Contacts of the strand formed by residues 127 - 132 (chain B) in PDB entry 1X7O
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 LEU 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP 3.2 0.8 + - - -
126B PHE* 1.3 76.6 - - - +
128B GLY* 1.3 64.7 + - - +
150B LEU 4.3 9.0 - - - +
151B GLY 4.3 2.7 - - - +
152B ALA* 3.4 29.1 - - + +
153B HIS* 2.8 46.9 + - + +
223B PHE* 5.4 1.6 - - + -
227B THR* 3.4 23.3 - - + +
229B LEU* 5.4 2.2 - - + -
271B LEU* 4.0 26.2 - - + +
274B ALA* 4.5 18.8 - - + -
275B VAL* 5.6 1.6 - - + +
278B ARG* 3.8 27.1 - - - +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 4.1 17.9 - - - -
127B LEU* 1.3 77.5 - - - +
129B VAL* 1.3 70.8 + - - +
152B ALA* 4.8 0.2 - - - -
154B GLY 3.6 10.1 - - - -
227B THR 2.9 11.0 + - - +
228B LEU* 3.7 8.7 - - - -
229B LEU* 2.9 23.0 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLY* 1.3 79.7 - - - +
130B LEU* 1.3 60.7 + - - +
131B PHE* 5.3 0.4 - - - -
143B ILE* 4.0 12.8 - - + -
147B ALA* 4.8 10.8 - - + -
152B ALA* 4.9 1.8 - - + -
154B GLY 3.1 9.1 + - - +
155B LEU* 3.4 23.7 - - + -
156B ILE* 2.8 33.3 + - - +
228B LEU* 3.8 6.5 - - - +
229B LEU* 3.4 8.5 - - + +
231B ILE* 3.7 27.8 - - + -
271B LEU* 4.1 33.4 - - + -
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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
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129B VAL* 1.3 75.3 - - - +
131B PHE* 1.3 59.0 + - - +
132B ASP* 3.9 9.0 - - + +
156B ILE* 3.2 18.6 - - + +
158B ALA* 3.9 10.1 - - + -
191B VAL* 3.8 17.9 - - + -
228B LEU* 4.3 11.9 - - + -
229B LEU 2.9 6.9 + - - +
230B LEU* 3.7 21.1 - - + -
231B ILE* 2.9 29.1 + - - +
242B TRP* 2.8 68.0 - - + +
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Residues in contact with PHE 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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129B VAL* 4.2 0.8 - - + -
130B LEU* 1.3 71.0 - - - +
132B ASP* 1.3 62.7 + - - +
134B PRO* 3.2 39.8 - - + +
139B ASN* 3.8 27.4 - - + -
140B ILE* 4.0 12.8 - - + -
143B ILE* 3.5 28.9 - - + -
155B LEU* 4.3 11.2 - - + +
156B ILE 2.8 12.6 + - - +
157B VAL* 3.7 5.5 - - + -
158B ALA 3.1 20.4 + - - -
231B ILE* 3.6 16.4 - - + -
232B GLY 3.5 24.5 - - - -
233B ASN 4.5 0.2 - - - -
234B GLU* 3.6 21.3 - - - -
263B ALA* 4.0 11.7 - - + -
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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
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130B LEU* 3.8 5.7 + - + -
131B PHE* 1.3 68.5 - - - +
133B ARG* 1.3 107.3 + - - +
134B PRO* 3.4 0.6 - - - -
158B ALA 3.9 5.1 - - - +
231B ILE 3.0 17.8 + - - +
232B GLY* 4.1 0.8 - - - -
233B ASN* 3.3 20.3 + - - +
237B GLY 4.4 0.5 - - - +
238B LEU* 3.7 9.2 - - + +
239B SER* 3.0 24.2 + - - -
242B TRP* 3.1 34.8 + - + +
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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