Contacts of the strand formed by residues 338 - 344 (chain A) in PDB entry 3RT0
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 HIS 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A TYR* 3.5 14.1 - - - -
220A LEU* 3.2 33.6 + - + +
225A GLU* 5.3 2.0 + - - -
333A LEU 3.9 0.7 - - - +
334A VAL* 3.7 0.9 - - - -
335A CYS* 3.1 37.2 + - - +
336A SER 3.7 1.0 - - - -
337A SER* 1.3 111.3 + - - +
339A ILE* 1.3 70.5 + - - +
340A VAL* 4.2 3.1 - - + -
417A PHE* 3.1 41.3 - + + -
418A MET 3.5 4.7 - - - +
419A PRO* 3.5 30.5 - - + +
420A ARG* 3.7 3.3 - - - +
370B ASP* 5.4 3.7 - - + +
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Residues in contact with ILE 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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332A ALA* 4.7 0.9 - - + -
333A LEU 3.4 9.0 - - - +
334A VAL* 4.4 11.9 - - + -
338A HIS* 1.3 78.7 - - - +
340A VAL* 1.3 64.1 + - - +
341A VAL* 3.9 13.2 - - + -
351A LEU* 4.0 18.6 - - + -
360A LEU* 3.9 23.3 - - + -
416A THR 3.8 0.7 - - - +
418A MET* 2.9 43.1 + - + +
420A ARG* 3.8 20.0 - - + -
424A ASP* 4.9 1.1 - - - +
427A LEU* 4.0 20.4 - - + -
501A LEU* 3.9 28.5 - - + -
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Residues in contact with VAL 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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215A LEU* 6.2 1.3 - - + -
220A LEU* 5.1 2.9 - - + -
286A TRP* 4.2 27.4 - - + -
290A PHE* 3.8 20.3 - - + -
331A VAL 3.8 0.5 - - - +
332A ALA* 3.2 2.8 - - - -
333A LEU* 2.8 50.9 + - + +
335A CYS* 6.5 0.2 - - - -
338A HIS* 4.8 6.3 - - + -
339A ILE* 1.3 80.3 - - - +
341A VAL* 1.3 63.8 + - - +
342A SER 4.3 0.2 + - - -
415A VAL* 3.8 20.2 - - + -
416A THR 3.4 10.5 - - - +
417A PHE* 4.0 24.2 - - + -
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Residues in contact with VAL 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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330A VAL* 4.2 7.6 - - + -
331A VAL 3.1 9.0 - - - +
332A ALA* 4.1 12.3 - - + -
339A ILE* 3.9 9.4 - - + -
340A VAL* 1.3 79.1 - - - +
342A SER* 1.3 68.7 + - - +
343A ASN 4.7 0.2 - - - +
349A ALA* 4.0 21.3 - - + -
360A LEU* 3.7 52.7 - - + +
361A SER* 4.4 5.2 - - - -
414A GLU 3.8 1.1 - - - +
415A VAL* 3.3 6.1 - - - +
416A THR* 2.8 38.3 + - + +
427A LEU* 5.2 0.7 - - + -
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Residues in contact with SER 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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290A PHE* 3.2 44.1 - - - +
294A PHE* 3.4 10.2 - - - -
329A ALA 3.8 1.4 - - - +
330A VAL* 3.6 1.7 - - - -
331A VAL* 2.9 40.4 + - - +
340A VAL 4.2 0.4 - - - -
341A VAL* 1.3 73.2 - - - +
343A ASN* 1.3 61.2 + - - +
413A PRO* 3.2 23.6 - - - +
414A GLU 3.6 3.8 - - - -
415A VAL* 4.1 3.2 - - - +
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Residues in contact with ASN 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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294A PHE* 4.5 0.2 - - - -
329A ALA 3.6 2.0 + - - -
330A VAL* 3.6 23.4 - - + +
341A VAL* 4.7 1.8 - - + -
342A SER* 1.3 78.3 + - - +
344A CYS* 1.3 66.3 + - - +
345A GLY 3.2 20.7 + - - +
347A SER 3.3 22.5 + - - +
361A SER* 3.5 26.6 - - - -
362A VAL 3.7 13.4 - - - +
364A HIS* 3.1 14.5 + - + -
413A PRO* 3.1 4.4 - - - +
414A GLU* 2.9 35.9 + - + +
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Residues in contact with CYS 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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294A PHE* 3.5 24.5 - - + -
328A THR* 3.3 5.5 - - - -
329A ALA* 2.8 37.1 + - + +
343A ASN* 1.3 75.2 - - - +
345A GLY* 1.3 58.3 + - - +
364A HIS* 3.7 3.8 - - - -
398A ARG* 3.8 8.0 - - - +
399A SER* 3.5 33.4 - - - -
400A ILE* 4.3 2.7 - - + -
411A PRO* 3.7 27.8 - - - -
412A GLU 4.2 3.1 - - - -
413A PRO* 4.3 2.0 - - + -
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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