Contacts of the strand formed by residues 380 - 387 (chain A) in PDB entry 5VXZ
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 GLN 380 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASP* 3.3 5.4 - - - +
325A PHE* 2.8 50.6 + - + +
326A ARG* 4.9 1.0 - - - +
373A VAL 4.5 0.2 - - - +
374A ILE* 3.1 61.6 + - - +
376A HIS* 3.4 20.6 + - + +
378A MET 3.4 3.4 + - - +
379A TRP* 1.3 76.3 - - - +
381A THR* 1.3 62.5 + - - +
382A ILE* 3.9 13.8 + - + +
395A VAL* 4.1 8.7 - - + +
396A ASN* 3.5 23.8 - - - +
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Residues in contact with THR 381 (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 GLU* 4.0 31.9 - - + +
323A PHE 3.6 1.6 - - - +
324A ASP* 2.7 25.6 + - - +
380A GLN* 1.3 71.9 - - - +
382A ILE* 1.3 66.4 + - - +
383A SER* 5.0 2.0 - - - +
394A LYS 3.7 0.5 - - - +
395A VAL* 3.4 6.4 - - - +
396A ASN* 2.9 44.3 + - - -
397A ARG* 4.7 11.5 + - + +
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Residues in contact with ILE 382 (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 GLU* 3.3 2.6 - - - +
323A PHE* 2.8 58.5 + - + -
325A PHE* 3.9 36.6 - - + -
334A LEU* 4.0 15.0 - - + -
348A LEU* 4.0 15.9 - - + -
355A LEU* 4.4 12.8 - - + -
374A ILE* 5.1 1.8 - - + -
380A GLN* 3.9 13.2 + - + +
381A THR* 1.3 80.4 - - - +
383A SER* 1.3 71.9 + - - +
384A VAL* 4.5 0.2 - - + -
393A ILE* 4.7 7.2 - - + -
394A LYS 3.4 5.6 - - - +
395A VAL* 4.3 14.6 - - + -
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Residues in contact with SER 383 (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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320A VAL* 6.5 0.4 - - - -
321A ALA 3.3 7.0 - - - -
322A GLU* 4.3 15.0 - - - +
381A THR* 4.3 2.4 - - - -
382A ILE* 1.3 74.7 - - - +
384A VAL* 1.3 68.6 + - - +
385A GLU* 4.5 8.5 + - - +
392A VAL 4.2 3.8 + - - -
393A ILE* 3.4 7.3 - - - +
394A LYS* 3.0 56.6 + - - +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.2 11.9 - - + +
320A VAL* 3.5 2.3 - - - +
321A ALA* 2.8 42.9 + - + +
323A PHE* 4.9 7.0 - - + -
335A LEU* 4.9 9.6 - - + -
346A ILE* 3.9 28.0 - - + -
348A LEU* 3.8 31.9 - - + -
357A LEU* 5.7 1.1 - - + -
382A ILE* 4.5 2.7 - - + -
383A SER* 1.3 77.7 + - - +
385A GLU* 1.3 66.8 + - - +
391A LEU* 5.0 3.6 - - + -
392A VAL 3.7 3.6 - - - -
393A ILE* 4.3 17.7 - - + -
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Residues in contact with GLU 385 (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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318A ARG* 2.8 35.0 + - - -
319A LEU* 3.5 9.9 - - - +
320A VAL* 3.9 11.7 - - + +
383A SER* 4.5 9.2 + - - +
384A VAL* 1.3 79.0 - - - +
386A GLU* 1.3 72.7 + - - +
387A LEU* 3.6 21.7 + - + +
391A LEU* 3.4 9.6 - - - +
392A VAL* 2.8 48.0 + - + +
394A LYS* 5.2 10.0 + - - +
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Residues in contact with GLU 386 (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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317A THR 4.4 3.1 - - - +
318A ARG* 3.5 34.8 + - + -
319A LEU* 3.0 40.5 + - + +
361A TYR* 4.4 3.5 + - - +
385A GLU* 1.3 77.8 - - - +
387A LEU* 1.3 59.4 + - - +
388A ALA 4.4 3.6 - - - +
390A ASN 3.7 6.1 - - - +
391A LEU* 3.9 15.0 - - + +
405A VAL* 5.7 4.5 - - + -
407A GLY 4.1 3.6 - - - +
408A ASP* 3.4 16.5 - - - +
409A LEU* 2.7 45.9 + - - +
410A PHE* 4.8 0.9 + - - -
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Residues in contact with LEU 387 (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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318A ARG* 4.6 8.7 - - - +
385A GLU* 3.6 31.2 - - + +
386A GLU* 1.3 74.6 - - - +
388A ALA* 1.3 64.8 + - + +
389A ARG 3.1 0.3 + - - -
390A ASN* 2.7 43.7 + - + +
392A VAL* 4.2 27.1 - - + -
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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