Contacts of the strand formed by residues 368 - 373 (chain B) in PDB entry 5D3V
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 LYS 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B ILE 3.9 0.7 - - - +
362B HIS* 3.4 2.8 - - - -
363B ASN* 2.8 36.9 + - + +
366B LYS* 3.6 44.6 - - + +
367B ASN* 1.3 78.3 - - - +
369B TRP* 1.3 62.7 + - - +
370B PHE* 5.2 4.8 - - + -
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Residues in contact with TRP 369 (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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282B SER* 4.1 11.1 - - - -
337B GLU* 4.4 7.4 - - + -
338B VAL 5.9 0.2 - - - -
339B GLU* 3.4 32.8 - - + -
349B HIS* 5.7 9.9 - + + +
360B LYS* 4.0 37.0 - - + +
361B ILE 3.3 11.4 - - - -
362B HIS* 3.2 60.4 + + + -
367B ASN* 4.3 8.2 + - - -
368B LYS* 1.3 76.5 - - - +
370B PHE* 1.3 66.9 + - - +
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Residues in contact with PHE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LYS* 3.7 39.5 - - + +
281B ILE 3.5 12.3 - - - +
282B SER* 4.2 8.5 - - - +
291B PHE* 4.0 12.3 - + - -
298B LEU* 5.1 0.4 - - + -
300B TYR* 4.2 17.0 - + - -
331B ILE* 3.9 22.9 - - + -
349B HIS 5.7 0.7 - - - -
360B LYS* 3.3 5.9 - - - +
361B ILE* 2.8 61.6 + - + -
363B ASN* 5.7 2.0 - - + -
368B LYS* 5.2 6.1 - - + -
369B TRP* 1.3 79.8 - - - +
371B VAL* 1.3 69.6 + - - +
372B CYS* 3.5 23.8 - - - -
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU 3.5 0.5 - - - +
280B LYS* 3.4 5.2 - - - -
281B ILE* 2.8 52.3 + - + +
341B VAL* 4.9 4.5 - - + -
349B HIS* 3.9 21.3 - - + +
350B SER* 4.8 6.3 - - - -
355B VAL* 4.2 28.7 - - + -
359B TRP 3.3 10.8 - - - +
360B LYS* 3.9 27.4 - - + -
370B PHE* 1.3 78.4 - - - +
372B CYS* 1.3 73.4 + - - +
373B MET* 5.0 0.4 - - + -
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Residues in contact with CYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 4.2 7.2 - - + -
279B LEU 3.4 4.9 - - - +
291B PHE* 3.9 18.6 - - - -
358B GLY* 3.0 4.0 - - - -
359B TRP* 2.8 64.4 + - + +
361B ILE* 3.7 20.4 - - - -
370B PHE* 3.5 29.8 - - - -
371B VAL* 1.3 75.0 - - - +
373B MET* 1.3 60.4 + - - +
374B ALA 4.3 0.2 - - - -
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Residues in contact with MET 373 (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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353A TYR* 3.9 28.2 - - + -
354A THR* 5.7 7.0 - - - +
278B LEU* 3.7 8.4 - - - +
279B LEU* 2.9 55.3 + - + +
281B ILE* 4.2 20.9 - - + -
354B THR 4.0 8.7 - - - +
355B VAL* 3.8 19.1 - - + -
356B THR* 3.0 48.9 - - - +
357B ASN 3.8 1.6 - - - +
371B VAL* 5.0 0.4 - - + -
372B CYS* 1.3 73.8 - - - +
374B ALA* 1.3 63.5 + - - +
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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