Contacts of the strand formed by residues 348 - 357 (chain B) in PDB entry 1RY7
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 SER 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B ARG* 3.5 26.5 + - - +
253B PRO* 2.7 34.8 + - - -
254B ILE* 4.7 0.2 - - - -
255B LEU* 3.7 13.3 + - - +
340B LEU* 3.6 4.9 - - - +
341B ALA 3.0 31.0 + - - +
347B PHE* 1.3 75.3 - - - +
349B HIS* 1.3 75.7 + - - +
350B HIS* 5.0 2.8 - - - -
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Residues in contact with HIS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG* 5.8 0.2 - - - +
255B LEU* 3.8 4.7 - - - -
338B THR* 4.0 11.7 - - + +
339B CYS 3.3 14.8 - - - +
340B LEU* 3.9 16.5 - - + +
347B PHE* 5.9 1.4 - - - +
348B SER* 1.3 86.9 + - - +
350B HIS* 1.3 88.1 + - - +
351B SER* 4.5 2.8 + - - -
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Residues in contact with HIS 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG* 6.0 3.1 - - - -
255B LEU* 2.8 42.0 + - + +
256B GLN 3.3 12.5 + - - -
257B ALA* 4.0 11.6 - - - +
258B GLY 4.7 1.1 - - - -
259B LEU 3.2 31.0 - - - +
260B PRO* 3.8 6.3 - - + +
338B THR* 2.9 16.5 - - - +
339B CYS* 3.0 14.7 + - + +
348B SER* 5.0 3.4 - - - -
349B HIS* 1.3 100.1 + - - +
351B SER* 1.3 72.0 + - - +
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Residues in contact with SER 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PRO* 3.5 14.6 - - - +
290B HIS* 4.0 1.0 + - - -
336B GLU* 3.1 20.0 + - - -
337B TYR 3.1 8.3 - - - -
338B THR* 2.5 29.7 + - - +
349B HIS* 4.5 4.0 + - - -
350B HIS* 1.3 81.1 + - - +
352B ALA* 1.3 67.5 + - - +
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Residues in contact with ALA 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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260B PRO* 3.6 21.8 - - + +
261B ALA 3.6 27.8 - - - +
262B ASN* 3.6 7.9 - - - +
273B PHE* 4.8 4.7 - - + -
336B GLU* 3.3 4.0 - - - +
337B TYR* 2.7 34.8 + - + +
351B SER* 1.3 80.6 - - - +
353B TRP* 1.3 68.4 + - - +
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Residues in contact with TRP 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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262B ASN* 2.7 35.5 + - + +
263B GLN 2.8 31.9 + - - -
273B PHE* 3.8 7.2 - - - -
297B LYS* 5.4 5.2 - - - -
334B ALA 4.1 7.4 - - - -
335B GLY* 3.6 25.6 - - - -
336B GLU* 3.2 41.2 - - + +
337B TYR* 4.9 0.4 - - - +
352B ALA* 1.3 80.6 - - - +
354B LEU* 1.3 59.1 - - - +
355B VAL* 5.4 6.1 - - + -
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Residues in contact with LEU 354 (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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263B GLN* 3.2 13.5 - - + +
265B ALA* 4.9 2.2 - - + -
271B VAL* 3.4 45.1 - - + -
273B PHE* 3.7 19.0 - - + -
326B LEU* 4.1 6.3 - - + -
329B VAL* 4.6 2.2 - - + -
333B ASP* 3.1 40.4 - - + +
334B ALA* 2.8 27.4 - - - +
335B GLY 3.5 5.1 + - - -
337B TYR* 4.6 3.6 - - + +
353B TRP* 1.3 75.1 - - - +
355B VAL* 1.3 70.7 + - - +
356B VAL* 3.6 26.0 - - + -
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Residues in contact with VAL 355 (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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263B GLN 3.3 5.7 + - - +
264B THR* 3.1 23.0 - - + +
265B ALA 2.9 24.6 + - - -
334B ALA* 4.7 6.7 - - + +
353B TRP* 5.4 7.9 - - + -
354B LEU* 1.3 84.5 - - - +
356B VAL* 1.3 68.8 - - - +
357B LEU* 4.6 9.2 - - + -
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Residues in contact with VAL 356 (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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265B ALA* 2.9 18.6 - - + +
266B VAL 4.2 4.9 - - - +
267B LEU 4.5 1.6 - - - +
329B VAL* 3.4 26.9 - - + +
330B THR 3.3 6.7 - - - +
331B PHE* 3.1 49.9 - - + +
334B ALA* 4.6 11.1 - - + +
354B LEU* 3.6 22.4 - - + -
355B VAL* 1.3 79.8 - - - +
357B LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 357 (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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264B THR* 3.6 25.8 - - + -
265B ALA 3.2 20.0 + - - +
266B VAL* 3.5 6.2 - - + -
267B LEU* 2.8 27.7 + - - +
331B PHE* 3.3 6.7 - - - -
355B VAL* 4.6 9.2 - - + -
356B VAL* 1.3 76.4 - - - +
358B PRO* 1.3 78.4 - - + +
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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