Contacts of the strand formed by residues 306 - 310 (chain B) in PDB entry 1YCH
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 ALA 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B LYS 3.4 2.0 + - - -
255B ALA* 3.4 19.6 - - + -
256B VAL 3.0 23.4 + - - -
304B ALA* 3.4 4.4 - - - +
305B ARG* 1.3 81.5 - - - +
307B VAL* 1.3 67.4 + - - +
308B LEU* 4.0 6.5 - - + -
338B VAL 3.2 8.1 - - - +
393B ILE* 3.8 28.5 - - + -
397B ILE* 3.9 10.3 - - + -
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 3.5 8.3 - - + +
258B ALA* 6.3 0.7 - - + -
301B ILE* 3.6 47.1 - - + -
304B ALA* 5.0 1.8 - - + -
306B ALA* 1.3 79.6 - - - +
308B LEU* 1.3 62.8 + - - +
309B VAL* 4.0 22.2 + - + +
329B LEU* 4.3 11.7 - - + -
337B LYS* 4.7 15.3 - - + -
338B VAL 3.0 10.2 + - - +
339B GLY* 3.3 18.2 - - - -
340B LEU 3.4 2.9 + - - +
359B LEU* 4.7 4.2 - - + +
364B ILE* 4.5 15.3 - - + -
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Residues in contact with LEU 308 (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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255B ALA* 4.7 4.9 - - + -
256B VAL 2.9 7.2 + - - +
257B ILE* 3.3 25.0 - - + +
258B ALA 2.9 25.6 + - - +
273B LEU* 4.0 24.9 - - + -
277B LEU* 4.3 14.4 - - + -
306B ALA* 4.0 16.2 - - + -
307B VAL* 1.3 88.4 - - - +
309B VAL* 1.3 61.4 + - - +
339B GLY* 4.9 1.1 - - - -
340B LEU* 3.3 20.2 - - + +
342B PHE* 4.2 10.1 - - + -
393B ILE* 3.8 31.0 - - + -
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ALA* 3.2 11.7 - - + +
307B VAL* 4.0 19.5 - - + -
308B LEU* 1.3 78.8 - - - +
310B GLY* 1.3 60.8 + - - +
322B VAL* 3.9 18.6 - - + -
325B LEU* 4.0 22.7 - - + -
326B LEU* 4.4 8.5 - - + -
329B LEU* 5.0 0.4 - - + -
340B LEU 3.0 7.3 + - - -
341B ALA* 3.2 23.7 - - - -
342B PHE* 3.3 4.6 + - - -
355B LEU* 3.8 26.0 - - + +
359B LEU* 4.4 22.2 - - + -
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Residues in contact with GLY 310 (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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258B ALA 3.0 9.7 + - - -
259B TYR* 3.3 19.3 - - - +
260B ASP 3.5 2.1 + - - -
266B THR* 3.9 5.8 - - - -
309B VAL* 1.3 77.4 - - - +
311B SER* 1.3 65.1 - - - -
322B VAL* 4.1 4.9 - - - +
342B PHE* 3.1 32.8 - - - -
355B LEU* 4.2 2.5 - - - -
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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