Contacts of the helix formed by residues 262 - 272 (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 HIS 262 (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 17.7 - - + +
251B ASN* 3.7 4.7 - - - +
253B ARG* 4.0 7.6 + - + -
259B ALA 4.9 0.7 - - - -
260B THR 2.8 12.8 + - - -
261B LEU* 1.3 78.0 - - - +
263B GLY* 1.3 68.4 + - - +
264B GLU* 3.3 2.0 - - - +
265B ILE* 3.1 1.9 + - + +
266B SER* 2.8 19.9 + - - -
291B CYS* 3.5 14.1 - - + -
293B MET* 3.6 10.6 - - + +
294B CYS* 3.6 11.4 - - - -
355B ASP* 2.7 55.8 + - - -
356B ILE* 5.0 3.1 - - + -
502B ZN 2.2 38.5 - - - -
503B ZN 3.8 6.7 - - - -
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Residues in contact with GLY 263 (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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233B ILE* 3.8 21.0 - - - +
234B GLY* 4.9 4.9 - - - -
249B GLY 4.1 2.8 - - - +
250B HIS* 3.8 1.3 - - - -
251B ASN* 3.5 28.5 - - - +
262B HIS* 1.3 73.9 - - - +
264B GLU* 1.3 61.3 + - - +
266B SER* 3.5 2.3 + - - -
267B THR* 2.8 32.7 + - - -
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Residues in contact with GLU 264 (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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233B ILE* 4.1 2.8 - - - +
235B GLY* 6.0 0.9 - - - -
263B GLY* 1.3 77.8 + - - +
265B ILE* 1.3 67.8 + - + +
267B THR* 3.3 9.1 + - - -
268B LEU* 3.1 28.1 + - + +
284B LEU* 4.1 24.9 - - + +
286B THR* 3.2 36.4 + - + +
288B LEU 3.6 2.8 - - - +
290B PRO* 3.4 30.1 - - + +
294B CYS* 3.5 33.5 - - + +
297B ALA* 6.2 0.2 - - + -
503B ZN 3.7 13.4 - - - -
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Residues in contact with ILE 265 (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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60A THR* 3.6 31.0 - - + +
65A ILE* 5.6 2.7 - - + -
93A MET* 4.6 8.1 - - - -
260B THR* 3.4 32.8 - - - +
261B LEU* 4.3 8.5 - - + -
262B HIS 3.1 5.7 + - - +
264B GLU* 1.3 74.8 - - - +
266B SER* 1.3 57.6 + - - +
268B LEU* 3.2 4.6 + - + -
269B GLU* 2.9 27.0 + - - +
293B MET* 3.9 17.0 - - + -
294B CYS* 3.8 26.0 - - - -
297B ALA* 3.8 28.3 - - + -
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Residues in contact with SER 266 (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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249B GLY* 4.6 0.2 - - - -
250B HIS 3.1 33.9 + - - -
252B MET* 3.8 13.0 - - - +
261B LEU* 3.9 21.0 - - - +
262B HIS 2.8 14.3 + - - -
263B GLY 3.7 2.5 - - - -
265B ILE* 1.3 75.4 - - - +
267B THR* 1.3 62.2 + - - +
269B GLU* 3.3 2.0 + - - +
270B ASN* 2.9 42.0 + - - +
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Residues in contact with THR 267 (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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235B GLY* 3.3 22.2 + - - +
236B CYS* 3.4 36.6 - - - +
237B LEU* 3.8 8.7 - - + +
247B GLY 3.9 5.6 - - - +
248B ARG* 4.2 2.3 + - - -
249B GLY* 3.5 14.1 + - - +
263B GLY 2.8 19.2 + - - -
264B GLU* 3.4 12.1 - - - -
265B ILE 3.2 0.2 - - - -
266B SER* 1.3 77.0 - - - +
268B LEU* 1.3 63.3 + - + +
270B ASN* 3.1 13.2 + - - +
271B CYS* 3.3 13.3 + - - -
284B LEU* 4.2 9.9 - - + -
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Residues in contact with LEU 268 (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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59A ALA* 4.0 10.6 - - + +
60A THR* 3.9 13.0 - - + -
93A MET* 5.7 0.2 - - - -
237B LEU* 4.2 22.0 - - + -
264B GLU* 3.1 16.0 + - + +
265B ILE* 3.6 8.3 - - - +
267B THR* 1.3 79.8 - - + +
269B GLU* 1.3 64.7 + - - +
271B CYS* 3.1 19.7 + - - +
272B GLY 3.7 2.3 + - - -
279B TYR* 4.3 12.9 + - + -
284B LEU* 4.9 10.3 - - + -
297B ALA* 3.8 29.2 - - + -
298B ILE 5.2 0.7 - - - +
301B TYR* 4.3 19.3 - - + -
303B ILE* 3.9 28.7 - - + -
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Residues in contact with GLU 269 (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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56A LYS* 5.2 3.5 + - - +
57A GLY 5.0 3.0 - - - +
58A SER* 2.7 36.8 + - - -
59A ALA* 3.3 4.3 + - - -
60A THR* 2.7 35.1 + - - +
61A LEU* 4.3 7.2 - - - +
261B LEU* 4.6 11.4 - - + -
265B ILE 2.9 14.4 + - - +
266B SER* 3.5 12.6 - - - +
268B LEU* 1.3 75.7 - - - +
270B ASN* 1.3 62.7 + - - +
272B GLY* 3.1 19.8 + - - -
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Residues in contact with ASN 270 (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 LEU 4.3 3.5 - - - +
247B GLY* 4.5 3.8 - - - -
248B ARG 2.7 32.4 + - - +
249B GLY* 3.5 10.9 - - - -
266B SER* 2.9 28.2 + - - +
267B THR 3.1 4.5 + - - +
269B GLU* 1.3 79.9 - - - +
271B CYS* 1.3 62.4 + - - +
272B GLY* 3.1 2.4 - - - -
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Residues in contact with CYS 271 (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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237B LEU* 3.8 31.4 - - + -
246B LEU* 3.4 15.6 - - - +
247B GLY* 3.6 24.5 - - - -
267B THR 3.4 15.0 - - - -
268B LEU* 3.1 13.4 + - - +
270B ASN* 1.3 77.4 - - - +
272B GLY* 1.3 63.0 + - - +
273B ARG 4.5 0.2 - - - +
274B LEU* 3.9 31.8 - - + +
279B TYR* 5.5 1.6 - - + +
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Residues in contact with GLY 272 (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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57A GLY 4.3 9.0 - - - -
59A ALA* 3.7 17.1 - - - +
268B LEU 3.7 0.8 + - - -
269B GLU 3.1 15.9 + - - -
270B ASN 3.1 2.1 - - - -
271B CYS* 1.3 84.0 - - - +
273B ARG* 1.3 65.6 + - - -
274B LEU* 3.5 7.1 + - - +
279B TYR* 4.0 1.9 + - - -
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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