Contacts of the helix formed by residues 280 - 288 (chain A) in PDB entry 1XTB
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 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A MET* 4.1 5.6 - - - -
163A PRO* 4.8 0.2 - - - -
275A LEU* 3.3 22.1 + - - -
277A SER 2.9 9.8 + - - -
279A ILE* 1.3 76.9 - - - +
281A LEU* 1.3 62.1 - - - +
282A SER 3.2 3.4 - - - -
283A ILE* 2.9 28.5 + - - +
284A ALA* 3.1 10.7 + - - +
292A PHE* 3.8 7.5 - - - -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 3.7 33.1 - - + +
131A PHE* 4.1 20.0 - - + -
132A CYS* 3.7 23.1 - - - -
206A ILE* 4.2 11.9 - - + -
243A VAL* 4.6 3.1 - - + -
245A LEU* 3.7 26.0 - - + -
263A PHE* 4.0 21.8 - - + -
278A ALA 3.0 16.8 + - - +
279A ILE 3.2 1.6 - - - -
280A GLY* 1.3 76.3 - - - +
282A SER* 1.3 57.3 + - - +
284A ALA* 3.1 2.8 + - + +
285A LEU* 2.8 35.2 + - + +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 4.9 6.5 - - - -
153A ASN* 4.1 19.9 + - - +
163A PRO* 3.3 28.1 - - - +
167A THR* 4.4 1.8 - - - -
180A VAL* 3.9 7.6 - - - +
182A PHE* 3.7 17.4 - - - -
206A ILE* 4.3 16.4 - - - +
279A ILE 4.3 1.7 + - - -
281A LEU* 1.3 78.7 - - - +
283A ILE* 1.3 63.6 + - - +
285A LEU* 3.8 5.7 - - - +
286A HIS* 3.0 25.1 + - - +
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Residues in contact with ILE 283 (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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163A PRO* 3.8 32.3 - - + +
166A VAL* 3.6 41.5 - - + -
167A THR* 3.9 10.1 - - + -
170A LEU* 5.0 1.6 - - + -
275A LEU* 4.2 16.6 - - + +
280A GLY* 2.9 23.6 + - - +
282A SER* 1.3 75.4 + - - +
284A ALA* 1.3 60.6 + - - +
286A HIS* 3.1 2.9 + - - +
287A VAL* 2.9 47.5 + - + +
292A PHE* 4.0 15.7 - - + -
295A LEU* 4.4 7.0 - - + -
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Residues in contact with ALA 284 (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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128A MET* 4.9 1.1 - - + -
132A CYS* 3.5 22.5 - - - +
136A ARG* 4.8 0.3 - - - -
280A GLY 3.1 7.4 + - - +
281A LEU* 3.5 8.7 - - + +
283A ILE* 1.3 79.6 - - - +
285A LEU* 1.3 56.2 + - - +
288A GLY* 2.6 42.9 + - - -
289A PHE* 3.8 24.4 + - + -
292A PHE* 4.1 15.0 - - + -
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Residues in contact with LEU 285 (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 PHE* 4.4 11.2 - - + -
132A CYS* 3.4 37.7 - - + +
135A VAL* 3.9 24.2 - - + -
136A ARG* 2.9 32.6 + - + +
151A VAL* 4.1 24.5 - - + -
178A PRO* 3.3 10.3 - - + +
180A VAL* 5.2 1.6 - - + -
204A LEU* 4.6 3.4 - - + -
206A ILE* 3.8 29.2 - - + -
281A LEU* 2.8 24.0 + - + +
282A SER* 3.8 5.2 - - - +
284A ALA* 1.3 77.1 - - - +
286A HIS* 1.3 56.9 + - - +
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Residues in contact with HIS 286 (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 ARG* 3.2 9.9 + - - -
167A THR* 3.8 31.6 - - + -
171A LYS* 3.1 34.6 + - + +
174A SER* 3.1 56.1 + - - +
177A GLY* 4.0 1.3 - - - -
178A PRO 3.3 22.0 + - - -
179A ARG* 5.0 2.7 - - - -
180A VAL* 3.6 20.2 - - + +
282A SER 3.0 18.1 + - - +
283A ILE 3.6 3.1 - - - +
285A LEU* 1.3 78.5 - - - +
287A VAL* 1.3 65.9 + - + +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 4.0 5.6 + - - -
167A THR* 5.6 2.5 - - + -
170A LEU* 3.5 38.4 - - + +
173A TYR* 3.2 22.1 - - + +
174A SER 4.2 0.9 - - - +
283A ILE* 2.9 35.2 + - + +
286A HIS* 1.3 89.3 - - + +
288A GLY* 1.3 64.6 + - - +
291A ASN* 2.7 49.8 + - + +
292A PHE 4.4 3.4 - - - +
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Residues in contact with GLY 288 (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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132A CYS* 6.0 0.4 - - - -
136A ARG* 3.4 27.9 - - - +
284A ALA 2.6 23.9 + - - +
287A VAL* 1.3 81.8 - - - +
289A PHE* 1.3 64.1 + - - -
290A ASP* 3.4 3.1 - - - -
291A ASN 3.4 0.6 + - - -
292A PHE* 3.3 16.6 + - - +
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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