Contacts of the strand formed by residues 373 - 380 (chain B) in PDB entry 3VI4
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 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ASP* 5.4 1.6 - - - +
103B LEU* 5.3 0.2 - - + -
369B LEU* 3.3 36.8 - - + +
370B SER* 3.2 35.8 + - - +
371B GLU 4.0 0.2 - - - -
372B GLY* 1.3 80.6 - - - +
374B THR* 1.3 66.6 + - - +
410B ILE* 3.6 27.4 - - + -
411B THR 3.3 4.3 - - - +
412B SER* 3.9 13.9 - - - -
416B PRO* 4.9 1.3 - - + -
421B ASP* 5.2 0.2 - - - +
438B LEU* 4.6 10.1 - - + -
440B TYR* 4.4 17.3 - - + +
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Residues in contact with THR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PRO* 5.3 14.4 - - + -
315A ASP* 6.2 1.1 - - - +
369B LEU* 4.2 2.5 - - - -
372B GLY 4.3 0.4 - - - -
373B VAL* 1.3 80.5 - - - +
375B ILE* 1.3 67.1 + - - +
410B ILE* 3.4 10.9 - - - +
411B THR* 2.7 51.3 + - - -
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Residues in contact with ILE 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PRO 5.3 3.1 - - - +
315A ASP* 4.6 13.0 - - - -
366B ASN* 4.0 20.2 - - - +
369B LEU* 4.1 15.5 - - + -
374B THR* 1.3 79.4 + - - +
376B SER* 1.3 71.6 + - - +
377B TYR* 4.2 16.0 - - + +
393B ARG* 5.7 1.8 - - - +
408B ILE* 4.0 14.6 - - + -
409B SER 3.3 13.5 - - - +
410B ILE* 3.8 19.3 - - + -
423B PHE* 4.3 12.6 - - + -
425B ILE* 4.2 15.5 - - + -
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Residues in contact with SER 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 1.3 74.3 + - - +
377B TYR* 1.3 69.3 + - - +
378B LYS* 4.3 2.2 - - - -
407B GLU 4.4 0.7 - - - -
408B ILE* 3.5 10.0 - - - +
409B SER* 2.8 44.8 + - - +
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Residues in contact with TYR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B LEU* 3.7 34.3 - - + -
365B GLU 4.2 0.3 - - - -
366B ASN* 3.4 20.8 + - - +
375B ILE* 4.2 17.5 - - + -
376B SER* 1.3 80.1 - - - +
378B LYS* 1.3 65.0 + - - +
389B GLY* 3.6 25.2 + - - +
392B GLY* 3.3 30.6 - - - -
393B ARG* 3.3 47.8 + - + +
406B PHE* 5.0 2.2 - + + -
407B GLU 3.8 1.6 - - - -
408B ILE* 4.0 19.7 - - + -
425B ILE* 3.3 32.0 - - + +
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B SER* 6.1 2.5 - - - -
377B TYR* 1.3 76.7 - - - +
379B SER* 1.3 59.2 + - - +
380B TYR* 3.5 31.4 + - + +
387B GLY 3.3 12.6 - - - +
388B THR* 4.2 21.4 - - + +
392B GLY 3.4 4.7 - - - +
406B PHE* 3.3 5.0 - - - +
407B GLU* 2.8 51.2 + - + +
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Residues in contact with SER 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B LYS* 1.3 72.1 - - - +
380B TYR* 1.3 69.8 + - - +
381B CYS* 3.8 4.6 - - - -
386B ASN* 3.3 6.8 - - - +
387B GLY* 2.9 45.6 + - - +
391B ASN 3.5 1.4 + - - -
392B GLY 3.1 16.1 + - - -
394B LYS 3.0 26.5 + - - -
395B CYS* 4.1 3.8 - - - -
405B GLN 3.8 3.6 - - - -
406B PHE* 3.8 12.3 - - - -
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Residues in contact with TYR 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B LYS* 3.5 45.9 + - + +
379B SER* 1.3 74.4 - - - +
381B CYS* 1.3 64.0 + - - +
386B ASN* 3.1 32.8 - - + +
387B GLY 5.9 0.2 - - - -
395B CYS* 4.0 1.7 - - - -
404B VAL* 3.9 5.7 - - - +
405B GLN* 2.9 50.3 + - + +
407B GLU* 3.6 38.6 + - + -
504B NAG 3.3 34.3 - - - -
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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