Contacts of the strand formed by residues 338 - 344 (chain B) in PDB entry 3ZVU
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 HIS 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B LEU* 3.2 42.1 + - + +
221B MET* 4.3 5.8 - - + -
333B LEU 3.8 1.0 - - - +
334B VAL* 3.8 0.2 - - - -
335B CYS* 3.0 33.4 + - - +
336B SER 3.7 0.6 - - - -
337B SER* 1.3 115.1 + - - +
339B ILE* 1.3 67.6 + - - +
340B VAL* 4.8 2.2 - - + +
417B PHE* 3.1 38.4 - + + -
418B MET 3.3 5.6 - - - +
419B PRO* 3.6 31.5 - - + +
420B ARG* 3.8 3.6 - - - -
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Residues in contact with ILE 339 (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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332B ALA* 4.8 0.7 - - + -
333B LEU 3.4 8.5 - - - +
334B VAL* 4.3 11.7 - - + -
338B HIS* 1.3 78.3 - - - +
340B VAL* 1.3 64.6 + - - +
341B VAL* 4.1 18.2 - - + -
351B LEU* 4.3 15.9 - - + -
353B ARG* 6.1 0.2 - - - +
360B LEU* 4.2 7.0 - - + -
416B THR 3.7 0.9 - - - +
418B MET* 2.7 47.5 + - + +
420B ARG* 3.9 19.5 - - + -
424B ASP* 4.7 2.7 - - - +
427B LEU* 3.8 26.0 - - + -
501B LEU* 3.7 33.4 - - + -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 6.0 1.6 - - + -
220B LEU* 5.2 2.2 - - + -
286B TRP* 4.1 30.5 - - + -
290B PHE* 3.9 17.1 - - + -
331B VAL 3.8 0.5 - - - +
332B ALA* 3.3 2.8 - - - -
333B LEU* 2.7 53.1 + - + +
335B CYS* 6.4 0.4 - - - -
338B HIS* 4.8 4.5 - - + -
339B ILE* 1.3 76.3 - - - +
341B VAL* 1.3 64.3 + - - +
415B VAL* 3.8 20.6 - - + -
416B THR 3.3 11.4 - - - +
417B PHE* 3.8 24.0 - - + -
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Residues in contact with VAL 341 (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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330B VAL* 4.3 6.5 - - + -
331B VAL 3.3 5.6 - - - +
332B ALA* 4.0 18.2 - - + -
339B ILE* 4.1 6.0 - - + -
340B VAL* 1.3 80.1 - - - +
342B SER* 1.3 69.5 + - - +
343B ASN 4.6 0.4 - - - +
349B ALA* 3.9 24.0 - - + -
360B LEU* 3.7 50.7 - - + +
361B SER* 4.4 5.4 - - - -
414B GLU 3.7 1.1 - - - +
415B VAL* 3.1 6.6 - - - +
416B THR* 2.7 39.8 + - - +
427B LEU* 5.1 1.1 - - + -
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Residues in contact with SER 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 3.3 50.2 - - - +
294B PHE* 3.5 8.9 - - - -
329B ALA 3.7 2.1 - - - +
330B VAL* 3.5 2.1 - - - -
331B VAL* 2.8 38.8 + - - +
341B VAL* 1.3 75.1 - - - +
343B ASN* 1.3 58.8 + - - +
413B PRO* 3.2 22.2 - - - +
414B GLU 3.6 3.6 - - - -
415B VAL* 3.8 2.6 - - - +
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Residues in contact with ASN 343 (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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294B PHE* 4.6 0.2 - - - -
329B ALA 3.5 3.1 - - - +
330B VAL* 3.4 19.9 - - + +
341B VAL* 4.2 0.9 - - + -
342B SER* 1.3 76.2 + - - +
344B CYS* 1.3 63.8 + - - +
345B GLY 3.3 22.4 + - - +
347B SER 3.3 18.1 + - - +
361B SER* 3.6 30.6 + - - -
362B VAL 3.7 19.4 + - - +
364B HIS* 3.2 11.8 + - - +
413B PRO* 3.1 6.0 - - - +
414B GLU* 2.9 38.2 + - + +
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Residues in contact with CYS 344 (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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294B PHE* 3.7 21.5 - - + -
328B THR* 3.3 4.5 - - - -
329B ALA* 2.8 36.6 + - + +
343B ASN* 1.3 76.4 - - - +
345B GLY* 1.3 58.0 + - - +
364B HIS* 3.5 4.7 - - - -
398B ARG* 3.8 9.0 - - - -
399B SER* 3.3 40.2 - - - -
400B ILE* 4.2 3.6 - - + -
410B ILE 3.8 5.4 - - - -
411B PRO* 3.9 16.4 - - - -
412B GLU 4.5 1.3 - - - -
413B PRO* 4.5 2.2 - - + -
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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