Contacts of the strand formed by residues 349 - 359 (chain B) in PDB entry 5YDJ
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 GLY 349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B ASN* 4.2 3.2 - - - +
270B ALA 3.4 9.4 - - - -
272B VAL* 3.9 7.0 - - - -
303B ILE* 3.6 16.4 - - - +
344B ILE* 2.9 13.4 + - - +
345B HIS* 3.2 26.7 + - - +
347B PHE 3.7 1.0 - - - -
348B GLY* 1.3 80.0 - - - +
350B ASP* 1.3 63.8 + - - -
351B PRO* 3.5 1.9 - - - +
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Residues in contact with ASP 350 (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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269B ASN* 3.2 32.1 - - - +
270B ALA 2.7 19.1 + - - +
272B VAL* 3.4 16.7 - - - +
344B ILE* 4.2 0.9 - - - -
349B GLY* 1.3 69.9 - - - -
351B PRO* 1.4 73.8 - - - +
352B SER* 2.7 28.1 + - - -
353B ARG* 3.2 37.4 + - + -
354B VAL* 3.9 0.7 - - - +
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Residues in contact with PRO 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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340B VAL 5.1 0.2 - - - +
341B ARG* 3.8 47.2 + - + +
344B ILE* 4.1 13.2 - - + -
345B HIS* 4.2 30.7 - - + -
349B GLY 3.5 7.8 - - - +
350B ASP* 1.4 92.3 - - - +
352B SER* 1.3 56.6 + - - +
353B ARG 3.3 0.2 - - - -
354B VAL* 3.3 21.2 + - + +
378B LEU 4.9 2.9 - - - +
379B PHE* 5.4 1.7 - - - -
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Residues in contact with SER 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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341B ARG* 5.2 4.7 - - - +
350B ASP* 2.7 27.2 + - - -
351B PRO* 1.3 78.1 - - - +
353B ARG* 1.3 61.2 + - - +
354B VAL 3.5 1.1 - - - -
379B PHE 5.3 0.6 - - - -
380B GLN* 3.4 30.3 + - - +
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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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269B ASN 3.3 19.4 + - - -
271B ALA* 3.6 26.7 - - + +
272B VAL 2.8 23.0 + - - +
350B ASP* 3.2 34.0 + - + +
351B PRO 3.3 0.8 - - - -
352B SER* 1.3 83.2 - - - +
354B VAL* 1.3 58.2 + - - +
355B THR* 3.5 3.7 + - - -
380B GLN* 3.6 20.4 - - - +
381B ARG* 6.0 0.2 - - - +
637B ALA 4.8 2.2 - - - +
638B LYS* 3.5 35.7 + - - +
803B SO4 2.7 45.0 + - - -
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 3.4 15.3 - - + +
274B LEU* 4.1 32.1 - - + -
337B LEU* 5.2 1.8 - - + -
340B VAL* 4.2 16.6 - - + +
341B ARG* 5.7 1.6 - - - +
350B ASP 3.9 10.1 - - - +
351B PRO* 3.3 24.0 - - + +
352B SER 3.5 3.0 + - - -
353B ARG* 1.3 74.1 - - - +
355B THR* 1.3 59.5 + - - +
356B LEU* 4.3 4.3 - - + -
378B LEU 4.4 7.6 - - - +
379B PHE* 3.5 24.1 - - + +
380B GLN* 2.8 29.1 + - - +
381B ARG 3.6 2.8 + - - -
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Residues in contact with THR 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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272B VAL 2.7 12.2 + - - -
273B MET* 3.5 4.2 - - + -
274B LEU* 2.9 26.3 + - - -
353B ARG 4.0 3.1 + - - -
354B VAL* 1.3 72.1 - - - +
356B LEU* 1.3 72.4 + - - +
357B PHE* 3.7 2.0 + - + -
380B GLN* 5.0 0.2 + - - -
381B ARG* 3.4 28.9 + - + +
383B ILE* 4.0 19.3 - - + -
636B PHE* 4.3 0.7 - - + -
637B ALA* 3.1 50.9 + - + +
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Residues in contact with LEU 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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274B LEU* 3.6 18.6 - - + +
276B ILE* 5.0 4.5 - - + -
337B LEU* 3.5 29.4 - - + -
354B VAL* 4.3 3.1 - - + -
355B THR* 1.3 74.4 - - - +
357B PHE* 1.3 56.5 + - - +
366B VAL* 3.8 24.5 - - + +
369B HIS* 3.8 25.1 - - + -
379B PHE* 3.5 53.8 - - + -
381B ARG 3.0 9.3 + - - +
382B ALA* 3.4 1.3 - - - -
383B ILE* 2.8 30.5 + - - +
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Residues in contact with PHE 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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273B MET* 3.5 32.8 - - + -
274B LEU 2.9 23.7 + - - +
275B TRP* 3.1 57.6 - + + -
276B ILE 3.0 22.5 + - - -
296B LEU* 3.9 19.7 - - + -
304B VAL* 4.9 1.6 - - + -
355B THR* 4.3 2.0 - - + +
356B LEU* 1.3 77.2 - - - +
358B GLY* 1.3 57.6 + - - +
366B VAL* 4.0 5.5 - - - +
383B ILE* 3.4 28.9 - - + -
385B GLN* 4.6 3.8 - - - +
607B VAL* 5.1 4.0 - - + -
608B PHE* 3.6 23.6 - + - -
633B TRP* 4.3 20.6 - + - -
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Residues in contact with GLY 358 (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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275B TRP* 3.5 11.1 - - - -
276B ILE 3.2 16.4 - - - -
357B PHE* 1.3 76.3 - - - +
359B GLU* 1.3 59.9 + - - -
362B GLY 3.8 10.3 - - - -
363B ALA* 3.5 8.2 - - - +
366B VAL* 4.0 1.4 - - - +
383B ILE 3.4 6.0 + - - +
385B GLN* 3.0 29.3 + - - +
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Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TRP* 3.7 14.4 - - + -
276B ILE 4.0 1.6 + - - -
278B GLY* 3.4 13.6 + - - +
291B TYR* 5.4 1.8 + - - +
358B GLY* 1.3 75.4 - - - +
360B SEB 1.3 94.6 + - - +
361B ALA 3.2 0.2 + - - -
362B GLY* 2.8 22.6 + - - -
363B ALA 3.4 1.7 - - - +
385B GLN* 3.2 22.9 - - + +
386B SER* 4.0 2.3 - - - -
600B HIS* 3.1 29.7 + - - -
601B GLY* 3.3 22.0 + - - -
603B GLU* 3.2 22.9 - - - +
604B ILE* 3.6 15.3 - - + +
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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