Contacts of the helix formed by residues 326 - 340 (chain R) in PDB entry 5C7L
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 PRO 326 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324R PRO* 3.6 10.1 - - + +
325R ALA* 1.3 93.4 - - - +
327R TYR* 1.3 67.5 + - - +
328R SER* 3.2 11.9 - - - +
329R ALA* 3.0 28.5 + - + +
330R ILE* 3.1 7.1 + - - +
377R ASP* 3.5 28.4 - - - +
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Residues in contact with TYR 327 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325R ALA 3.5 0.6 + - - -
326R PRO* 1.3 73.3 - - - +
328R SER* 1.3 57.4 + - - +
330R ILE* 2.9 22.6 + - + +
331R LYS* 2.8 54.2 + - + +
367R PHE* 3.7 18.9 - + - -
368R ASP 3.9 0.5 + - - -
369R ALA* 2.7 33.2 + - - -
372R GLY* 3.6 27.6 + - - -
373R ILE 4.8 1.8 - - - -
374R ALA* 4.8 23.1 - - + +
380R VAL* 5.3 0.4 - - + -
381R LYS 4.9 0.2 - - - -
382R LEU* 3.9 22.3 - - + +
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Residues in contact with SER 328 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326R PRO* 4.3 11.8 - - - +
327R TYR* 1.3 78.9 - - - +
329R ALA* 1.3 58.2 + - - -
331R LYS* 3.5 18.9 + - - +
332R GLU* 3.0 32.1 + - - +
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Residues in contact with ALA 329 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239R ARG* 4.4 13.3 + - - +
240R PHE* 3.5 20.9 - - + -
326R PRO* 3.0 24.6 + - + +
328R SER* 1.3 77.1 + - - +
330R ILE* 1.3 66.1 + - - +
332R GLU* 3.9 7.1 - - - +
333R ALA* 3.0 23.9 + - - +
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Residues in contact with ILE 330 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236R ILE* 3.9 22.7 - - + -
240R PHE* 3.8 20.6 - - + -
321R LEU* 4.6 2.7 - - + -
325R ALA* 3.2 28.0 - - + +
326R PRO 3.1 7.0 + - - +
327R TYR* 2.9 30.6 + - + +
329R ALA* 1.3 76.6 - - - +
331R LYS* 1.3 62.9 + - - +
333R ALA* 3.2 3.5 + - - +
334R VAL* 3.1 27.3 + - + +
367R PHE* 4.3 12.6 - - + -
380R VAL* 4.0 26.2 - - + -
382R LEU* 4.1 17.5 - - + -
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Residues in contact with LYS 331 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327R TYR* 2.8 43.4 + - + +
328R SER* 3.7 23.3 - - - +
330R ILE* 1.3 76.3 - - - +
332R GLU* 1.3 63.3 + - + +
334R VAL* 3.3 2.3 + - - -
335R LYS* 3.0 31.1 + - - +
348R TYR* 3.6 29.3 - - + +
350R GLU* 4.3 13.9 + - - -
367R PHE* 4.6 3.6 - - + -
369R ALA* 4.0 13.9 - - + -
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Residues in contact with GLU 332 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328R SER* 3.0 22.8 + - - +
329R ALA* 4.0 7.6 - - - +
330R ILE 3.3 0.4 - - - -
331R LYS* 1.3 77.1 - - - +
333R ALA* 1.3 63.9 + - - +
335R LYS* 3.0 36.0 + - - +
336R ALA* 3.1 24.6 + - - +
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Residues in contact with ALA 333 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235R VAL* 3.7 16.0 - - + +
236R ILE* 5.5 0.9 - - + -
239R ARG* 4.0 28.5 - - + +
240R PHE* 4.3 6.3 - - + -
329R ALA 3.0 18.0 + - - +
330R ILE 3.2 4.7 + - - +
332R GLU* 1.3 77.3 - - - +
334R VAL* 1.3 61.5 + - + +
336R ALA* 3.5 5.6 + - - +
337R ALA* 3.1 22.7 + - - +
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Residues in contact with VAL 334 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232R LEU* 4.4 5.4 - - + -
235R VAL* 4.2 9.2 - - + -
236R ILE* 4.4 17.5 - - + -
330R ILE* 3.1 19.1 + - + +
331R LYS 3.9 3.4 - - - +
333R ALA* 1.3 72.6 - - - +
335R LYS* 1.3 61.6 + - - +
337R ALA* 3.2 3.5 + - - +
338R ALA* 2.9 27.5 + - - +
346R LEU* 4.1 18.3 - - + +
348R TYR* 3.9 13.5 - - + -
367R PHE* 3.5 52.0 - - + -
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Residues in contact with LYS 335 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331R LYS* 3.0 16.9 + - - +
332R GLU* 3.0 39.2 + - - +
334R VAL* 1.3 77.2 - - - +
336R ALA* 1.3 57.1 + - - +
338R ALA* 3.2 2.0 + - - +
339R LYS* 2.9 61.4 + - + +
348R TYR* 3.6 48.3 + - + -
350R GLU* 3.9 11.9 + - - -
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Residues in contact with ALA 336 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332R GLU 3.1 17.8 + - - +
333R ALA* 3.8 6.7 - - - +
335R LYS* 1.3 76.0 - - - +
337R ALA* 1.3 62.8 + - - +
339R LYS* 3.6 7.6 + - - +
340R GLY* 3.1 19.9 + - - -
341R PRO* 3.9 4.3 - - - +
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Residues in contact with ALA 337 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235R VAL* 3.6 32.3 - - + -
333R ALA 3.1 12.5 + - - +
334R VAL 3.2 6.9 + - - +
336R ALA* 1.3 76.7 - - - +
338R ALA* 1.3 61.6 + - - +
340R GLY 3.3 5.4 + - - -
341R PRO* 4.3 11.0 - - + -
342R MET* 2.9 37.5 + - + +
346R LEU* 4.2 4.9 - - + -
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Residues in contact with ALA 338 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334R VAL 2.9 16.4 + - - +
335R LYS 3.2 4.0 + - - +
337R ALA* 1.3 78.3 - - - +
339R LYS* 1.3 60.8 + - + +
342R MET* 4.5 1.3 - - - -
343R ALA* 3.3 22.5 - - - +
346R LEU* 3.3 28.4 - - + +
347R ALA* 4.0 14.6 - - - -
348R TYR* 4.1 13.7 - - + +
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Residues in contact with LYS 339 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335R LYS* 2.9 45.9 + - + +
336R ALA* 4.0 6.3 - - - +
338R ALA* 1.3 77.4 - - + +
340R GLY* 1.3 58.4 + - - +
343R ALA* 4.4 5.6 - - - +
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Residues in contact with GLY 340 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336R ALA 3.1 10.3 + - - -
337R ALA 3.3 0.2 + - - -
338R ALA 3.3 1.2 - - - -
339R LYS* 1.3 78.2 - - - +
341R PRO* 1.3 74.7 - - - +
342R MET 3.1 3.0 + - - -
343R ALA* 3.1 18.2 + - - +
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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