Contacts of the strand formed by residues 325 - 334 (chain B) in PDB entry 1JV1
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 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B VAL* 4.1 15.0 - - + -
77B LEU* 5.1 4.3 - - + -
279B VAL* 3.9 23.3 - - + -
291B VAL* 3.4 5.9 - - - +
292B VAL* 3.0 49.3 + - + +
323B PHE* 3.6 3.0 - - - +
324B ASN* 1.3 75.8 + - - +
326B GLY* 1.3 63.2 + - - +
327B ASN 3.4 0.2 + - - -
394B VAL* 4.8 3.8 - - + -
396B GLU* 6.3 0.9 - - - -
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Residues in contact with GLY 326 (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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279B VAL* 3.1 6.8 - - - +
280B VAL* 2.9 45.5 + - - -
282B LYS* 4.4 6.1 - - - -
289B VAL* 4.0 17.9 - - - -
290B GLY 3.6 6.3 - - - -
291B VAL* 4.8 1.1 - - - -
324B ASN 3.1 3.0 + - - -
325B ALA* 1.3 70.8 - - - +
327B ASN* 1.3 67.1 + - - -
328B ILE* 3.3 3.8 + - - +
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Residues in contact with ASN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 5.2 3.3 - - - +
278B LYS 4.4 2.9 - - - +
279B VAL* 4.2 7.9 - - - -
289B VAL* 3.9 4.2 - - - +
290B GLY 2.8 24.8 + - - +
292B VAL* 4.6 7.6 - - + -
301B VAL* 4.3 11.8 - - + +
325B ALA 3.4 2.4 + - - -
326B GLY* 1.3 71.2 - - - -
328B ILE* 1.3 61.7 + - - +
329B ALA* 3.0 21.5 + - - +
331B HIS* 3.3 18.5 + - - -
383B PHE* 3.6 21.0 - - - -
902B UD1 2.7 60.2 + - - +
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Residues in contact with ILE 328 (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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251B CYS* 4.9 2.1 - - - +
254B ASN* 4.9 2.5 + - - +
278B LYS* 3.5 45.6 + - + +
280B VAL* 3.6 40.4 - - + +
289B VAL* 5.5 0.2 - - + -
326B GLY 3.3 6.6 + - - +
327B ASN* 1.3 75.0 + - - +
329B ALA* 1.3 70.5 + - - +
330B ASN* 3.0 25.4 + - + +
397B VAL* 4.4 3.8 - - + -
402B GLU* 4.2 20.2 - - + +
403B PHE* 3.6 37.8 - - + -
902B UD1 4.2 3.8 - - - -
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Residues in contact with ALA 329 (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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108B LEU* 5.6 5.2 - - + +
249B VAL 4.4 0.4 - - - -
250B TYR* 3.4 4.2 - - - -
251B CYS* 3.2 38.0 + - + +
327B ASN* 3.0 18.1 + - - +
328B ILE* 1.3 79.1 - - - +
330B ASN* 1.3 65.5 + - - +
331B HIS* 3.8 15.3 - - + -
902B UD1 4.1 32.3 - - - +
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Residues in contact with ASN 330 (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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248B HIS* 3.0 28.5 + - + -
249B VAL 3.4 4.5 - - - -
250B TYR* 3.8 4.4 - - - +
251B CYS* 4.7 2.8 + - - +
254B ASN* 4.7 5.9 - - - +
257B VAL* 3.4 24.5 - - - +
258B LYS 4.8 1.9 + - - +
264B PHE* 3.9 4.2 - - + -
278B LYS* 2.9 52.0 + - + +
327B ASN* 4.4 0.2 + - - -
328B ILE* 3.0 36.6 + - + +
329B ALA* 1.3 79.5 + - - +
331B HIS* 1.3 65.1 + - - +
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Residues in contact with HIS 331 (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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108B LEU* 6.0 0.9 - - + -
247B ILE 3.7 0.3 - - - +
248B HIS* 3.5 6.8 + - - -
249B VAL* 2.8 41.3 + - + +
264B PHE* 3.8 4.5 - - - -
276B GLY 3.3 7.4 - - - +
277B ALA* 4.2 7.0 - - + -
327B ASN* 3.3 24.3 + - - -
329B ALA* 3.8 15.3 - - - -
330B ASN* 1.3 83.8 + - - +
332B PHE* 1.3 61.8 + - - +
333B PHE* 3.9 27.2 - - + -
382B VAL* 3.7 34.0 - - + +
383B PHE* 4.2 8.9 - + + +
386B PHE* 3.6 27.5 - + - -
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Residues in contact with PHE 332 (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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246B SER* 3.4 37.0 - - - -
247B ILE 3.5 6.5 - - - -
248B HIS* 4.8 1.1 - - + +
264B PHE* 3.7 12.3 - - + -
265B ILE* 4.3 20.9 - - + -
268B CYS* 3.6 45.5 - - + -
269B ILE* 3.9 18.4 - - + -
273B ALA 3.6 22.2 - - - -
274B ASP 4.1 2.2 - - - -
275B CYS* 3.2 4.1 - - - -
276B GLY 2.9 34.7 + - - +
331B HIS* 1.3 74.1 - - - +
333B PHE* 1.3 69.6 + - - +
334B THR* 3.8 22.0 - - + -
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Residues in contact with PHE 333 (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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226B LEU* 5.2 1.1 - - + -
227B TYR* 3.6 18.2 - + - -
246B SER* 4.0 0.5 - - - -
247B ILE* 2.9 34.1 + - + +
249B VAL* 3.6 32.1 - - + -
274B ASP 3.6 3.1 - - - -
275B CYS* 3.4 27.8 - - - -
331B HIS* 3.9 19.7 - - + -
332B PHE* 1.3 84.5 - - - +
334B THR* 1.3 63.9 + - - +
337B PHE* 3.9 11.2 - + + -
338B LEU* 4.0 34.3 - - + -
382B VAL* 4.5 6.5 - - + -
385B ILE* 3.6 18.8 - - + -
386B PHE* 3.8 14.4 - + - -
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Residues in contact with THR 334 (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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245B TRP* 3.2 40.9 - - + +
246B SER* 4.7 0.9 - - - +
247B ILE* 5.0 0.2 - - - -
273B ALA 3.6 23.1 - - - +
274B ASP* 3.2 18.5 + - + +
332B PHE* 3.8 9.2 - - + -
333B PHE* 1.3 76.9 - - - +
335B VAL* 1.3 65.6 + - - +
336B PRO* 3.7 10.4 - - - +
337B PHE* 3.2 22.1 + - - +
338B LEU* 3.1 19.9 + - - +
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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