Contacts of the strand formed by residues 391 - 398 (chain A) in PDB entry 4X8P
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 VAL 391 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLU* 3.7 37.7 - - + +
331A ILE 3.5 4.5 - - - +
332A THR* 3.6 27.4 - - + +
389A GLY 4.3 7.9 - - - +
390A ASP* 1.3 74.1 - - - +
392A LEU* 1.3 63.0 + - - +
393A GLY 4.0 0.3 + - - -
450A TYR 4.7 0.2 - - - -
451A LYS* 4.0 0.2 - - - -
452A ASN* 2.8 37.5 + - - +
453A GLY 4.6 1.0 + - - -
489A LYS* 3.9 17.3 - - + -
490A TYR* 3.6 28.9 - - + +
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Residues in contact with LEU 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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330A GLU* 3.2 9.0 - - - +
331A ILE 2.8 40.5 + - - +
333A VAL* 3.7 21.8 - - + -
344A LEU* 4.3 4.7 - - + -
366A TRP* 3.7 31.2 - - + -
386A TYR* 3.5 46.2 - - + -
390A ASP* 3.8 11.4 - - + +
391A VAL* 1.3 77.4 - - - +
393A GLY* 1.3 58.7 + - - +
394A PHE* 3.5 23.7 - - + -
450A TYR 3.3 1.1 - - - +
451A LYS* 3.8 14.4 - - + -
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Residues in contact with GLY 393 (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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328A TYR* 3.1 28.5 - - - -
329A PHE 3.8 2.2 - - - -
330A GLU* 4.5 2.5 - - - -
391A VAL 4.0 0.6 + - - -
392A LEU* 1.3 70.7 - - - +
394A PHE* 1.3 69.2 + - - -
395A TYR 4.2 0.4 - - - -
449A PHE* 3.4 7.1 - - - +
450A TYR* 2.8 36.7 + - - +
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Residues in contact with PHE 394 (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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328A TYR* 3.2 11.7 - - - -
329A PHE* 2.9 71.7 + + + +
331A ILE* 3.7 17.0 - - + -
344A LEU* 3.5 39.7 - - + -
345A GLY* 3.8 10.1 - - - -
346A TRP* 3.6 10.1 - - - +
366A TRP* 4.2 7.6 - + - -
392A LEU* 3.5 38.6 - - + -
393A GLY* 1.3 71.6 - - - -
395A TYR* 1.3 59.8 + - - +
448A ILE 3.9 1.6 - - - -
449A PHE* 3.4 33.9 - + - -
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Residues in contact with TYR 395 (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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326A ALA* 3.8 14.4 - - + +
327A TRP 3.4 10.5 - - - -
328A TYR* 3.9 13.0 - + + -
346A TRP* 3.5 10.3 + - - +
394A PHE* 1.3 73.7 - - - +
396A ILE* 1.3 62.1 + - - +
397A ASN* 3.5 39.1 + - + +
446A GLU* 4.4 8.9 + - + -
447A ILE* 3.6 2.3 - - - -
448A ILE* 2.9 68.3 + - + +
450A TYR* 3.9 12.8 - - + -
492A PRO* 6.2 0.2 - - + -
495A LEU* 3.9 29.4 - - + +
496A THR 3.6 21.5 + - - -
497A TYR* 4.3 10.5 - + + -
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Residues in contact with ILE 396 (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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322A VAL* 3.9 15.7 - - + -
326A ALA* 3.2 4.2 - - - +
327A TRP* 2.9 40.8 + - + +
346A TRP* 3.6 40.8 - - + -
395A TYR* 1.3 78.7 - - - +
397A ASN* 1.3 62.7 + - - +
398A LEU* 4.2 16.6 - - + -
446A GLU 3.3 10.3 - - - +
447A ILE* 3.8 14.6 - - + -
463A ILE* 3.8 16.4 - - + -
468A TYR* 3.7 35.9 - - + -
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Residues in contact with ASN 397 (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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325A GLY* 3.5 11.5 - - - +
326A ALA* 3.6 11.1 - - - +
395A TYR* 3.5 27.0 + - + +
396A ILE* 1.3 73.6 - - - +
398A LEU* 1.3 67.0 + - - +
399A PRO* 3.5 26.0 - - - +
444A GLY 4.2 5.9 + - - -
445A SER* 3.1 9.9 - - - -
446A GLU* 2.9 42.8 + - + +
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Residues in contact with LEU 398 (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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322A VAL* 3.6 39.3 - - + +
323A ARG* 3.4 26.0 - - - +
324A LYS* 3.3 9.3 - - - +
325A GLY 2.8 35.8 + - - +
396A ILE* 4.2 8.7 - - + -
397A ASN* 1.3 79.2 + - - +
399A PRO* 1.4 67.3 - - - +
445A SER* 4.4 5.4 - - - -
463A ILE* 3.8 32.8 - - + -
465A GLU* 6.3 1.3 - - - -
466A GLY 4.3 4.5 - - - +
468A TYR* 4.1 17.9 - - + -
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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