Contacts of the helix formed by residues 252 - 257 (chain B) in PDB entry 5WN1
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B ALA* 3.2 4.8 + - - -
251B ASP* 1.3 71.5 - - - +
253B PHE* 1.3 63.8 + - - +
255B HIS* 3.5 9.5 + - - +
256B LEU* 3.5 19.4 + - - +
285B PHE* 2.9 33.6 + - - +
287B LEU* 4.3 9.9 - - - -
292B LEU* 5.7 0.7 - - - -
295B LEU* 4.1 17.8 - - - +
298B SER* 2.6 33.9 + - - -
314B LEU* 3.8 13.6 - - - +
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Residues in contact with PHE 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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45B TYR* 3.7 17.3 - - - -
47B ASP* 4.4 1.8 - - - -
251B ASP* 3.2 3.0 + - - +
252B SER* 1.3 82.9 + - - +
254B ARG* 1.3 89.0 + - - +
256B LEU 3.3 2.3 + - - -
257B TYR* 2.9 58.0 + + + +
260B THR* 4.6 4.3 - - - -
263B ALA* 3.6 28.5 - - + -
281B ARG* 3.9 32.3 - - - +
285B PHE 5.8 0.4 - - - +
298B SER* 3.7 30.7 - - - +
300B ILE* 4.0 18.4 - - + -
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Residues in contact with ARG 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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215B HIS* 6.4 2.0 - - + -
218B ILE* 3.2 37.8 + - - +
219B ASP* 2.4 31.6 + - - +
251B ASP* 2.9 24.9 + - + +
253B PHE* 1.3 89.7 - - - +
255B HIS* 1.3 62.2 + - - +
257B TYR 3.3 20.9 + - - -
258B PRO* 3.0 45.7 - - + +
260B THR 2.8 25.2 + - - -
263B ALA* 5.0 4.2 + - - +
281B ARG* 3.5 18.8 - - - +
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Residues in contact with HIS 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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248A PRO* 3.8 29.6 - - + -
289A HIS* 3.1 27.8 + - + +
290A SER* 3.8 17.7 + - - -
250B ALA* 5.1 5.6 - - + +
251B ASP 2.9 18.0 + - - +
252B SER* 3.7 6.7 - - - +
254B ARG* 1.3 78.1 - - - +
256B LEU* 1.3 73.9 + - + +
258B PRO* 4.4 0.9 - - - +
292B LEU* 3.8 28.2 + - + +
295B LEU* 3.9 14.1 - - + +
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Residues in contact with LEU 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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289A HIS* 4.4 18.6 - - + +
290A SER* 3.5 25.4 - - - +
292A LEU* 6.1 0.9 - - + -
293A PRO* 4.4 6.6 - - + +
51B GLN* 5.1 10.3 - - - +
55B PRO* 6.5 0.9 - - + -
252B SER 3.5 10.9 + - - +
253B PHE 3.3 2.7 + - - +
254B ARG 3.2 0.4 - - - -
255B HIS* 1.3 97.5 - - + +
257B TYR* 1.3 82.9 + - + +
258B PRO* 3.5 4.4 - - - +
295B LEU* 4.0 21.3 - - + +
296B CYS 4.3 3.8 - - - +
297B ASP* 3.6 38.4 - - - +
298B SER* 3.9 6.7 - - - +
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Residues in contact with TYR 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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293A PRO* 4.1 27.4 - - + +
45B TYR* 6.1 0.2 - - - -
47B ASP* 5.8 0.2 - - - -
48B PRO* 3.6 35.2 - - + +
49B PRO 4.9 0.3 + - - -
51B GLN* 5.6 0.7 - - - +
253B PHE* 2.9 40.6 + + + +
254B ARG* 3.3 15.0 + - - -
256B LEU* 1.3 95.9 - - + +
258B PRO* 1.3 65.9 - - - +
259B ASN 2.9 4.8 + - - -
260B THR* 3.2 33.0 + - + +
297B ASP* 2.9 31.6 + - - -
298B SER 3.8 13.2 - - - -
299B LYS* 3.7 1.4 + - - -
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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