Contacts of the helix formed by residues 324 - 332 (chain A) in PDB entry 5LLU
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 ASN 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A TYR* 3.9 5.6 + - - -
318A PHE* 3.9 17.5 - - - -
323A LYS* 1.4 70.1 - - - +
325A PRO* 1.4 70.2 - - + +
326A PHE* 3.4 3.3 + - + +
327A VAL* 3.6 32.3 + - + +
328A PHE* 3.7 7.3 + - - +
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Residues in contact with PRO 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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314A PRO* 3.3 49.4 - - + +
317A TYR* 3.6 21.5 - - + -
318A PHE* 3.7 15.9 - - + -
323A LYS 3.3 8.7 - - - +
324A ASN* 1.4 86.0 - - + +
326A PHE* 1.3 67.8 + - + +
327A VAL 3.3 1.3 - - - -
328A PHE* 3.4 4.5 + - + +
329A ILE* 3.0 32.4 + - + +
469A LEU* 4.3 4.4 - - + +
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Residues in contact with PHE 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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310A LEU* 3.2 51.1 - - + -
314A PRO* 3.7 25.6 - - + -
324A ASN* 3.4 2.5 - - + +
325A PRO* 1.3 84.6 - - + +
327A VAL* 1.4 61.4 + - + +
329A ILE* 4.0 20.1 - - + +
330A ALA* 3.6 16.6 + - - +
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Residues in contact with VAL 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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324A ASN* 3.8 29.2 - - + +
325A PRO 3.3 0.6 - - - -
326A PHE* 1.4 77.7 - - + +
328A PHE* 1.3 63.4 + - - +
329A ILE 3.4 0.4 - - - -
330A ALA* 3.5 17.8 + - + +
331A GLY* 3.5 4.9 + - - -
360A ASN* 4.4 2.9 - - - +
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Residues in contact with PHE 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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317A TYR* 3.3 28.3 - + + +
324A ASN 3.7 11.1 + - - +
325A PRO* 3.4 9.2 - - + +
327A VAL* 1.3 77.2 - - - +
329A ILE* 1.4 61.7 + - + +
330A ALA 3.3 0.2 - - - -
331A GLY 3.2 9.7 + - - -
332A ILE* 3.4 8.4 + - + +
356A LEU* 3.5 17.3 - - + -
360A ASN* 3.3 37.3 + - + -
362A VAL* 4.1 14.8 - - + -
468A ALA* 3.2 40.6 - - + -
469A LEU* 3.6 24.2 - - + -
472A GLY* 4.0 17.3 - - - -
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Residues in contact with ILE 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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309A GLY 4.8 3.8 - - - +
310A LEU* 5.3 7.4 - - + -
314A PRO* 4.4 10.1 - - + -
325A PRO* 3.0 22.4 + - + +
326A PHE* 4.0 33.2 - - + +
327A VAL 3.4 0.4 - - - -
328A PHE* 1.4 75.0 - - - +
330A ALA* 1.3 56.7 + - - +
332A ILE* 3.5 9.3 + - + +
333A LEU* 3.0 36.7 + - + +
336A LEU* 4.0 19.2 - - + +
465A LEU* 3.8 23.6 - - + -
469A LEU* 4.3 20.6 - - + -
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Residues in contact with ALA 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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51A LEU* 3.7 12.5 - - - +
326A PHE 3.6 14.6 + - - +
327A VAL* 3.5 15.7 + - + +
328A PHE 3.3 0.2 - - - -
329A ILE* 1.3 76.1 - - - +
331A GLY* 1.3 63.1 + - - +
333A LEU* 3.4 25.5 - - + +
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Residues in contact with GLY 331 (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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51A LEU* 5.2 1.0 - - - +
327A VAL 3.5 5.0 + - - -
328A PHE 3.2 4.2 + - - -
330A ALA* 1.3 78.7 - - - +
332A ILE* 1.3 57.1 + - - +
333A LEU 3.2 3.8 + - - -
334A GLN* 4.4 2.1 + - - +
355A CYS* 3.7 1.6 - - - +
359A ASN* 2.8 43.6 + - - -
360A ASN* 3.5 20.2 - - - -
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Residues in contact with ILE 332 (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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328A PHE* 3.4 16.9 + - + +
329A ILE* 3.5 8.3 - - + +
331A GLY* 1.3 71.5 - - - +
333A LEU* 1.3 61.2 + - - +
334A GLN 3.3 2.7 - - - -
335A ALA* 3.2 15.9 + - + +
336A LEU* 3.3 38.7 + - + +
352A THR* 4.8 2.9 - - + +
355A CYS* 3.7 20.9 - - + -
356A LEU* 3.7 27.4 - - + +
360A ASN* 3.5 19.1 - - - +
464A VAL* 5.4 2.2 - - + -
465A LEU* 3.9 12.3 - - + -
468A ALA* 3.7 26.9 - - + -
469A LEU* 6.0 0.2 - - + -
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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