Contacts of the helix formed by residues 291 - 302 (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 CYS 291 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A MET* 3.7 15.0 - - + -
262B HIS* 3.5 13.0 - - + -
289B SER 3.8 1.6 + - - -
290B PRO* 1.3 73.6 - - - +
292B ASP* 1.3 62.1 + - - +
293B MET* 3.3 23.3 - - - -
294B CYS 3.5 3.1 - - - -
295B THR* 2.8 25.7 + - - -
314B PHE* 4.0 18.3 - - + -
316B SER* 3.4 12.3 - - - -
356B ILE* 5.3 2.9 - - + -
502B ZN 2.4 36.6 - - - -
503B ZN 4.1 3.4 - - - -
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Residues in contact with ASP 292 (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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96A GLY* 3.3 23.5 - - - +
99A ILE* 3.5 15.9 - - + +
100A MET* 4.3 9.7 - - + +
121A TYR* 4.3 4.8 + - + -
125A ARG* 3.0 41.7 + - - -
291B CYS* 1.3 76.1 - - - +
293B MET* 1.3 57.9 + - - +
295B THR* 3.6 7.3 - - - +
296B GLY* 3.0 21.0 + - - -
316B SER* 3.7 11.6 + - - -
317B LYS* 4.1 1.0 + - - +
318B GLY* 3.7 17.8 + - - -
321B TYR* 6.0 0.3 - - - -
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Residues in contact with MET 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.7 7.9 - - - -
93A MET* 4.1 11.6 - - + +
96A GLY 3.4 18.7 + - - +
97A ALA* 3.8 28.3 - - + +
100A MET* 4.1 13.6 - - + +
101A TYR* 5.3 2.2 - - - -
259B ALA 5.2 0.4 - - - +
260B THR* 3.4 38.4 - - - +
262B HIS* 3.6 34.1 - - + +
265B ILE* 3.9 15.9 - - + -
291B CYS* 3.2 8.1 - - - -
292B ASP* 1.3 78.4 - - - +
294B CYS* 1.3 64.2 + - - +
296B GLY* 3.1 3.5 + - - -
297B ALA* 3.1 19.6 + - - +
502B ZN 4.3 0.7 - - - -
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Residues in contact with CYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B HIS* 3.6 13.7 - - - -
264B GLU* 3.5 45.6 - - + +
265B ILE* 3.8 18.8 - - - -
290B PRO* 3.8 9.6 - - + -
291B CYS* 3.5 2.0 + - - +
293B MET* 1.3 77.2 - - - +
295B THR* 1.3 66.1 + - - +
297B ALA* 3.2 3.7 + - - +
298B ILE* 3.1 26.9 + - - +
502B ZN 2.3 34.3 - - - -
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Residues in contact with THR 295 (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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290B PRO* 3.5 14.0 + - - +
291B CYS 2.8 21.7 + - - -
292B ASP* 3.6 6.1 - - - +
294B CYS* 1.3 75.9 - - - +
296B GLY* 1.3 65.3 + - - +
298B ILE* 3.2 8.8 + - - +
299B ILE* 3.0 40.0 + - + +
318B GLY* 3.3 40.6 + - - +
321B TYR* 4.1 10.1 - - + -
322B LEU* 3.6 17.9 - - + -
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Residues in contact with GLY 296 (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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92A ASP* 3.3 23.2 - - - +
93A MET* 3.4 9.2 + - - -
292B ASP 3.0 14.5 + - - -
293B MET 3.1 5.3 + - - -
295B THR* 1.3 77.8 - - - +
297B ALA* 1.3 50.3 + - - +
299B ILE* 3.3 10.6 + - - +
300B MET* 2.8 35.7 + - - +
321B TYR* 6.2 0.4 - - - -
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Residues in contact with ALA 297 (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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93A MET* 3.7 31.8 - - + +
264B GLU* 6.2 0.7 - - + -
265B ILE* 3.8 15.5 - - + -
268B LEU* 3.8 22.6 - - + +
293B MET 3.1 6.0 + - - +
294B CYS* 3.2 9.2 + - - +
296B GLY* 1.3 74.5 - - - +
298B ILE* 1.3 65.8 + - + +
300B MET* 3.3 1.5 + - - +
301B TYR* 3.0 30.1 + - + +
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Residues in contact with ILE 298 (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 GLU* 5.5 1.1 - - + -
268B LEU* 6.0 0.4 - - + -
284B LEU* 3.6 27.6 - - + -
290B PRO* 4.5 6.7 - - + -
294B CYS 3.1 16.0 + - - +
295B THR* 3.5 7.4 - - - +
297B ALA* 1.3 76.5 - - + +
299B ILE* 1.3 58.4 + - - +
301B TYR 3.7 0.2 + - - -
302B GLY 3.0 22.3 + - - -
303B ILE* 3.1 47.7 + - + +
306B CYS* 3.7 36.8 - - + -
322B LEU* 3.9 21.1 - - + -
327B HIS* 3.5 11.3 - - + +
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Residues in contact with ILE 299 (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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92A ASP* 3.5 27.9 - - + +
295B THR* 3.0 24.1 + - + +
296B GLY* 3.5 9.9 - - - +
298B ILE* 1.3 73.2 - - - +
300B MET* 1.3 66.3 + - - +
302B GLY* 3.1 12.6 + - - -
321B TYR* 3.5 40.2 - - + +
322B LEU* 3.8 13.9 - - + -
325B ARG* 3.5 27.8 - - + +
327B HIS* 3.6 21.3 + - + +
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Residues in contact with MET 300 (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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62A HIS* 3.7 24.0 - - + +
91A CYS* 3.6 26.5 - - + -
92A ASP* 4.4 9.9 - - + +
93A MET* 4.1 23.6 - - + +
155A ASP 4.1 0.4 - - - +
156A ILE* 3.8 39.8 - - + +
157A GLY* 5.0 0.3 - - - -
280B LYS* 5.3 0.9 + - - -
296B GLY 2.8 21.2 + - - +
297B ALA 3.3 2.4 + - - +
299B ILE* 1.3 75.7 - - - +
301B TYR* 1.3 100.5 + - + +
302B GLY 3.3 0.3 + - - -
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Residues in contact with TYR 301 (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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53A ARG* 2.8 19.9 + - - -
59A ALA* 2.5 35.7 + - + +
60A THR* 5.4 0.4 - - + -
93A MET* 5.3 2.7 - - - -
154A GLU 4.3 6.1 - - - -
157A GLY* 3.9 22.4 - - - -
268B LEU* 4.3 20.2 - - + -
274B LEU 5.7 0.2 - - - -
279B TYR* 3.3 62.7 + + + +
280B LYS* 2.8 25.2 + - - +
297B ALA* 3.0 17.7 + - - +
300B MET* 1.3 102.7 - - + +
302B GLY* 1.3 62.5 + - - +
303B ILE* 4.2 8.5 - - + -
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR 4.5 0.4 - - - -
280B LYS* 3.6 23.5 - - - +
298B ILE 3.0 7.5 + - - -
299B ILE 3.1 12.1 + - - -
300B MET 3.2 1.0 - - - -
301B TYR* 1.3 78.1 - - - +
303B ILE* 1.3 65.9 + - - +
304B PRO* 3.0 12.0 - - - +
327B HIS* 4.1 7.4 - - - -
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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