Contacts of the strand formed by residues 385 - 392 (chain A) in PDB entry 4X61
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 ARG 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A LYS 4.1 14.6 + - - +
355A ASP* 3.6 36.0 + - - +
356A THR 5.1 2.4 + - - -
357A ASN 3.9 7.4 + - - +
358A VAL* 3.3 40.0 - - + +
359A GLN* 2.7 30.3 + - - +
384A ARG* 1.3 78.4 - - - +
386A ILE* 1.3 58.3 + - - +
412A GLN* 5.8 0.4 - - - +
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Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.7 30.7 - - + -
358A VAL* 3.9 6.1 - - - +
359A GLN* 3.0 12.8 - - + +
361A LEU* 4.0 17.0 - - + -
375A SER 3.5 26.5 - - - +
376A LEU* 4.4 5.6 - - + +
379A ALA* 3.7 20.2 - - + -
384A ARG 4.0 0.9 + - - +
385A ARG* 1.3 82.0 - - - +
387A LYS* 1.3 60.5 + - - +
388A LEU* 3.8 31.6 - - + -
412A GLN* 3.0 37.2 + - - +
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Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL* 4.0 13.2 - - + +
359A GLN 2.6 12.7 + - - +
360A VAL* 3.4 10.6 - - + +
361A LEU* 2.7 33.4 + - - +
386A ILE* 1.3 73.0 - - - +
388A LEU* 1.3 62.1 + - - +
389A TYR* 3.7 19.1 + - + +
411A SER 5.8 3.8 - - - +
412A GLN* 4.2 10.5 - - - +
414A THR* 5.1 7.6 - - - +
427A GLU* 2.9 32.4 + - - +
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Residues in contact with LEU 388 (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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361A LEU* 3.6 26.9 - - + +
363A VAL* 4.2 17.5 - - + -
372A VAL* 4.0 13.0 - - + +
375A SER* 3.9 16.4 - - - -
376A LEU* 3.7 35.2 - - + -
386A ILE* 3.8 18.3 + - + +
387A LYS* 1.3 74.6 - - - +
389A TYR* 1.3 58.5 + - - +
412A GLN* 3.0 18.8 + - + +
413A VAL* 3.8 21.8 - - + -
414A THR* 2.8 34.1 + - - -
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Residues in contact with TYR 389 (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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360A VAL* 3.9 15.9 - - + -
361A LEU 2.9 7.6 + - - +
362A MET* 3.5 31.8 - - + -
363A VAL* 2.9 29.9 + - - +
387A LYS* 3.7 18.8 + - + -
388A LEU* 1.3 79.7 - - - +
390A ALA* 1.3 60.2 + - - +
391A VAL* 4.0 3.8 - - + -
413A VAL* 4.9 0.2 - - - -
414A THR* 3.2 35.2 - - + -
416A VAL* 4.4 1.3 - - + -
423A TRP* 3.6 25.1 - + + -
426A PRO* 3.3 35.1 - - + +
427A GLU* 2.7 34.9 + - + +
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Residues in contact with ALA 390 (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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363A VAL* 3.8 5.2 - - - -
366A ALA* 4.0 10.8 - - + -
372A VAL* 4.0 26.0 - - + -
389A TYR* 1.3 73.6 - - - +
391A VAL* 1.3 61.3 + - - +
392A GLU 3.8 0.5 + - - -
401A LEU* 4.3 9.4 - - + +
409A TRP* 5.1 0.4 - - + -
413A VAL* 4.0 13.0 - - + -
414A THR 2.7 14.0 + - - +
415A VAL* 3.6 11.4 - - + +
416A VAL 2.9 24.8 + - - +
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Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL 2.9 10.4 + - - +
364A LEU* 3.8 17.9 - - + -
365A GLY 2.7 31.2 + - - -
366A ALA 3.1 5.6 + - - -
389A TYR* 4.8 3.1 - - + -
390A ALA* 1.3 75.4 - - - +
392A GLU* 1.3 60.6 + - - +
416A VAL* 3.2 24.5 - - + +
418A SER* 3.5 23.1 - - - +
420A MET* 4.4 19.3 - - + +
423A TRP* 3.7 35.4 - - + -
701A SAM 4.7 1.8 - - + -
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Residues in contact with GLU 392 (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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324A TYR* 4.4 0.2 - - - -
365A GLY 3.5 2.3 - - - -
366A ALA 3.2 7.4 + - - +
367A GLY* 2.6 38.9 + - - +
390A ALA 3.8 0.2 + - - -
391A VAL* 1.3 75.3 - - - +
393A LYS* 1.3 62.8 + - - +
394A ASN* 2.7 37.6 + - + +
397A ALA* 4.4 0.9 - - + -
398A VAL* 3.5 9.8 - - + +
401A LEU* 3.7 21.1 - - + -
416A VAL 2.9 7.1 + - - -
417A SER* 3.5 8.5 - - - -
418A SER 3.0 23.1 + - - -
701A SAM 2.5 42.8 + - - -
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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