Contacts of the helix formed by residues 252 - 257 (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 MET 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B GLU* 5.0 1.6 - - - +
250B HIS* 3.2 38.8 - - + +
251B ASN* 1.3 79.0 - - - +
253B ARG* 1.3 67.0 + - - +
254B PHE 3.3 2.5 - - - -
255B GLN* 3.5 24.0 - - + -
256B LYS* 2.8 47.0 + - + +
257B GLY 3.8 0.2 + - - -
258B SER* 3.8 4.7 + - - -
261B LEU* 2.9 33.0 + - + -
266B SER* 3.8 13.0 - - - +
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Residues in contact with ARG 253 (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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73A ARG* 3.5 22.8 - - - +
74A LEU 5.2 2.2 + - - +
79A TYR* 5.6 0.6 + - - -
101A TYR* 2.8 29.5 + - - -
251B ASN* 2.8 21.6 + - - +
252B MET* 1.3 69.8 - - - +
254B PHE* 1.3 78.1 + - + +
257B GLY* 2.8 30.5 + - - -
258B SER 3.0 25.9 + - - +
259B ALA* 3.6 10.7 + - - +
261B LEU 4.2 2.7 + - - +
262B HIS* 4.0 4.6 + - + -
354B GLU* 3.1 40.0 + - - +
355B ASP* 2.8 56.3 + - - +
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Residues in contact with PHE 254 (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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73A ARG* 3.4 39.5 + - - +
228B GLU 6.0 0.2 - - - +
229B GLY 4.1 12.6 - - - +
230B GLY* 4.2 7.4 - - - -
231B VAL* 3.7 30.7 - - + -
251B ASN* 4.5 0.2 + - - -
252B MET 3.3 0.2 - - - -
253B ARG* 1.3 91.9 - - + +
255B GLN* 1.3 71.1 + - - +
256B LYS 3.5 0.2 + - - -
257B GLY* 3.9 3.8 + - - -
344B PHE* 5.1 0.2 - + - -
348B ARG* 3.4 24.9 - - - -
351B ASP* 3.4 39.7 - - + -
354B GLU* 4.5 1.6 - - - -
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Residues in contact with GLN 255 (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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225B GLY* 3.9 9.3 + - - -
228B GLU* 2.9 49.7 + - + +
230B GLY* 3.9 15.3 - - - -
250B HIS* 3.5 8.9 - - - -
251B ASN* 3.3 26.3 + - - +
252B MET* 3.4 28.7 + - + +
253B ARG 4.1 0.2 + - - -
254B PHE* 1.3 81.0 + - - +
256B LYS* 1.3 60.0 + - + +
257B GLY 3.7 0.2 - - - -
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Residues in contact with LYS 256 (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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69A GLU* 5.1 2.1 - - - +
252B MET* 2.8 39.2 + - + +
255B GLN* 1.3 78.4 - - + +
257B GLY* 1.3 66.7 + - - +
258B SER* 3.1 8.7 - - - -
261B LEU* 3.9 23.8 - - + +
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Residues in contact with GLY 257 (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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69A GLU* 4.8 3.5 - - - +
72A GLY* 4.4 6.6 - - - -
73A ARG* 3.8 29.7 + - - +
253B ARG 2.8 13.7 + - - -
254B PHE 3.9 4.3 + - - -
255B GLN 3.7 1.4 - - - -
256B LYS* 1.3 79.6 - - - +
258B SER* 1.3 59.7 + - - +
259B ALA 4.0 1.0 + - - -
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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