Contacts of the helix formed by residues 334 - 348 (chain B) in PDB entry 1YSD
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 ASP 334 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B MET* 3.6 9.1 - - + +
309B GLY* 2.6 17.2 + - - +
332B VAL* 3.3 13.1 - - + +
333B ASP* 1.3 70.3 - - - +
335B GLU* 1.3 59.3 + - - +
336B ARG* 2.9 69.8 + - - +
337B CYS* 3.1 23.5 + - - +
338B LYS* 3.1 28.3 + - - +
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Residues in contact with GLU 335 (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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333B ASP* 3.3 15.2 + - - +
334B ASP* 1.3 70.5 + - - +
336B ARG* 1.3 66.9 + - + +
338B LYS* 2.9 40.0 + - - +
339B LYS* 2.9 43.2 + - + +
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Residues in contact with ARG 336 (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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212B GLN* 5.3 4.2 - - - +
215B MET* 3.9 20.0 + - - +
216B ASP* 3.0 32.5 + - - +
219B TYR* 3.5 53.7 + - + +
334B ASP* 2.9 30.7 + - - +
335B GLU* 1.3 78.5 - - + +
337B CYS* 1.3 60.9 + - - +
339B LYS* 3.1 18.0 + - - +
340B LEU* 3.2 23.4 + - - +
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Residues in contact with CYS 337 (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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215B MET* 4.3 9.0 - - - -
219B TYR* 4.1 17.3 - - - -
287B THR* 3.7 52.0 - - - +
309B GLY* 4.6 0.2 - - - -
310B GLU* 4.2 6.1 - - + -
334B ASP* 3.1 31.6 + - + +
336B ARG* 1.3 79.0 - - - +
338B LYS* 1.3 65.5 + - - +
340B LEU* 3.3 5.5 + - - +
341B MET* 3.0 25.3 + - - +
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Residues in contact with LYS 338 (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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310B GLU* 3.3 31.6 - - + +
312B VAL* 3.8 28.6 - - + +
313B ASN* 3.2 6.0 - - - +
333B ASP* 2.9 32.5 + - - +
334B ASP 3.1 8.9 + - - +
335B GLU* 2.9 44.0 + - - +
336B ARG 3.4 0.2 - - - -
337B CYS* 1.3 76.5 - - - +
339B LYS* 1.3 57.6 + - + +
342B LYS* 2.9 35.2 + - - +
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Residues in contact with LYS 339 (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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219B TYR* 5.4 1.2 + - - -
335B GLU* 2.9 41.5 + - + +
336B ARG* 3.1 24.5 + - - +
338B LYS* 1.3 77.4 - - + +
340B LEU* 1.3 62.7 + - - +
342B LYS* 3.5 17.1 + - - +
343B GLN* 3.1 27.1 + - - +
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Residues in contact with LEU 340 (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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219B TYR* 4.1 9.9 - - + +
222B ALA* 3.8 24.2 - - + -
223B LEU* 3.9 27.4 - - + -
226B TYR* 3.8 37.1 - - + -
232B PRO* 3.8 24.2 - - + +
336B ARG 3.2 15.3 + - - +
337B CYS* 3.7 5.8 - - - +
339B LYS* 1.3 80.1 - - - +
341B MET* 1.3 63.1 + - - +
343B GLN* 3.4 11.2 + - - +
344B PHE* 3.1 20.8 + - - +
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Residues in contact with MET 341 (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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231B VAL* 4.3 1.1 - - + -
232B PRO* 4.0 19.5 + - - +
233B ILE* 4.0 23.3 - - + -
288B LEU* 4.0 17.9 - - + -
310B GLU* 3.6 12.3 - - - +
313B ASN* 3.7 15.0 - - + +
337B CYS 3.0 16.6 + - - +
340B LEU* 1.3 74.2 - - - +
342B LYS* 1.3 65.9 + - - +
344B PHE* 3.2 21.1 + - + +
345B ILE* 2.9 37.8 + - + +
352B TRP* 3.5 43.3 - - + -
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Residues in contact with LYS 342 (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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313B ASN* 3.6 21.9 + - - +
338B LYS 2.9 18.1 + - - +
339B LYS* 3.8 18.5 - - - +
341B MET* 1.3 76.8 - - - +
343B GLN* 1.3 57.0 + - - +
345B ILE* 3.4 4.4 + - - +
346B ASP* 3.0 28.3 + - + +
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Residues in contact with GLN 343 (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 TYR* 3.5 17.0 + - + +
339B LYS* 3.1 19.1 + - - +
340B LEU* 3.6 10.0 + - - +
341B MET 3.2 0.2 - - - -
342B LYS* 1.3 75.9 - - - +
344B PHE* 1.3 59.4 + - - +
346B ASP* 3.2 7.1 + - + +
347B GLU* 2.9 61.7 + - + +
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Residues in contact with PHE 344 (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 TYR* 4.5 11.8 + + + -
230B GLY 4.1 2.5 - - - -
231B VAL* 3.9 35.0 - - + -
232B PRO* 3.4 35.0 - - + -
340B LEU 3.1 7.8 + - - +
341B MET* 3.2 25.5 + - + +
343B GLN* 1.3 78.0 - - - +
345B ILE* 1.3 60.8 + - - +
347B GLU* 3.9 8.2 - - - +
348B ARG* 2.8 68.8 + - + -
351B ASP* 4.2 18.6 - - + -
352B TRP* 3.9 24.0 - - + -
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Residues in contact with ILE 345 (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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313B ASN* 3.7 40.4 - - + +
341B MET* 2.9 36.7 + - + +
342B LYS* 3.8 4.0 - - - +
344B PHE* 1.3 78.9 - - + +
346B ASP* 1.3 64.6 + - - +
348B ARG 4.7 0.2 - - - +
349B PRO* 3.3 25.3 - - + +
352B TRP* 3.8 42.8 - - + +
353B PHE* 5.8 1.8 - - + -
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Residues in contact with ASP 346 (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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342B LYS* 3.0 15.7 + - + +
343B GLN* 3.3 12.1 - - + +
345B ILE* 1.3 82.3 - - - +
347B GLU* 1.3 64.8 + - + +
349B PRO* 3.3 6.8 - - - +
504B CA 2.5 50.2 - - - -
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 2.6 31.3 + - - -
343B GLN* 2.9 44.8 + - + +
344B PHE* 3.9 3.6 - - - +
346B ASP* 1.3 82.1 - - + +
348B ARG* 1.3 69.9 + - + +
349B PRO* 3.5 5.6 - - - +
504B CA 4.4 1.6 - - - -
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Residues in contact with ARG 348 (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 TYR* 6.0 3.6 - - - -
229B GLY* 2.9 32.3 + - - -
230B GLY* 4.3 2.0 + - - +
254B PHE* 3.4 32.0 - - - -
344B PHE* 2.8 46.5 + - + +
345B ILE 3.8 2.9 - - - -
347B GLU* 1.3 89.5 - - + +
349B PRO* 1.3 65.4 - - - +
350B GLN 3.3 2.7 - - - -
351B ASP* 2.6 39.6 + - + +
352B TRP* 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