Contacts of the helix formed by residues 129 - 140 (chain A) in PDB entry 1XB2
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A CYS 3.2 2.0 - - - -
128A PRO* 1.3 82.0 - - - +
130A HIS* 1.3 66.3 + - - -
131A ALA 3.4 2.0 - - - -
132A ASP* 3.1 25.9 + - - +
133A TYR* 3.2 17.4 + - - -
139B ASP* 3.5 13.5 - - - -
140B PHE* 3.5 12.1 - - - -
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Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLY* 1.3 71.0 - - - -
131A ALA* 1.3 67.6 + - + +
133A TYR* 3.0 14.9 + - - +
134A VAL* 3.0 26.0 + - + +
163A GLU* 4.8 2.8 + - - +
166A LEU* 5.3 3.1 - - + -
167A LEU* 3.7 33.8 - - + +
170A GLN* 3.6 32.2 + - - -
139B ASP* 2.8 21.6 + - - +
140B PHE* 3.5 21.0 - - + -
143B ARG* 3.3 51.7 + - - +
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A HIS* 1.3 84.9 - - + +
132A ASP* 1.3 59.6 + - - +
134A VAL* 4.0 4.9 - - - +
135A LYS* 3.0 32.2 + - - +
403A ASP* 4.8 12.8 - - - +
117B GLU* 6.2 0.4 - - - +
139B ASP* 3.1 14.2 + - - +
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A CYS* 3.8 17.9 - - + -
128A PRO* 3.4 17.1 - - - +
129A GLY* 3.1 27.5 + - - +
130A HIS 3.0 0.8 + - - -
131A ALA* 1.3 77.6 - - - +
133A TYR* 1.3 60.2 + - - +
135A LYS* 3.5 17.0 + - - +
136A ASN* 3.0 35.9 + - - +
139B ASP* 5.3 0.7 - - - +
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY* 4.8 1.3 - - - -
62A THR 3.3 22.2 + - - -
63A ILE* 4.3 18.6 - - + -
125A THR* 3.9 11.6 + - + -
126A ASP* 3.4 4.0 - - - -
127A CYS* 2.8 54.0 + - + -
129A GLY 3.2 19.8 + - - -
130A HIS 3.0 6.7 + - - +
132A ASP* 1.3 76.4 - - - +
134A VAL* 1.3 61.1 + - - +
136A ASN* 3.1 10.2 + - + +
137A MSE 2.9 27.9 + - - +
142A ALA 6.0 0.2 - - - -
144A LEU* 3.7 33.7 - - + -
167A LEU* 3.8 30.3 - - + -
171A ILE* 4.3 9.5 - - + +
140B PHE* 4.3 6.7 - + - -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A HIS* 3.0 35.4 + - + +
131A ALA* 4.0 5.8 - - - +
133A TYR* 1.3 74.3 - - - +
135A LYS* 1.3 65.0 + - - +
137A MSE 3.1 10.9 + - + +
138A ILE* 2.9 36.5 + - + +
167A LEU* 4.0 8.7 - - + -
170A GLN* 3.7 20.2 - - - +
171A ILE* 4.2 11.7 - - + -
355A GLN* 4.5 4.3 - - - +
403A ASP* 3.6 30.1 - - - +
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ALA* 3.0 20.9 + - - +
132A ASP* 3.6 17.9 + - - +
133A TYR 3.2 0.2 - - - -
134A VAL* 1.3 78.5 - - - +
136A ASN* 1.3 62.8 + - - +
138A ILE* 3.8 5.6 - - - +
139A THR* 2.9 41.2 + - - +
357A TYR* 3.2 61.7 + - + -
363A GLU* 3.3 15.2 + - - +
403A ASP* 5.6 1.3 + - - -
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Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR* 4.6 3.6 - - - +
127A CYS* 3.2 33.1 - - - -
132A ASP* 3.0 12.9 + - - +
133A TYR* 3.5 11.5 - - + +
135A LYS* 1.3 84.5 - - - +
137A MSE 1.3 56.6 + - - +
139A THR* 4.7 0.7 - - - -
140A GLY* 2.9 23.2 + - - -
141A THR* 3.2 24.4 + - - +
142A ALA* 3.7 34.1 + - - +
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Residues in contact with MSE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A TYR 2.9 13.2 + - - +
134A VAL* 3.5 17.9 - - + +
136A ASN* 1.3 76.6 - - - +
138A ILE* 1.3 80.8 + - + +
140A GLY 3.0 3.3 + - - -
142A ALA 4.9 0.4 + - - -
143A PRO* 4.9 12.8 - - + -
144A LEU 6.2 0.2 - - - +
170A GLN* 4.6 5.2 - - + +
171A ILE* 3.8 45.8 - - + +
355A GLN* 4.4 17.5 - - + -
421A ARG* 2.6 34.4 + - - +
435A LEU* 4.2 18.2 - - + -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 2.9 30.2 + - + +
135A LYS* 3.8 3.8 - - - +
137A MSE 1.3 86.1 - - + +
139A THR* 1.3 58.3 + - - +
355A GLN* 3.6 53.8 - - + +
356A VAL 4.0 3.4 - - - +
357A TYR* 4.1 10.8 - - + +
403A ASP* 4.0 15.7 - - + -
421A ARG* 3.0 24.8 + - - +
433A THR* 3.6 27.3 - - - +
434A GLY* 4.0 11.8 - - - +
435A LEU* 4.1 6.9 - - - +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 2.9 28.2 + - - +
138A ILE* 1.3 76.2 - - - +
140A GLY* 1.3 60.3 + - - +
141A THR* 3.0 24.9 - - - +
357A TYR* 4.9 4.5 - - - -
421A ARG* 3.6 8.5 - - - -
433A THR* 4.1 30.9 + - + +
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN 2.9 9.1 + - - -
137A MSE 3.0 5.1 + - - -
138A ILE 3.1 0.4 - - - -
139A THR* 1.3 76.8 - - - +
141A THR* 1.3 64.1 + - - +
142A ALA 3.4 2.7 - - - -
143A PRO* 3.3 15.6 - - - +
421A ARG* 3.1 28.0 - - - -
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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