Contacts of the strand formed by residues 345 - 356 (chain I) in PDB entry 6RAR
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 ILE 345 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344I PHE* 1.3 78.8 - - - +
346I GLU* 1.3 73.9 + - - +
347I VAL* 4.7 8.5 - - + -
379I TYR* 5.1 1.6 - - - +
410I ARG* 3.3 2.3 - - - +
411I ALA* 2.7 44.3 + - + +
412I ASP 4.3 7.6 - - - +
413I ALA* 3.7 7.9 - - + -
414I LYS* 3.7 31.6 - - + +
425I LEU* 3.9 15.0 - - + -
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Residues in contact with GLU 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344I PHE* 3.8 11.1 - - + -
345I ILE* 1.3 83.2 - - - +
347I VAL* 1.3 68.1 + - - +
374I ASP* 4.7 2.6 - - - +
408I GLU* 4.3 16.0 - - + +
409I ILE 3.1 9.4 - - - +
410I ARG* 2.8 50.8 + - + +
431I LYS* 4.0 12.6 - - - -
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Residues in contact with VAL 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I ILE* 4.7 9.6 - - + -
346I GLU* 1.3 80.9 - - - +
348I THR* 1.3 62.6 + - - +
349I LEU* 3.8 20.4 + - + -
374I ASP* 3.6 29.8 - - + +
379I TYR* 4.1 21.5 - - + +
407I VAL 3.5 1.0 - - - +
408I GLU* 3.4 4.0 - - - -
409I ILE* 2.8 36.7 + - + +
425I LEU* 3.7 35.0 - - + -
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Residues in contact with THR 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347I VAL* 1.3 73.2 + - - +
349I LEU* 1.3 69.4 + - - +
373I GLU 4.1 6.4 - - - +
374I ASP* 3.1 22.4 + - - +
406I LEU* 3.8 37.2 - - + +
407I VAL 3.2 11.2 - - - +
408I GLU* 4.0 18.1 - - + +
434I ARG* 4.7 10.5 + - + +
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Residues in contact with LEU 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347I VAL* 3.8 22.8 + - + -
348I THR* 1.3 80.6 - - - +
350I LYS* 1.3 59.6 + - - +
370I VAL* 3.6 32.1 - - + -
371I GLU 3.5 5.2 - - - +
372I GLY* 3.6 38.8 - - - +
373I GLU 4.3 0.7 - - - +
374I ASP* 4.6 3.6 - - + -
379I TYR* 3.8 21.5 - - + -
381I LEU* 3.8 18.4 - - + -
406I LEU* 3.3 8.9 - - - -
407I VAL* 2.7 39.1 + - + +
409I ILE* 4.8 3.1 - - + -
425I LEU* 4.7 2.2 - - + -
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Residues in contact with LYS 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349I LEU* 1.3 74.3 - - - +
351I VAL* 1.3 68.8 + - - +
352I VAL* 4.0 4.6 - - + +
370I VAL* 3.2 5.0 - - - -
371I GLU 2.8 39.0 + - - +
372I GLY* 4.9 1.5 - - - -
404I GLY* 4.7 8.5 - - - +
405I GLN 3.3 6.5 - - - +
406I LEU* 3.9 16.4 - - + -
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Residues in contact with VAL 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350I LYS* 1.3 75.0 - - - +
352I VAL* 1.3 62.0 + - - +
353I SER 3.9 19.3 - - - +
354I VAL* 4.1 17.3 - - + -
368I ILE* 4.4 12.1 - - + -
369I LEU 3.8 6.1 - - - +
370I VAL* 4.3 1.3 - - - -
402I LEU* 3.5 24.9 - - + +
403I LEU* 4.4 3.1 - - - +
404I GLY* 2.9 26.0 + - - -
405I GLN 2.8 18.6 + - - +
407I VAL* 4.1 12.8 - - + -
433I PHE* 3.7 29.8 - - + -
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Residues in contact with VAL 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350I LYS* 3.4 11.4 + - + +
351I VAL* 1.3 75.4 - - - +
353I SER* 1.3 68.3 + - - +
369I LEU* 2.9 16.5 + - + +
371I GLU* 4.1 36.3 - - + +
403I LEU* 2.9 16.9 - - - +
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Residues in contact with SER 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351I VAL* 3.9 1.3 - - - +
352I VAL* 1.3 83.7 - - - +
354I VAL* 1.3 67.7 + - - +
355I GLU* 3.2 13.4 + - - -
368I ILE* 3.4 4.7 - - - +
369I LEU* 2.9 63.3 + - - +
403I LEU* 3.7 7.8 - - - +
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Residues in contact with VAL 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351I VAL* 4.1 16.4 - - + -
353I SER* 1.3 79.8 - - - +
355I GLU* 1.3 68.2 + - - +
356I GLU 4.2 0.3 + - - -
365I LEU* 3.5 33.9 - - + -
367I ALA 3.8 2.7 - - - +
368I ILE* 4.3 5.6 - - + -
395I TYR 4.5 1.6 - - - +
396I TRP* 4.0 19.0 - - + -
399I ARG* 4.0 42.0 - - + +
402I LEU* 4.3 9.2 - - + -
403I LEU* 4.5 5.0 - - + +
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Residues in contact with GLU 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353I SER* 3.2 28.3 + - - +
354I VAL* 1.3 82.7 - - - +
356I GLU* 1.3 54.4 - - - +
365I LEU* 3.8 3.5 - - - -
366I GLY 2.7 29.6 + - - -
367I ALA* 2.8 29.4 + - + +
369I LEU* 4.0 30.2 - - + +
396I TRP* 3.9 3.1 - - - -
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Residues in contact with GLU 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355I GLU* 1.3 76.6 - - - +
357I GLY* 1.3 70.3 + - - +
358I THR* 5.0 2.9 - - - +
362I LYS* 3.8 11.8 - - - +
363I GLY* 2.7 33.2 + - - +
364I ARG 3.4 14.8 - - - +
366I GLY* 4.0 1.1 - - - -
396I TRP* 3.6 30.1 - - + -
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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