Contacts of the helix formed by residues 323 - 330 (chain A) in PDB entry 5JHQ
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 ASP 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A ALA 2.8 20.6 + - - +
291A ILE 3.8 9.2 + - - +
292A LYS 5.1 0.9 - - - -
293A GLY* 3.6 24.3 - - - +
321A LEU 3.8 0.4 + - - -
322A ALA* 1.3 73.4 - - - +
324A PRO* 1.4 71.4 - - - +
325A SER* 3.1 32.6 + - - -
326A ALA 3.1 2.7 + - - +
327A LYS* 2.7 31.7 + - - +
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Residues in contact with PRO 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ALA 4.1 3.8 - - - +
323A ASP* 1.4 95.7 - - - +
325A SER* 1.3 61.5 + - - +
327A LYS* 3.7 18.7 - - + +
328A ALA* 4.0 5.0 + - - +
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Residues in contact with SER 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLY 5.0 2.7 - - - -
295A ILE* 3.7 19.7 - - - +
323A ASP* 3.1 15.1 + - - -
324A PRO* 1.3 74.3 - - - +
326A ALA* 1.3 65.0 + - - +
327A LYS 3.2 1.3 - - - -
328A ALA* 3.2 22.3 + - - +
329A VAL* 4.0 2.3 + - - +
334A TYR* 4.7 4.4 - - - -
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ALA* 3.6 37.7 - - + +
293A GLY* 4.2 9.6 - - - -
295A ILE* 3.4 20.5 - - + +
298A CYS* 4.1 9.4 - - - -
322A ALA* 4.4 2.0 - - - -
323A ASP* 3.1 4.8 + - - +
325A SER* 1.3 76.3 - - - +
327A LYS* 1.3 63.9 + - - +
328A ALA 3.2 0.4 - - - -
329A VAL* 3.3 6.0 + - - +
330A LEU* 3.3 25.8 + - - +
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.5 43.4 - - + +
322A ALA* 4.0 11.2 - - + +
323A ASP 2.7 20.7 + - - +
324A PRO* 3.7 13.7 - - + +
325A SER 3.2 0.4 - - - -
326A ALA* 1.3 72.5 - - - +
328A ALA* 1.3 61.8 + - - +
330A LEU 3.5 1.0 + - - -
331A THR* 3.3 32.3 + - + +
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A PRO 4.0 5.3 + - - +
325A SER* 3.2 14.1 + - - +
327A LYS* 1.3 79.2 - - - +
329A VAL* 1.3 56.5 + - - +
331A THR* 3.1 17.2 + - - -
333A GLU* 3.2 23.4 + - + +
334A TYR* 3.2 24.0 + - + +
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ILE* 3.8 37.9 - - + -
298A CYS* 4.2 11.9 - - + -
299A ILE* 3.7 25.1 - - + -
302A LEU* 3.9 19.5 - - + +
325A SER 4.5 0.2 - - - +
326A ALA* 3.3 8.8 + - - +
328A ALA* 1.3 74.6 - - - +
330A LEU* 1.3 59.0 + - + +
331A THR 3.2 1.6 - - - -
332A GLY* 3.0 19.8 + - - -
334A TYR* 3.6 31.2 - - + -
356A THR* 4.7 4.4 + - + -
358A LEU* 4.1 6.6 - - - +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU* 3.9 32.3 - - + -
290A ALA* 3.8 17.0 - - + -
298A CYS* 4.7 7.2 - - - -
302A LEU* 4.1 17.7 - - + -
308A PRO* 4.7 12.0 - - + +
318A ALA* 3.6 14.8 - - + +
319A LEU* 3.6 51.6 - - + +
322A ALA* 4.2 2.9 - - + -
326A ALA 3.3 15.1 + - - +
327A LYS 3.5 0.4 + - - -
329A VAL* 1.3 75.7 - - + +
331A THR* 1.3 60.7 + - - +
332A GLY 3.5 0.2 - - - -
358A LEU* 3.6 17.0 - - - +
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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