Contacts of the helix formed by residues 254 - 258 (chain B) in PDB entry 1WUU
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 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ASN* 3.5 9.4 - - - +
49B GLN* 2.9 33.0 + - - -
247B ALA* 4.3 5.8 - - - -
252B LYS* 4.0 3.3 - - - +
253B GLU* 1.3 78.7 - - - +
255B LEU* 1.4 56.4 + - - +
256B ARG* 2.7 20.1 + - - +
257B GLU* 2.4 52.2 + - - +
258B VAL 4.0 0.2 + - - -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 3.8 17.0 + - + +
243B CYS* 3.6 28.5 - - + +
246B VAL* 4.1 7.2 - - + -
247B ALA* 3.3 38.3 - - + +
254B SER* 1.4 70.2 - - - +
256B ARG* 1.3 59.4 + - - +
257B GLU 2.9 2.2 + - - -
258B VAL* 3.1 32.1 + - + +
263B LEU* 6.3 0.2 - - + -
278B ALA* 3.8 33.7 - - + +
281B VAL* 3.9 27.8 - - + -
282B VAL* 3.9 9.9 - - + +
285B ILE* 4.6 5.0 - - - +
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Residues in contact with ARG 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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48B ASN 3.1 14.5 + - - +
49B GLN* 2.7 38.4 + - + +
50B GLY 3.8 4.8 + - - -
51B LEU* 4.6 12.8 - - - +
202B ASP* 2.9 28.4 + - - -
204B ARG* 2.9 68.1 + - + +
254B SER* 2.7 15.5 + - - +
255B LEU* 1.3 76.9 - - - +
257B GLU* 1.3 59.2 + - - +
258B VAL 3.3 4.1 + - - +
259B GLN* 4.8 4.7 - - - +
285B ILE* 4.1 28.6 - - - +
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Residues in contact with GLU 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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49B GLN* 4.5 2.4 - - - +
204B ARG* 3.3 30.7 + - - +
252B LYS* 3.5 48.3 + - + +
253B GLU* 4.2 22.4 - - + +
254B SER* 2.4 64.1 + - - +
256B ARG* 1.3 72.3 - - - +
258B VAL* 1.3 58.0 + - - +
259B GLN* 5.0 3.3 - - - +
262B GLU* 3.9 7.1 - - - +
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Residues in contact with VAL 258 (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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247B ALA* 5.3 0.2 - - - -
250B LEU* 4.7 19.3 - - + -
252B LYS* 4.3 16.2 - - + -
254B SER 4.3 2.5 - - - +
255B LEU* 3.1 41.5 + - + +
256B ARG 4.2 2.4 - - - +
257B GLU* 1.3 80.3 - - - +
259B GLN* 1.3 80.9 + - - +
262B GLU* 4.0 9.2 - - + +
263B LEU* 3.0 40.4 - - + +
282B VAL* 3.6 13.4 - - + +
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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