Contacts of the strand formed by residues 237 - 242 (chain A) in PDB entry 1T8U
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 LYS 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A GLN* 3.0 17.2 + - + +
155A ALA* 3.3 9.3 - - + -
156A ILE 3.0 25.6 + - - -
211A ILE* 6.3 0.9 - - + -
235A ASP 3.3 8.0 + - - +
236A THR* 1.3 77.8 - - - +
238A LEU* 1.3 60.3 + - - +
239A ILE* 5.4 0.2 - - - -
305A ARG 5.5 2.2 + - - -
306A GLN* 3.6 13.9 - - + +
329A PHE* 3.4 49.7 + - + +
330A LEU* 4.1 21.5 - - + +
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 3.6 4.9 - - + +
158A ILE* 4.1 29.6 - - + -
229A ILE* 4.3 14.6 - - + -
236A THR* 3.9 23.6 - - + +
237A LYS* 1.3 80.8 - - - +
239A ILE* 1.3 58.0 + - - +
240A VAL* 5.1 0.4 - - - -
298A TRP* 3.6 30.5 - - + -
302A PHE* 3.7 24.0 - - + -
306A GLN 2.8 13.6 + - - +
307A MET* 3.1 23.9 - - + +
308A LEU 2.8 31.7 + - - -
329A PHE* 3.8 2.8 - - - -
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Residues in contact with ILE 239 (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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155A ALA* 5.1 1.3 - - + -
156A ILE 2.9 12.5 + - - +
157A ILE* 3.4 10.8 - - + +
158A ILE* 3.0 25.6 + - - +
159A GLY 4.0 0.9 - - - +
168A LEU* 3.8 17.0 - - + -
172A LEU* 4.8 1.3 - - + -
213A MET* 4.0 26.0 - - + -
237A LYS 5.4 1.6 - - - +
238A LEU* 1.3 76.3 - - - +
240A VAL* 1.3 69.4 + - - +
241A VAL* 4.2 0.7 - - + -
308A LEU* 3.4 7.2 - - + +
310A VAL* 3.8 27.6 - - + -
326A VAL* 4.1 13.7 - - + -
329A PHE* 3.8 17.7 - - + -
330A LEU* 4.1 24.7 - - + -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 3.5 28.7 - - + -
159A GLY 3.4 7.2 - - - +
160A VAL* 3.5 29.4 - - + -
220A PHE* 4.2 17.0 - - + -
238A LEU 5.1 0.4 - - - -
239A ILE* 1.3 80.5 - - - +
241A VAL* 1.3 63.6 + - - +
242A VAL* 3.5 13.4 + - + +
307A MET* 4.3 6.1 - - + -
308A LEU 2.7 10.0 + - - +
309A PHE* 3.3 29.0 - - + -
310A VAL 2.8 25.2 + - - -
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Residues in contact with VAL 241 (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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157A ILE* 4.5 3.8 - - + -
159A GLY 2.7 15.4 + - - +
160A VAL* 2.9 25.7 + - - +
163A GLY* 3.2 31.9 - - - +
164A GLY* 4.0 12.3 - - - +
165A THR* 4.4 8.7 - - + -
168A LEU* 3.5 38.6 - - + -
239A ILE* 4.7 0.4 - - + -
240A VAL* 1.3 71.3 - - - +
242A VAL* 1.3 62.4 + - - +
310A VAL* 3.5 15.7 - - + +
312A GLY* 4.0 14.8 - - - -
315A LEU* 4.3 4.0 - - + -
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Residues in contact with VAL 242 (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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160A VAL* 4.1 8.3 - - + -
163A GLY* 4.7 0.2 - - - -
220A PHE* 5.8 0.4 - - + -
240A VAL* 3.5 26.7 + - + +
241A VAL* 1.3 73.5 - - - +
243A ARG* 1.3 58.0 + - - +
291A TYR* 3.9 13.9 - - + -
309A PHE* 4.5 2.7 - - + -
310A VAL 2.9 14.5 + - - +
311A SER* 4.2 0.2 - - - -
312A GLY* 2.7 34.7 + - - -
313A GLU* 4.3 0.9 - - - +
394A PHE* 3.8 21.8 - - + -
402A PHE* 3.7 28.3 - - + -
404A TRP* 3.8 21.5 - - + -
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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