Contacts of the strand formed by residues 392 - 400 (chain B) in PDB entry 1JV5
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 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B LYS* 3.6 24.0 - - + -
339B LEU 3.5 12.8 - - - +
340B ARG* 3.5 21.5 - - + +
341B PRO* 5.2 2.9 - - - -
390B ASP 3.0 6.6 + - - +
391B SER* 1.3 75.9 - - - +
393B LEU* 1.3 60.6 + - - +
394B TYR* 3.5 9.9 - - + -
413B LEU* 3.7 10.0 - - - +
414B VAL 2.9 27.8 + - - +
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 4.0 9.9 - - - +
42A GLY* 6.1 1.1 - - - -
308B GLY 5.3 0.4 - - - +
337B VAL 3.9 0.5 - - - +
338B LYS* 3.5 3.1 - - - -
339B LEU* 2.7 54.4 + - + +
341B PRO* 5.4 2.4 - - + +
392B ALA* 1.3 72.5 - - - +
394B TYR* 1.3 62.2 + - - +
395B TYR* 3.2 40.8 + - + +
410B GLN 5.1 3.1 - - - +
411B GLY* 4.4 5.2 - - - -
412B THR 3.8 7.2 - - - +
413B LEU* 3.6 39.7 - - + +
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Residues in contact with TYR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLN* 3.0 9.8 - - - +
320B LEU* 3.9 16.4 - - + -
336B TRP* 4.9 3.8 - - + -
337B VAL 3.5 2.9 - - - +
338B LYS* 3.7 42.9 + - + -
348B ILE* 4.0 8.5 - - + -
364B PHE* 5.9 1.0 - + - -
381B MET* 3.5 27.8 - - + -
383B LEU* 3.6 23.2 - - + +
390B ASP* 2.8 34.8 + - - +
392B ALA 3.5 19.3 - - - -
393B LEU* 1.3 74.2 - - - +
395B TYR* 1.3 62.0 + - - +
412B THR* 2.9 36.7 + - - +
414B VAL* 3.6 24.9 - - + -
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 2.7 26.7 + - - -
42A GLY* 3.1 26.3 + - - -
44A VAL* 3.6 16.1 - - + +
306B GLN* 3.7 4.3 - - - +
336B TRP* 3.3 8.3 - - - -
337B VAL* 2.9 45.3 + - + +
339B LEU* 4.3 17.0 - - + -
345B LEU* 5.4 0.7 - - + -
393B LEU* 3.2 33.5 - - + +
394B TYR* 1.3 78.3 - - - +
396B CYS* 1.3 61.3 + - - +
408B TRP* 3.6 28.9 - + + -
409B GLY 3.2 24.7 - - - -
410B GLN 3.6 8.7 + - - -
411B GLY 3.6 6.7 - - - -
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Residues in contact with CYS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.8 10.9 - - - +
306B GLN* 3.6 21.0 - - - +
322B CYS* 2.0 52.7 - - + -
334B ILE* 4.5 3.8 - - + -
335B ASN 2.9 11.7 - - - +
336B TRP* 4.0 17.0 - - + -
395B TYR* 1.3 76.8 - - - +
397B ALA* 1.3 61.3 + - - +
408B TRP* 3.7 0.7 - - - -
409B GLY 3.0 24.6 + - - -
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Residues in contact with ALA 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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304B LEU* 3.8 4.5 - - - -
334B ILE* 3.6 2.7 - - - +
335B ASN* 2.6 42.2 + - + +
337B VAL* 5.5 0.9 - - + -
396B CYS* 1.3 76.1 - - - +
398B GLY* 1.3 57.2 + - - +
405B PHE* 3.8 27.8 - - + -
407B TYR 2.9 15.9 - - - +
408B TRP* 3.8 25.8 - - + +
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Residues in contact with GLY 398 (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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304B LEU* 3.6 11.1 - - - +
327B TYR* 5.4 4.0 - - - -
332B TYR* 5.9 0.2 - - - -
333B TRP 3.5 8.3 - - - -
334B ILE* 4.5 7.0 - - - -
397B ALA* 1.3 74.8 - - - +
399B GLN* 1.3 63.5 + - - -
404B TRP 3.5 4.4 - - - +
406B ALA 2.9 24.8 + - - -
407B TYR* 2.7 23.5 + - - -
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Residues in contact with GLN 399 (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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327B TYR* 5.3 1.9 - - - -
331B SER 4.6 1.2 - - - +
332B TYR* 3.3 37.4 - - - +
333B TRP* 3.1 49.5 + - + +
335B ASN* 4.9 0.2 - - - +
398B GLY* 1.3 73.9 - - - -
400B TYR* 1.3 70.9 + - - +
402B ASN* 4.9 12.5 - - - +
403B LEU 3.1 22.9 - - - +
404B TRP* 3.6 40.8 + - + +
407B TYR* 5.2 0.2 - - - -
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Residues in contact with TYR 400 (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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55A HIS* 5.9 0.2 + - - -
302B VAL* 4.5 10.6 - - + +
327B TYR* 4.5 18.6 - + + +
332B TYR* 3.4 45.7 + + - -
399B GLN* 1.3 78.8 - - - +
401B GLY* 1.3 71.7 + - - +
402B ASN 3.2 1.8 - - - -
403B LEU* 2.9 17.6 + - - +
406B ALA* 3.4 12.8 - - + +
407B TYR* 3.2 46.4 - + + -
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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