Contacts of the strand formed by residues 337 - 345 (chain A) in PDB entry 5INQ
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 337 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 5.0 0.7 - - + -
230A PHE* 5.0 1.1 - - + -
266A THR* 3.7 28.9 - - + -
267A VAL 4.7 0.2 - - - +
268A ILE* 4.1 5.8 - - + -
296A PHE* 5.1 1.9 - - - -
330A PHE* 3.5 47.8 - - + -
332A ALA* 3.4 20.5 - - + +
335A GLY* 3.3 2.0 - - - +
336A HIS* 1.3 79.4 - - - +
338A ILE* 1.3 66.1 + - - +
339A PRO* 3.5 9.6 - - + +
366A LEU* 3.9 33.9 - - + -
367A ASN 3.4 16.4 - - - +
368A VAL* 4.3 12.1 - - + -
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Residues in contact with ILE 338 (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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296A PHE* 4.3 20.4 - - + -
335A GLY* 3.5 32.5 - - - +
337A LEU* 1.3 78.3 - - - +
339A PRO* 1.3 74.1 - - - +
340A GLN* 3.1 22.3 + - - +
366A LEU* 4.3 1.3 - - - -
367A ASN* 2.9 35.4 + - + +
369A VAL* 4.1 16.8 - - + -
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Residues in contact with PRO 339 (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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293A ALA* 4.4 6.5 - - + -
296A PHE* 3.6 33.3 - - + -
297A LEU* 3.7 26.6 - - + +
330A PHE* 3.4 33.9 - - + -
337A LEU* 3.5 10.1 - - + +
338A ILE* 1.3 89.1 - - - +
340A GLN* 1.3 65.1 + - - +
364A CYS* 5.2 0.7 - - - -
365A THR 4.6 0.2 - - - +
366A LEU* 3.3 26.2 - - + -
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Residues in contact with GLN 340 (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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297A LEU* 4.1 8.8 - - - +
338A ILE* 3.1 40.0 + - - +
339A PRO* 1.3 76.3 + - - +
341A SER* 1.3 62.2 + - - +
365A THR* 2.7 25.5 + - - +
366A LEU 4.2 0.9 - - - -
367A ASN* 3.2 46.5 + - - +
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Residues in contact with SER 341 (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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297A LEU* 3.9 9.3 - - - +
339A PRO 3.9 0.6 - - - -
340A GLN* 1.3 80.3 - - - +
342A LEU* 1.3 61.5 - - - +
343A ASP* 4.1 13.8 + - - -
363A LEU* 4.4 2.3 + - - +
364A CYS* 3.4 10.4 - - - -
365A THR* 2.6 50.0 + - - +
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Residues in contact with LEU 342 (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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293A ALA* 4.6 2.0 - - + -
294A TRP* 3.7 40.8 - - + +
297A LEU* 3.6 15.2 - - + +
300A PRO* 5.4 2.0 - - + -
302A HIS* 2.9 24.9 + - - -
303A CYS* 3.6 23.0 - - - +
328A ILE* 3.6 30.7 - - + -
341A SER* 1.3 75.4 - - - +
343A ASP* 1.3 65.3 + - - +
362A LEU* 4.0 22.0 - - + -
363A LEU 3.4 15.5 - - - +
364A CYS* 3.7 9.2 - - + -
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Residues in contact with ASP 343 (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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302A HIS* 3.3 19.7 + - + -
303A CYS* 4.3 5.2 - - - -
341A SER* 4.1 17.5 + - - -
342A LEU* 1.3 81.4 - - - +
344A LEU* 1.3 67.6 + - - +
362A LEU* 3.5 4.8 - - - +
363A LEU* 2.8 51.9 + - + +
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Residues in contact with LEU 344 (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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153A TYR* 5.5 0.9 + - - -
302A HIS* 3.4 21.5 - - - +
303A CYS* 3.7 21.9 - - + +
305A TYR 3.9 14.6 - - - +
306A THR* 4.2 3.8 - - + -
343A ASP* 1.3 79.7 - - - +
345A VAL* 1.3 65.9 + - - +
347A LEU* 3.8 28.2 - - + +
360A TRP* 3.9 30.1 - - + +
361A GLY 3.3 7.6 - - - +
362A LEU* 3.7 24.2 - - + -
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Residues in contact with VAL 345 (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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127A ILE* 4.4 9.0 - - + -
129A TRP* 4.2 10.5 - - + -
149A CYS* 3.6 21.8 - - - -
153A TYR* 3.8 31.4 - - + +
343A ASP* 5.7 0.4 - - + -
344A LEU* 1.3 79.1 - - - +
346A GLY* 1.3 63.1 + - - +
347A LEU* 3.5 10.5 - - - +
348A GLU* 5.9 0.4 - - - -
360A TRP* 3.6 1.0 - - - -
361A GLY* 2.9 50.3 + - - -
362A LEU 4.2 2.2 - - - +
363A LEU* 4.0 21.1 - - + -
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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