Contacts of the helix formed by residues 328 - 333 (chain K) in PDB entry 4UJ3
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 328 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452E LYS* 3.5 9.7 + - - -
324K ILE* 3.0 13.8 + - - +
326K GLN 3.5 0.4 - - - -
327K GLU* 1.3 94.5 - - - +
329K ILE* 1.3 64.6 + - - +
331K PRO* 3.4 4.5 - - - +
332K CYS* 3.2 28.6 + - - +
445K ARG* 2.3 51.8 + - - +
448K MET* 3.5 28.0 - - + +
449K SER* 3.6 11.6 + - - -
452K LYS* 5.0 2.7 - - - +
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Residues in contact with ILE 329 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324K ILE* 3.0 22.9 + - + +
325K TYR* 3.6 58.8 - - + +
328K ASP* 1.3 73.7 - - - +
330K PHE* 1.3 66.3 + - - +
332K CYS* 3.0 17.3 + - - +
333K LEU* 3.0 26.3 + - + +
345K LEU* 4.5 4.7 - - + -
414K VAL* 3.7 19.5 - - + -
417K PHE* 4.3 9.4 - - + -
418K PHE* 4.0 16.4 - - + -
448K MET* 4.3 15.0 - - + -
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Residues in contact with PHE 330 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316K ARG* 4.3 20.6 - - - -
325K TYR* 2.8 54.1 + + + +
326K GLN* 3.9 29.2 - - - +
329K ILE* 1.3 75.8 - - + +
331K PRO* 1.3 70.6 - - + +
333K LEU* 3.1 17.5 + - + +
334K THR* 3.2 15.8 + - - -
345K LEU* 4.4 22.4 - - + -
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Residues in contact with PRO 331 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E ASP* 4.3 2.3 - - - +
323E LYS* 5.2 8.5 - - - +
327E GLU* 4.1 13.2 - - - +
326K GLN 3.1 21.5 - - - +
327K GLU 3.1 27.1 - - - +
328K ASP 3.4 12.1 - - - +
329K ILE 3.6 0.7 - - - -
330K PHE* 1.3 93.5 - - + +
332K CYS* 1.3 49.9 + - - +
334K THR* 3.5 14.8 + - - +
410K ARG* 2.7 27.7 + - - -
452K LYS* 3.8 22.5 - - + +
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Residues in contact with CYS 332 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328K ASP 3.2 14.3 + - - +
329K ILE 3.0 10.9 + - - +
331K PRO* 1.3 81.8 - - - +
333K LEU* 1.3 58.6 + - - +
334K THR 3.3 0.4 - - - -
335K PHE* 3.2 13.3 - - - -
410K ARG* 3.0 32.3 + - - +
414K VAL* 3.8 17.7 - - + -
448K MET* 3.2 41.3 - - - -
451K ALA* 3.9 12.6 - - - -
452K LYS* 3.8 11.4 - - - +
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Residues in contact with LEU 333 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329K ILE* 3.0 32.3 + - + +
330K PHE* 3.1 10.4 + - + +
332K CYS* 1.3 78.8 - - - +
334K THR* 1.3 55.8 + - - +
335K PHE* 3.1 26.6 - - + -
341K ALA* 3.6 22.9 - - - +
344K VAL* 4.8 11.9 - - + -
345K LEU* 4.1 35.4 - - + +
348K VAL* 5.1 5.6 - - + -
410K ARG 4.8 0.2 - - - +
411K ILE* 4.5 19.1 - - + -
414K VAL* 4.1 25.1 - - + -
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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