.1 + - - +
137I GLN* 3.1 9.0 + - - +
138I TYR* 2.8 63.9 + - + +
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Residues in contact with CYS 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I ILE* 6.5 0.2 - - - -
109I VAL* 5.1 7.0 - - - -
131I LEU* 2.8 47.2 + - - +
132I SER 3.7 4.5 - - - +
134I ARG* 1.3 68.6 - - - +
136I ALA* 1.3 67.7 + - - +
137I GLN 3.0 0.3 + - - -
138I TYR* 3.0 6.5 + - - +
139I LYS* 2.8 26.3 + - - +
177I ILE* 4.8 0.4 - - - -
178I CYS* 4.0 30.1 - - - -
181I ASN* 3.7 22.0 - - + +
183I ILE* 3.6 16.8 - - + +
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Residues in contact with ALA 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I SER 3.0 8.4 + - - +
133I GLU* 3.4 12.8 - - - +
135I CYS* 1.3 77.4 - - - +
137I GLN* 1.3 56.5 + - - +
139I LYS* 3.6 6.8 + - - +
140I LYS* 3.1 36.3 + - - +
181I ASN* 3.5 22.3 + - - +
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Residues in contact with GLN 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I TYR* 4.6 1.8 + - - +
133I GLU 3.0 13.2 + - - +
134I ARG* 3.3 11.0 - - - +
135I CYS 3.0 0.2 - - - -
136I ALA* 1.3 73.7 - - - +
138I TYR* 1.3 70.9 + - + +
140I LYS* 2.9 37.9 + - - +
141I ASP* 2.9 51.3 + - - +
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Residues in contact with TYR 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I HIS* 2.6 45.6 + + - +
84I LEU* 3.7 16.3 - - + +
85I TYR* 3.6 15.7 - - - -
107I ILE* 3.8 36.7 - - + +
108I LYS 4.9 1.3 + - - -
109I VAL* 4.0 21.8 - - + -
134I ARG* 2.8 58.7 + - + +
135I CYS* 3.6 7.4 - - - +
137I GLN* 1.3 76.1 - - + +
139I LYS* 1.3 62.4 + - - +
141I ASP* 2.9 15.5 + - - +
142I GLY 3.2 0.7 + - - -
143I ALA* 3.0 22.4 + - + +
183I ILE* 4.5 1.8 - - + -
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Residues in contact with LYS 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PRO* 5.0 6.6 - - - +
15I GLU* 2.9 29.0 + - - -
19I ILE* 3.7 5.5 - - - +
135I CYS 2.8 19.8 + - - +
136I ALA* 3.6 6.7 - - - +
138I TYR* 1.3 71.1 - - - +
140I LYS* 1.3 60.5 + - - +
142I GLY* 2.9 22.0 + - - -
143I ALA 3.2 20.4 + - - +
144I ASP* 2.9 22.2 + - - +
181I ASN 4.0 10.5 - - - +
182I GLY* 2.7 32.5 + - - +
183I ILE* 3.9 9.6 - - + +
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Residues in contact with LYS 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PRO* 4.9 6.2 - - - +
243A LYS* 4.4 12.1 - - - -
136I ALA* 3.1 19.1 + - - +
137I GLN* 2.9 36.2 + - - +
139I LYS* 1.3 78.8 - - - +
141I ASP* 1.3 64.8 + - - +
142I GLY 3.4 1.0 + - - -
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Residues in contact with ASP 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PRO 5.8 1.8 - - - -
243A LYS* 3.8 22.2 + - - +
84I LEU* 4.7 9.0 - - + +
85I TYR* 2.6 43.1 + - + +
95I VAL* 3.8 19.8 - - - +
137I GLN* 2.9 30.9 + - - +
138I TYR* 2.9 10.9 + - - +
140I LYS* 1.3 85.5 - - - +
142I GLY* 1.3 56.2 + - - +
143I ALA 3.7 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