Contacts of the helix formed by residues 244 - 251 (chain C) in PDB entry 4PS1
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 PHE 244 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241C ASN* 3.6 25.1 - - + -
242C HIS 3.3 10.8 - - - -
243C ASN* 1.3 71.9 - - - +
245C ALA* 1.3 65.0 + - - +
246C LYS 3.2 2.0 - - - -
247C ALA* 3.2 11.5 + - + -
248C ARG* 3.0 38.0 + - - +
257C ILE* 3.8 15.3 - - + -
258C ARG 3.9 6.1 - - - +
259C ASP* 2.9 8.3 + - - +
260C ARG* 3.5 21.8 - - + -
316C SER* 3.4 24.9 - - - -
317C HIS* 3.5 27.8 - + - -
324C TYR* 4.3 8.5 - - + -
325C GLY 3.5 21.1 - - - -
326C THR* 3.8 16.6 - - + -
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Residues in contact with ALA 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ASN* 3.0 22.5 + - - +
244C PHE* 1.3 78.6 - - - +
246C LYS* 1.3 62.7 + - - +
248C ARG* 3.3 24.6 + - - +
249C GLU* 3.1 22.7 + - - +
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Residues in contact with LYS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ASN 4.9 1.2 + - - +
244C PHE* 3.2 0.8 - - - +
245C ALA* 1.3 77.1 - - - +
247C ALA* 1.3 59.4 + - - +
249C GLU* 3.0 33.0 + - - +
250C LYS* 2.9 57.9 + - + +
288C THR* 5.7 1.1 - - + -
326C THR* 3.7 11.9 + - - +
327C ASP* 3.7 24.0 - - + -
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C PHE* 3.2 13.9 + - + +
246C LYS* 1.3 76.7 - - - +
248C ARG* 1.3 62.0 + - - +
250C LYS 4.5 0.2 - - - +
251C VAL* 3.1 29.1 + - - +
254C LEU* 3.9 8.3 - - + +
257C ILE* 4.0 16.2 - - + -
326C THR 3.0 20.6 + - - +
327C ASP 3.5 11.0 - - - -
328C GLY* 3.5 21.1 - - - +
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Residues in contact with ARG 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C PHE* 3.0 15.4 + - - +
245C ALA* 3.3 32.7 + - - +
247C ALA* 1.3 77.5 - - - +
249C GLU* 1.3 61.6 + - - +
251C VAL 4.8 1.7 - - - +
254C LEU 3.4 13.5 - - - +
255C HIS* 3.5 38.0 - - - +
256C SER* 4.3 3.1 - - - +
257C ILE* 2.8 35.4 + - + +
258C ARG* 4.1 0.4 - - - +
259C ASP* 2.8 46.2 + - - +
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Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ALA 3.1 11.1 + - - +
246C LYS* 3.0 37.9 + - - +
248C ARG* 1.3 80.0 - - - +
250C LYS* 1.3 87.3 + - + +
251C VAL 5.4 0.2 - - - -
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C LYS* 2.9 43.5 + - + +
249C GLU* 1.3 113.0 + - + +
251C VAL* 1.3 63.5 + - + +
252C PRO* 3.4 10.2 - - - +
327C ASP* 4.3 11.2 - - + +
329C GLN* 6.1 1.3 - - - +
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Residues in contact with VAL 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C ALA 3.1 7.1 + - - +
248C ARG 4.8 1.1 - - - +
249C GLU 3.8 1.1 - - - -
250C LYS* 1.3 80.9 - - + +
252C PRO* 1.3 72.4 - - + +
253C LYS* 4.1 18.4 - - + -
254C LEU* 2.8 42.4 + - + +
255C HIS* 3.6 4.2 + - - -
327C ASP 3.7 17.0 - - - +
328C GLY* 3.6 25.6 - - - +
329C GLN* 4.3 11.4 - - - +
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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