Contacts of the helix formed by residues 127 - 138 (chain B) in PDB entry 1XR2
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 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B MET* 5.1 1.1 - - - -
124B LEU* 3.6 18.9 - - + +
126B GLU* 1.3 71.7 - - - +
128B LYS* 1.3 60.2 + - - +
129B PRO* 3.3 9.8 - - - +
130B LEU* 2.9 44.5 + - + +
131B GLU* 3.0 27.6 + - + +
184B VAL* 3.6 29.0 + - - +
187B LYS* 4.0 16.0 - - - +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG* 6.3 0.4 - - - +
59B ASN* 3.7 12.8 - - - +
61B LEU 5.8 4.3 - - - +
62B SER* 6.2 1.1 - - - -
63B TYR* 5.8 7.5 - - - -
69B ASP* 4.2 37.5 - - + +
72B VAL* 5.2 9.1 - - - +
73B MET* 5.9 2.5 - - + -
84B TYR* 5.6 2.8 + - - -
90B TYR* 5.4 5.7 - - - -
126B GLU* 2.9 33.8 + - + +
127B ASN* 1.3 73.6 - - - +
129B PRO* 1.3 70.9 - - + +
131B GLU* 3.4 18.3 + - + +
132B ASP* 2.9 27.2 + - + +
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Residues in contact with PRO 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B SER* 5.0 0.5 + - - -
59B ASN* 3.6 31.2 - - + +
73B MET* 3.9 29.4 - - + -
127B ASN* 3.3 11.4 - - - +
128B LYS* 1.3 95.4 - - + +
130B LEU* 1.3 56.7 + - - +
132B ASP* 3.6 1.7 + - - +
133B TYR* 3.0 27.9 + - - +
145B PRO* 4.3 17.3 - - + +
147B VAL* 4.1 9.0 - - + -
184B VAL* 4.2 11.7 - - + -
188B LEU* 3.8 7.5 - - + +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN* 2.9 41.2 + - + +
129B PRO* 1.3 76.0 - - - +
131B GLU* 1.3 61.2 + - + +
133B TYR* 3.0 2.4 + - + +
134B LEU* 2.8 57.6 + - + +
187B LYS* 4.2 14.6 - - + +
188B LEU* 3.7 20.4 - - + +
191B ASN* 3.6 27.4 - - + +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLU* 3.5 28.6 - - - +
127B ASN* 3.0 20.8 + - + +
128B LYS* 3.4 23.3 + - + +
130B LEU* 1.3 78.2 - - + +
132B ASP* 1.3 57.8 + - - +
134B LEU* 3.5 7.4 + - - +
135B PHE* 3.0 27.0 + - - +
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.0 35.4 + - - +
58B SER* 4.6 1.3 - - - -
59B ASN* 2.5 39.8 + - - +
60B GLU 4.3 1.6 + - - -
61B LEU* 5.4 1.4 + - - +
128B LYS* 2.9 19.1 + - + +
129B PRO 4.0 3.1 - - - +
131B GLU* 1.3 76.2 - - - +
133B TYR* 1.3 64.7 + - - +
135B PHE* 3.3 6.0 + - - +
136B PHE* 3.0 48.0 + - - -
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Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B SER* 4.4 1.7 + - - -
129B PRO 3.0 19.6 + - - +
130B LEU* 3.0 4.9 + - + +
132B ASP* 1.3 76.5 - - - +
134B LEU* 1.3 73.1 + - + +
136B PHE* 3.4 3.1 + - - +
137B LYS* 3.1 43.2 + - + +
141B ILE 4.8 0.2 - - - +
142B GLU* 2.9 30.7 + - - -
143B THR* 3.4 42.4 - - - -
145B PRO* 4.3 4.9 - - + -
188B LEU* 3.7 17.7 - - + -
191B ASN* 3.4 25.6 - - + -
192B GLY 3.0 18.2 + - - -
193B CYS* 3.5 26.0 - - + -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 2.8 41.4 + - + +
131B GLU* 3.9 5.2 - - - +
133B TYR* 1.3 79.5 - - + +
135B PHE* 1.3 64.7 + - - +
137B LYS* 3.5 16.7 - - + +
138B SER* 3.1 24.3 + - - -
191B ASN* 3.7 33.2 - - + +
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN* 3.6 43.3 - - + -
42B ARG* 3.7 28.9 - - + -
43B MET* 4.4 13.2 - - + -
131B GLU 3.0 17.8 + - - +
132B ASP* 3.5 10.1 - - - +
133B TYR 3.2 0.2 - - - -
134B LEU* 1.3 77.1 - - - +
136B PHE* 1.3 84.8 + + - +
138B SER* 2.6 25.7 + - - -
139B LYS* 3.7 8.5 + - + +
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG* 3.6 39.5 - - + -
43B MET* 4.2 7.4 - - - -
46B VAL* 3.4 38.1 - - + -
58B SER* 3.7 21.5 - - - -
132B ASP* 3.0 48.6 + - - -
133B TYR 4.1 2.7 - - - +
135B PHE* 1.3 86.2 - + - +
137B LYS* 1.3 64.5 + - - +
139B LYS* 2.9 12.8 + - - +
141B ILE* 2.8 43.1 + - + +
143B THR* 3.6 12.1 - - + -
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B TYR* 3.1 45.3 + - + +
134B LEU* 3.5 21.1 - - + +
135B PHE 3.2 0.2 - - - -
136B PHE* 1.3 78.2 - - - +
138B SER* 1.3 53.9 + - - +
140B GLY* 2.7 25.0 + - - -
141B ILE 3.5 9.6 + - - +
142B GLU* 2.9 31.0 - - + +
191B ASN 3.4 19.0 + - - -
192B GLY* 4.9 2.0 - - - -
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU 3.1 11.6 + - - -
135B PHE* 2.6 27.5 + - - -
137B LYS* 1.3 75.9 - - - +
139B LYS* 1.3 56.5 + - - +
140B GLY 3.3 1.1 - - - -
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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