Contacts of the strand formed by residues 348 - 353 (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 ARG 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B VAL* 4.0 7.6 - - - +
346B ASP 4.8 0.4 + - - +
347B SER* 1.3 75.8 - - - +
349B ALA* 1.3 68.3 + - - +
350B VAL* 3.7 11.9 - - + -
359B PRO* 4.8 2.5 - - - -
361B SER* 3.4 24.0 - - - +
363B ASP* 2.8 36.7 + - - +
429B LEU* 3.5 2.1 - - - +
430B ALA 3.0 33.7 + - - +
435B TRP* 3.4 54.7 + - + +
438B MET 5.0 1.0 + - - -
439B ASN* 5.7 1.0 - - - +
440B ASN* 2.7 45.8 + - - +
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Residues in contact with ALA 349 (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* 3.8 16.5 - - + +
341B VAL* 3.9 26.7 - - + -
348B ARG* 1.3 73.7 - - - +
350B VAL* 1.3 66.2 + - - +
359B PRO* 3.7 0.7 - - - +
360B LEU* 2.8 25.1 + - + -
361B SER* 3.1 11.0 + - - +
427B LEU* 4.6 2.2 - - + -
428B ILE 3.3 5.4 - - - -
429B LEU* 3.8 22.2 - - + -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG* 3.7 12.8 - - - -
349B ALA* 1.3 80.8 - - - +
351B LEU* 1.3 64.1 + - - +
357B ALA* 4.1 0.4 - - + -
358B MET 3.6 18.8 - - - +
359B PRO* 4.1 4.3 - - + -
427B LEU* 3.4 5.7 - - - +
428B ILE* 2.9 36.8 + - + +
435B TRP* 3.6 22.0 - - + -
440B ASN* 3.5 39.5 - - + +
444B CYS* 3.6 25.1 - - - -
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Residues in contact with LEU 351 (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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339B ILE* 4.3 9.6 - - + -
350B VAL* 1.3 73.0 - - - +
352B PHE* 1.3 71.5 + - - +
353B ARG* 3.7 22.6 + - + +
356B GLU 3.5 0.7 - - - +
357B ALA* 3.5 1.4 - - - -
358B MET* 2.6 55.7 + - + +
360B LEU* 3.9 18.9 - - + +
418B MET* 4.2 18.4 - - + -
424B ASP* 3.7 20.4 - - - +
426B CYS 3.3 17.3 - - - +
427B LEU* 4.2 4.7 - - + +
444B CYS* 4.4 1.8 - - - -
501B LEU* 3.4 25.6 - - + -
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Residues in contact with PHE 352 (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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350B VAL 4.1 0.6 + - - -
351B LEU* 1.3 75.2 - - - +
353B ARG* 1.3 53.6 + - - +
354B GLY 3.9 13.2 - - - -
355B LYS* 3.4 35.2 - - + -
356B GLU 3.5 15.7 - - - -
357B ALA 3.9 0.9 - - - -
424B ASP* 3.7 1.9 - - - -
425B GLU* 2.7 49.5 + - + -
426B CYS* 2.7 28.0 + - - +
441B GLN* 4.0 8.7 - - - -
444B CYS* 3.4 47.5 - - + -
445B GLU* 3.9 19.5 - - + -
448B ARG* 3.7 25.8 - - + -
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Residues in contact with ARG 353 (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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339B ILE* 6.1 0.2 - - - +
351B LEU* 3.7 17.1 + - + +
352B PHE* 1.3 71.5 - - - +
354B GLY* 1.3 62.2 + - - +
355B LYS 3.1 0.5 + - - -
356B GLU* 2.9 37.5 + - - +
358B MET* 3.9 29.1 - - + +
418B MET* 3.8 17.6 - - - +
419B PRO 3.0 25.1 + - - -
421B SER* 3.6 19.0 - - - +
423B GLU* 3.8 22.7 - - + +
424B ASP* 2.6 36.7 + - - +
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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