Contacts of the helix formed by residues 127 - 135 (chain B) in PDB entry 1XV9
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 THR 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B THR* 4.0 24.3 + - + +
123B ARG 5.7 0.5 - - - -
124B HIS 5.3 2.4 + - - -
125B MET 2.8 14.1 + - - +
126B GLY* 1.3 72.7 - - - -
128B MET* 1.3 60.6 + - - +
129B PHE 3.1 7.3 + - - -
130B GLU* 3.3 25.9 + - - +
131B GLN* 4.4 7.1 + - - +
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Residues in contact with MET 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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124B HIS 3.7 15.7 + - - +
125B MET* 4.0 15.1 - - + -
127B THR* 1.3 80.0 + - - +
129B PHE* 1.3 92.9 + - + +
130B GLU 3.2 0.9 - - - -
131B GLN* 3.2 25.8 + - - +
132B PHE* 3.0 25.9 - - + -
167B PHE* 3.7 13.7 - - + -
168B MET* 3.7 41.3 - - + +
171B GLN* 4.1 23.8 - - + -
172B VAL* 6.1 2.2 - - + -
202B CYS* 5.6 3.8 - - - +
205B VAL* 4.4 12.3 - - + -
206B LEU 5.6 0.2 - - - +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY* 3.0 25.8 - - - +
127B THR 3.1 0.4 - - - -
128B MET* 1.3 96.1 - - + +
130B GLU* 1.3 68.2 + - - +
131B GLN 3.1 6.4 + - - -
132B PHE* 3.6 23.2 + + - +
133B VAL 5.2 0.2 + - - -
205B VAL* 3.4 38.4 - - + -
206B LEU* 3.5 37.2 - - + -
208B THR* 4.5 4.0 - - - -
209B THR* 3.2 29.6 - - + -
219B CYS* 3.3 45.0 - - + +
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Residues in contact with GLU 130 (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 GLY 5.8 0.2 - - - +
127B THR* 3.7 20.6 - - - +
128B MET 3.2 1.2 - - - -
129B PHE* 1.3 84.1 - - + +
131B GLN* 1.3 61.2 + - + +
132B PHE 3.5 0.7 - - - -
133B VAL* 4.0 17.8 - - - +
134B GLN* 4.7 0.7 - - - +
209B THR* 5.8 1.0 - - - +
218B LEU 5.1 1.0 - - - +
219B CYS* 4.7 0.8 - - - -
220B GLY* 3.1 36.4 + - - -
221B PRO* 4.7 3.1 - - + +
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Residues in contact with GLN 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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124B HIS 5.5 0.7 - - - +
127B THR* 4.5 4.6 + - - +
128B MET* 3.3 27.9 - - - +
129B PHE 3.1 0.4 - - - -
130B GLU* 1.3 80.4 - - - +
132B PHE* 1.3 61.2 + - - +
133B VAL 3.1 3.6 + - - -
134B GLN* 3.1 38.4 + - - +
135B PHE* 2.9 23.1 - - + -
167B PHE* 4.1 22.7 - - + -
171B GLN* 5.4 3.4 + - - +
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Residues in contact with PHE 132 (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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128B MET* 3.0 28.3 - - + -
129B PHE* 3.6 28.3 - + - +
130B GLU 3.5 0.6 - - - -
131B GLN* 1.3 77.9 - - - +
133B VAL* 1.3 60.8 + - - +
134B GLN 3.1 1.4 + - - -
135B PHE* 3.2 17.7 + - - -
160B HIS* 3.2 18.9 - - - -
164B ILE* 4.1 20.6 - - + -
167B PHE* 3.5 23.1 - + - -
168B MET* 3.9 28.5 - - + -
206B LEU* 5.2 2.9 - - + -
219B CYS* 3.9 26.5 - - + -
222B LEU* 3.8 7.0 - - + -
224B TYR* 3.5 28.0 - + - +
1001D CI2 4.9 4.0 - - + -
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Residues in contact with VAL 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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130B GLU 4.0 15.7 - - - +
132B PHE* 1.3 77.6 - - - +
134B GLN* 1.3 69.3 + - + +
135B PHE 3.2 1.3 - - - -
136B ARG 4.1 0.2 + - - -
137B PRO* 2.7 32.6 - - + +
142B PHE* 4.2 7.4 - - + -
219B CYS 4.8 1.8 - - - +
221B PRO* 3.1 39.5 - - + -
222B LEU* 3.7 17.9 - - + -
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Residues in contact with GLN 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 GLU 4.7 0.3 - - - +
131B GLN* 3.1 51.2 + - - +
132B PHE 3.1 1.4 + - - -
133B VAL* 1.3 86.3 - - + +
135B PHE* 1.3 69.9 + - + +
136B ARG* 3.3 15.2 + - - +
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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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131B GLN* 2.9 31.6 - - + -
132B PHE* 3.2 13.2 + - - +
133B VAL 3.2 3.2 - - - -
134B GLN* 1.3 88.2 - - + +
136B ARG* 1.3 97.7 + - - +
137B PRO 3.3 1.3 - - - -
160B HIS* 2.9 31.6 + - + +
163B ASP* 4.0 21.6 - - + +
164B ILE* 3.7 9.4 - - + -
167B PHE* 3.6 50.5 - + + -
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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