Contacts of the strand formed by residues 250 - 255 (chain C) in PDB entry 1YAA
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 VAL 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C ALA 3.8 5.4 - - - +
221C PHE* 3.8 31.2 - - + -
242C VAL* 4.0 29.6 - - + +
244C LEU* 3.7 39.7 - - + +
248C SER 3.9 2.0 - - - +
249C PRO* 1.3 75.0 - - - +
251C PHE* 1.3 63.9 + - - +
252C VAL* 3.9 7.1 + - + +
269C ALA* 2.9 51.4 + - - +
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Residues in contact with PHE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C SER* 3.9 11.9 - - - +
118C PHE* 4.2 13.7 - + - -
119C PHE* 3.5 33.0 - + - -
218C ILE* 3.8 24.7 - - + -
219C ALA 3.2 5.2 + - - +
220C LEU* 3.3 21.5 - - + -
221C PHE 2.8 25.0 + - - -
249C PRO* 3.7 25.8 - - + -
250C VAL* 1.3 75.9 - - - +
252C VAL* 1.3 64.5 + - - +
253C CYS* 4.2 0.7 - - - -
269C HIS* 3.6 47.8 - + + +
5D LEU* 5.9 0.9 - - + -
6D PHE* 4.0 20.0 - + - -
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ILE* 3.4 32.5 - - + -
88C PHE* 3.9 19.7 - - + -
221C PHE* 3.5 7.0 - - + +
223C THR* 3.7 9.2 - - - +
240C VAL* 3.9 22.7 - - + -
250C VAL* 4.3 11.9 - - + +
251C PHE* 1.3 77.9 - - - +
253C CYS* 1.3 66.3 + - - +
254C GLN 3.6 3.7 + - - +
269C HIS* 2.9 55.9 + - - +
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Residues in contact with CYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLY* 4.2 5.5 - - - +
111C ALA* 3.6 20.2 - - + -
112C LEU* 3.1 51.8 - - + -
115C SER* 3.7 14.8 - - - -
220C LEU* 4.0 11.9 - - - -
221C PHE 3.0 11.4 + - - +
222C ASP* 3.7 5.7 - - - +
223C THR* 2.8 31.4 + - - +
252C VAL* 1.3 72.2 - - - +
254C GLN* 1.3 59.3 + - - +
269C PHE* 4.7 2.0 - - - -
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Residues in contact with GLN 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ALA* 3.1 35.3 + - - +
86C ILE* 3.7 17.8 - - - +
87C ILE* 3.9 16.8 - - + +
107C SER 4.0 0.2 - - - +
108C GLY* 4.0 7.7 + - - -
111C ALA* 4.4 0.2 - - - +
223C THR* 3.5 8.7 - - + +
226C GLN* 4.4 3.1 + - - +
252C VAL* 3.6 5.8 + - + -
253C CYS* 1.3 73.3 - - - +
255C SER* 1.3 65.7 + - - +
256C PHE* 3.5 21.6 - - + -
259C ASN* 6.3 0.2 - - - +
268C GLY* 3.4 4.2 - - - -
269C CYS* 2.9 69.8 + - - +
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Residues in contact with SER 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLY* 3.9 9.6 - - - +
223C THR 3.0 11.4 + - - +
224C ALA* 3.7 32.8 + - - +
253C CYS 5.3 0.4 - - - -
254C GLN* 1.3 79.3 - - - +
256C PHE* 1.3 68.2 + - - +
257C ALA* 3.1 14.6 + - - +
258C LYS* 4.6 0.9 - - - +
259C ASN* 3.7 16.8 + - - +
267C VAL 4.3 1.6 - - - -
907C PLP 2.7 27.5 + - - -
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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