Contacts of the strand formed by residues 388 - 397 (chain B) in PDB entry 3VBB
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 ALA 388 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382B TRP* 3.5 8.9 - - - -
383B PHE* 2.8 35.8 + - - +
386B SER* 3.3 11.4 - - - +
387B GLY* 1.3 81.2 - - - +
389B PHE* 1.3 66.3 + - - +
390B ARG* 4.1 25.4 - - + +
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Residues in contact with PHE 389 (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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158B ILE* 5.7 0.4 - - + -
162B CYS* 3.6 40.6 - - + -
360B HIS* 3.5 51.4 - + + +
380B GLU* 3.5 34.9 - - + +
381B ALA 3.1 10.5 - - - -
382B TRP* 3.8 22.2 - + + -
388B ALA* 1.3 75.3 - - - +
390B ARG* 1.3 77.0 + - - +
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Residues in contact with ARG 390 (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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170B HIS* 6.4 0.9 - - - -
316B PHE* 3.4 40.8 - - + -
317B ARG* 6.0 1.4 - - - +
380B GLU* 3.3 4.9 - - - -
381B ALA* 2.9 31.0 + - - +
383B PHE* 3.8 24.0 - - + -
386B SER* 5.7 4.9 - - - -
388B ALA* 4.1 22.2 - - + +
389B PHE* 1.3 90.1 + - - +
391B GLU* 1.3 63.8 + - - +
392B LEU* 3.3 1.6 + - - +
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Residues in contact with GLU 391 (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 LYS* 5.2 2.6 + - - -
378B ASP* 3.6 25.9 - - - +
379B LEU 4.3 0.7 - - - +
380B GLU* 3.7 19.5 - - + +
390B ARG* 1.3 71.8 - - - +
392B LEU* 1.3 61.9 + - - +
393B VAL* 3.6 23.0 + - - +
394B SER* 4.1 15.3 + - - -
429B THR* 4.9 2.9 + - - -
435B ARG* 2.8 41.7 + - - +
601B MG 3.4 23.4 - - - -
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Residues in contact with LEU 392 (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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316B PHE* 4.9 1.3 - - + -
352B TYR* 3.2 44.1 + - + +
357B ILE* 4.5 0.4 - - + -
379B LEU* 3.2 12.7 + - + +
381B ALA* 3.4 33.9 - - + -
383B PHE* 4.4 11.4 - - + -
390B ARG 3.3 1.0 + - - +
391B GLU* 1.3 80.5 - - - +
393B VAL* 1.3 66.3 + - + +
429B THR* 3.9 8.1 + - - +
430B MET 4.3 3.1 - - - +
432B ALA* 4.5 14.6 + - - +
435B ARG* 4.0 37.2 - - + +
436B THR* 4.3 5.4 - - - +
439B ALA* 4.1 11.9 - - + -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ILE* 4.5 7.9 - - + -
348B ALA* 4.2 21.3 - - + -
352B TYR* 3.7 18.8 - - + -
378B ASP* 3.1 5.5 - - - -
379B LEU* 2.9 43.1 + - + +
391B GLU* 3.6 9.1 - - - +
392B LEU* 1.3 83.2 - - + +
394B SER* 1.3 74.8 + - - +
428B ALA* 4.9 4.7 - - + -
429B THR* 3.1 15.9 - - - +
430B MET* 3.1 27.6 - - - +
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Residues in contact with SER 394 (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 LYS* 3.5 20.5 - - - +
377B LEU 3.4 4.5 - - - -
378B ASP* 3.3 19.1 - - - -
391B GLU* 4.1 13.0 + - - -
393B VAL* 1.3 75.6 - - - +
395B CYS* 1.3 61.7 + - - +
396B SER* 4.8 2.3 + - - -
427B ASN* 4.1 2.2 + - - +
428B ALA* 3.2 4.3 - - - +
429B THR* 3.0 38.2 + - - +
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Residues in contact with CYS 395 (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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341B PHE* 3.7 18.7 - - - -
344B MET* 4.0 25.6 - - - -
345B ILE* 3.9 30.7 - - + -
376B LYS* 3.2 6.5 - - - +
377B LEU* 2.7 42.8 + - + +
393B VAL* 5.0 0.2 - - + -
394B SER* 1.3 76.2 + - - +
396B SER* 1.3 65.3 + - - +
427B ASN 3.7 3.1 - - - -
428B ALA* 3.7 18.6 - - + -
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Residues in contact with SER 396 (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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341B PHE* 3.6 6.4 - - - -
344B MET* 5.0 0.3 - - - +
370B ASN* 5.5 0.7 + - - -
373B ALA* 4.6 7.7 - - - +
375B LYS 3.5 7.9 - - - -
376B LYS* 3.5 23.2 - - - +
394B SER* 4.8 1.9 + - - -
395B CYS* 1.3 78.7 + - - +
397B ASN* 1.3 63.3 + - - +
398B CYS* 4.0 7.8 + - - -
426B LEU* 3.3 8.5 - - - +
427B ASN* 3.0 47.6 + - - -
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Residues in contact with ASN 397 (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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337B SER* 2.8 33.6 + - - -
338B TRP* 3.4 45.9 - - + -
341B PHE* 3.5 10.9 - - + -
373B ALA* 3.7 1.0 - - - -
374B SER* 2.8 29.5 + - - -
375B LYS 3.4 6.9 + - - -
396B SER* 1.3 73.4 - - - +
398B CYS* 1.3 59.8 + - - +
399B THR* 2.8 29.9 + - - +
424B HIS* 4.7 0.2 - - - +
425B MET 3.7 1.0 - - - +
426B LEU* 3.6 17.1 - - + +
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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