Contacts of the helix formed by residues 315 - 323 (chain B) in PDB entry 4PK5
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 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B MET* 3.3 7.9 - - - +
275B VAL 6.1 0.4 - - - -
276B LEU 5.5 0.4 - - - -
278B GLY* 4.8 8.3 - - - -
313B ASN 3.6 1.8 + - - -
314B PRO* 1.3 71.0 - - - +
316B VAL* 1.3 62.5 + - - +
317B ARG* 3.4 9.5 + - - +
318B GLU* 3.2 44.3 + - - +
319B PHE 3.2 18.0 + - - -
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 3.8 19.7 - - + -
185B PHE* 4.2 13.7 - - + -
188B MET* 3.4 28.9 - - + -
196B LEU* 5.3 4.0 - - + -
200B LEU* 4.2 26.0 - - + -
276B LEU* 3.5 27.7 + - + +
277B LEU* 5.0 2.0 - - + -
314B PRO 3.4 0.8 + - - -
315B SER* 1.3 67.9 + - - +
317B ARG* 1.3 66.4 + - - +
319B PHE* 3.7 0.8 - - + +
320B VAL* 3.1 32.0 + - + +
332B TYR* 4.5 8.7 - - + -
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 5.7 6.9 - - - +
277B LEU 3.7 16.0 + - - +
278B GLY 3.9 16.8 - - - +
280B GLN* 6.5 0.4 - - - -
315B SER* 3.3 9.3 + - - +
316B VAL* 1.3 79.9 - - - +
318B GLU* 1.3 59.4 + - - +
320B VAL* 3.6 1.7 - - - +
321B LEU* 2.6 59.4 + - + +
332B TYR* 3.4 28.6 + - + +
397B LYS 4.0 5.0 + - - -
398B SER* 3.0 42.6 + - - +
399B LEU 3.8 4.6 + - - -
400B LEU* 3.3 22.8 - - + +
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Residues in contact with GLU 318 (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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315B SER* 3.2 32.4 + - - +
317B ARG* 1.3 82.3 + - - +
319B PHE* 1.3 67.6 + - - +
321B LEU* 3.1 17.8 + - - +
322B SER* 2.8 27.8 + - - -
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA 4.7 3.1 - - - -
188B MET* 3.4 65.7 - - + -
191B GLN* 4.0 19.1 - - - -
192B GLU 6.2 0.2 - - - -
193B ARG* 5.9 6.3 - - + -
196B LEU* 3.6 30.7 - - + -
315B SER 3.2 4.0 + - - +
316B VAL 3.7 4.7 - - - +
318B GLU* 1.3 79.7 - - - +
320B VAL* 1.3 70.9 + - + +
322B SER* 2.8 20.6 + - - -
323B LYS* 3.2 42.7 + - + +
328B LEU* 4.4 6.1 - - + -
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 4.7 1.6 - - + -
200B LEU* 4.5 7.4 - - + -
316B VAL* 3.1 27.8 + - + +
317B ARG 3.8 2.2 - - - +
319B PHE* 1.3 88.9 - - + +
321B LEU* 1.3 64.9 + - - +
322B SER 3.1 0.2 + - - -
323B LYS* 3.2 12.1 + - - +
324B GLY 4.3 2.6 + - - -
325B ASP* 5.3 2.1 + - - +
328B LEU* 4.0 24.1 - - + +
329B ARG* 3.8 33.1 + - + +
332B TYR* 4.1 17.9 - - + -
400B LEU* 3.7 22.0 - - + -
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Residues in contact with LEU 321 (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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317B ARG* 2.6 47.9 + - + +
318B GLU* 3.4 20.6 - - - +
320B VAL* 1.3 74.8 - - - +
322B SER* 1.3 59.8 + - - +
323B LYS 3.4 1.0 + - - -
324B GLY* 4.2 5.5 + - - -
329B ARG* 5.4 9.2 + - - -
400B LEU* 3.4 31.6 - - + +
401B LYS* 6.3 0.7 - - - +
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU 2.8 16.7 + - - -
319B PHE* 2.8 19.8 + - - -
321B LEU* 1.3 71.0 - - - +
323B LYS* 1.3 74.6 + - - +
324B GLY 3.6 1.1 + - - -
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Residues in contact with LYS 323 (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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191B GLN* 3.2 24.2 + - - +
319B PHE* 3.2 58.3 - - + +
320B VAL 3.2 7.7 + - - +
322B SER* 1.3 92.9 + - - +
324B GLY* 1.3 66.6 - - - +
325B ASP* 3.2 17.3 + - + +
328B LEU* 4.4 8.3 - - + -
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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