Contacts of the helix formed by residues 267 - 272 (chain B) in PDB entry 1YGY
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 SER 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B GLU* 4.8 7.3 + - - +
259B PHE* 5.1 1.6 - - - -
264B CYS* 3.8 22.9 - - - -
265B THR 3.8 0.8 - - - -
266B ASP* 1.3 82.2 + - - +
268B PRO* 1.3 66.3 - - - +
269B LEU* 2.8 34.7 + - - +
270B PHE* 3.1 38.9 + - - +
271B GLU* 4.1 5.7 - - - +
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Residues in contact with PRO 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLU* 6.4 1.6 - - + -
240B ALA* 6.5 0.9 - - - -
243B ALA* 5.2 10.5 - - + +
266B ASP 3.9 4.5 - - - +
267B SER* 1.3 85.9 - - - +
269B LEU* 1.3 65.0 + - + +
270B PHE 3.0 2.1 + - - -
271B GLU* 3.4 20.4 + - + +
272B LEU* 3.8 13.8 - - - +
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Residues in contact with LEU 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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126A ARG* 4.0 1.0 + - - -
239B GLU* 3.7 42.2 - - + +
242B LEU* 4.2 13.7 - - + -
243B ALA* 3.8 32.5 - - + +
256B LEU* 4.0 16.4 - - + -
259B PHE* 5.1 2.7 - - + -
267B SER* 2.8 18.4 + - - +
268B PRO* 1.3 79.3 - - + +
270B PHE* 1.3 66.7 + - + +
271B GLU 3.2 0.4 - - - -
272B LEU* 3.2 36.0 + - + +
275B VAL* 4.0 26.5 - - + +
277B VAL* 4.9 1.2 - - + +
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Residues in contact with PHE 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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125A LEU* 3.3 38.1 - - + +
126A ARG* 3.1 32.7 + - - +
128A HIS* 4.8 2.2 - + + -
259B PHE* 3.7 25.6 - + - -
264B CYS* 3.7 24.9 - - - -
265B THR* 3.8 18.6 - - - -
266B ASP 4.7 0.2 - - - -
267B SER* 3.4 32.8 - - - +
268B PRO 3.0 1.6 - - - -
269B LEU* 1.3 82.9 - - + +
271B GLU* 1.3 70.5 + - - +
272B LEU 3.2 2.0 - - - -
277B VAL* 3.6 35.9 - - + -
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 4.6 1.0 - - - +
128A HIS* 3.2 30.6 + - - -
267B SER 4.1 3.6 - - - +
268B PRO* 3.4 17.6 + - + +
269B LEU 3.2 1.0 - - - -
270B PHE* 1.3 91.9 - - - +
272B LEU* 1.3 67.1 + - + +
273B ALA 4.1 1.4 + - - -
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Residues in contact with LEU 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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126A ARG* 3.0 16.9 + - - -
243B ALA* 4.0 24.7 - - + +
246B ILE* 3.9 28.5 - - + -
247B THR* 4.0 23.8 - - + +
268B PRO 3.8 16.6 - - - +
269B LEU* 3.2 9.9 + - + +
270B PHE 3.2 0.8 - - - -
271B GLU* 1.3 87.3 - - + +
273B ALA* 1.3 64.3 + - - +
274B GLN* 3.2 11.9 - - - +
275B VAL* 3.1 27.9 + - + +
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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