Contacts of the strand formed by residues 199 - 205 (chain B) in PDB entry 1YIT
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 TYR 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27660 A 6.1 0.7 - - - -
194B PHE* 5.4 0.7 - - - -
197B GLY 4.7 6.3 - - - -
198B GLU* 1.3 76.3 - - - +
200B ALA* 1.3 60.0 + - - +
266B ASN* 4.2 21.1 - - + +
267B LYS 3.5 2.5 - - - +
268B ARG* 3.5 44.4 - - + -
298B LYS* 6.1 0.4 - - + -
313B PRO* 3.9 3.5 - - - +
314B ALA* 2.9 34.8 + - + +
317B PRO* 4.8 8.5 - - + -
318B ASN 5.8 0.2 - - - -
319B ASP* 3.6 48.1 + - + +
320B GLN 4.1 10.1 - - - -
321B PRO* 4.8 6.9 - - + +
322B ARG* 2.9 28.2 + - - -
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Residues in contact with ALA 200 (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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194B PHE* 3.9 19.7 - - + -
198B GLU 3.9 0.6 + - - -
199B TYR* 1.3 75.1 - - - +
201B ASP* 1.3 64.7 + - - +
202B VAL* 3.9 1.8 - - + -
267B LYS* 2.7 49.1 + - - +
269B LEU* 4.0 21.8 - - + -
311B PHE* 4.4 12.6 - - + -
312B ARG 3.1 11.7 - - - +
313B PRO* 4.5 0.2 - - - -
314B ALA* 4.5 0.2 - - - -
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Residues in contact with ASP 201 (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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26B PHE* 3.8 4.5 - - - -
200B ALA* 1.3 71.7 - - - +
202B VAL* 1.3 61.2 + - - +
263B THR* 4.5 5.8 - - + -
264B GLU 3.6 5.6 - - - +
265B LEU* 3.4 12.8 - - - +
266B ASN* 3.1 24.1 + - - +
310B ARG 3.5 4.7 - - - +
311B PHE* 3.5 1.8 - - - -
312B ARG* 2.5 73.7 + - - +
314B ALA* 3.5 14.2 - - - +
315B VAL* 3.0 21.1 + - - +
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Residues in contact with VAL 202 (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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74B ILE* 5.2 0.2 - - + -
200B ALA* 4.5 2.7 - - + +
201B ASP* 1.3 76.2 - - - +
203B ALA* 1.3 68.5 + - - +
262B ARG 3.9 0.5 - - - +
263B THR* 4.5 0.9 - - - -
264B GLU* 2.8 37.1 + - + +
267B LYS* 3.8 31.0 - - + -
269B LEU* 5.9 0.2 - - + -
297B VAL* 4.6 9.4 - - + -
301B VAL* 3.4 34.1 - - + -
302B PRO* 4.3 5.2 - - + +
309B VAL* 4.2 9.6 - - + -
310B ARG 3.2 10.1 - - - +
311B PHE* 4.2 23.6 - - + -
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Residues in contact with ALA 203 (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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24B PRO* 3.6 20.5 - - + +
25B ARG 5.6 0.2 - - - +
26B PHE* 3.5 29.6 - - + +
201B ASP 4.0 0.6 + - - -
202B VAL* 1.3 75.0 - - - +
204B GLY* 1.3 58.5 + - - +
261B GLN* 5.2 2.7 - - + +
262B ARG 3.1 10.5 - - - +
263B THR* 3.8 11.7 - - - +
302B PRO* 4.3 2.5 - - - -
309B VAL* 3.5 7.1 - - - +
310B ARG* 3.0 30.5 + - + +
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Residues in contact with GLY 204 (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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24B PRO* 3.4 15.7 - - - +
203B ALA* 1.3 76.0 - - - +
205B VAL* 1.3 62.1 + - - -
206B THR 3.6 1.8 + - - -
260B HIS 3.5 1.0 - - - +
261B GLN* 3.3 1.2 - - - +
262B ARG* 2.8 35.3 + - - +
302B PRO* 3.7 20.5 - - - +
308B LEU 4.6 5.4 - - - -
309B VAL* 4.9 2.0 - - - -
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Residues in contact with VAL 205 (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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19B SER* 4.0 13.2 - - - +
21B SER 3.5 16.6 - - - +
22B GLU* 3.2 27.8 + - - +
24B PRO* 4.0 9.3 - - + +
204B GLY* 1.3 72.6 - - - +
206B THR* 1.3 60.3 + - - +
259B TYR* 3.6 50.7 - - + +
260B HIS 3.1 3.8 - - - +
261B GLN* 4.4 7.0 - - + -
303B GLY* 4.5 0.9 - - - -
307B ARG* 2.4 46.8 + - - +
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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