Contacts of the strand formed by residues 326 - 333 (chain C) in PDB entry 3V81
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 ILE 326 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B VAL 5.9 3.4 - - - +
324C ASP* 4.6 10.8 - - + +
325C LEU* 1.3 83.2 - - - +
327C ALA* 1.3 66.2 + - - +
328C GLU 4.3 0.2 + - - -
340C GLN 3.7 1.4 - - - +
341C ILE* 3.2 5.1 - - - -
342C TYR* 2.9 70.6 + - + +
343C GLN 5.1 6.3 - - - +
387C PRO* 4.5 0.2 - - - -
388C LYS* 3.3 24.5 - - + +
390C LYS* 3.5 29.2 - - + -
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C ILE* 1.3 75.3 - - - +
328C GLU* 1.3 55.7 + - - +
329C ILE* 4.3 0.4 - - + -
339C TYR* 5.2 3.1 - - + -
340C GLN 3.3 4.5 - - - +
341C ILE* 3.6 22.4 - - + -
375C ILE* 4.0 8.7 - - + -
387C PRO* 4.0 9.8 - - + +
388C LYS 2.9 6.3 + - - -
389C PHE* 3.2 32.4 - - + -
390C LYS 2.8 30.0 + - - +
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Residues in contact with GLU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ALA* 1.3 75.2 - - - +
329C ILE* 1.3 62.7 + - - +
330C GLN* 3.7 18.0 + - - +
339C TYR* 3.1 3.5 - - - -
340C GLN* 2.9 41.7 + - - +
342C TYR* 3.3 31.1 + - + +
390C LYS* 3.2 43.0 + - + +
417C VAL* 3.6 20.1 - - + +
419C THR* 4.0 9.0 + - - +
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Residues in contact with ILE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ALA* 5.0 0.4 - - + -
328C GLU* 1.3 80.4 - - - +
330C GLN* 1.3 71.2 + - - +
337C TRP* 4.1 15.7 - - + -
338C THR 3.3 14.4 - - - +
339C TYR* 4.0 10.1 - - + -
368C LEU* 4.0 19.7 - - + -
371C ALA* 4.3 6.3 - - + -
372C VAL* 4.0 14.1 - - + -
375C ILE* 3.4 26.9 - - + -
389C PHE* 4.5 5.4 - - + -
390C LYS 3.1 7.1 + - - +
391C LEU* 3.8 24.5 - - + -
392C PRO* 2.9 34.0 - - + +
417C VAL* 4.9 2.4 - - - +
419C THR* 5.5 0.9 - - - -
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Residues in contact with GLN 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C GLU* 3.7 25.8 + - - +
329C ILE* 1.3 80.1 - - - +
331C LYS* 1.3 63.5 + - - +
332C GLN* 5.1 2.5 - - + +
337C TRP* 3.7 3.2 - - - -
338C THR* 2.8 49.3 + - - +
340C GLN* 2.7 46.4 + - - -
392C PRO* 4.7 1.8 - - - -
419C THR* 4.1 25.8 - - + +
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Residues in contact with LYS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ILE 4.3 0.2 - - - -
330C GLN* 1.3 74.3 - - - +
332C GLN* 1.3 62.9 + - - +
333C GLY* 3.8 23.5 - - - +
334C GLN 5.1 1.0 - - - +
335C GLY* 5.9 2.0 - - - +
336C GLN 4.4 0.9 - - - +
337C TRP* 3.4 37.6 - - + -
364C ASP* 3.0 35.0 + - - +
392C PRO* 4.5 7.3 - - + +
419C THR 5.6 1.2 + - - -
421C PRO* 3.9 55.2 + - + +
422C LEU 5.1 3.4 - - - +
423C VAL* 4.5 7.2 - - + -
426C TRP* 6.4 0.2 - - - -
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Residues in contact with GLN 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C GLY* 3.8 13.0 + - - +
275C LYS* 3.3 46.5 + - + +
330C GLN* 4.1 5.3 - - + +
331C LYS* 1.3 77.2 - - - +
333C GLY* 1.3 62.8 + - - +
334C GLN* 3.9 7.1 + - - -
336C GLN* 3.0 26.2 + - + +
337C TRP 4.7 0.6 - - - -
338C THR* 2.9 45.2 + - + +
421C PRO* 5.9 1.3 - - - -
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Residues in contact with GLY 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C LYS* 3.6 25.1 - - - +
332C GLN* 1.3 74.8 - - - +
334C GLN* 1.3 82.5 + - - +
335C GLY 3.2 3.6 - - - -
336C GLN* 3.0 28.2 + - - +
421C PRO* 5.8 0.6 - - - +
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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