Contacts of the strand formed by residues 329 - 333 (chain C) in PDB entry 4BUR
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 GLU 329 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301C LYS 2.8 16.6 + - - +
302C SER* 3.0 21.9 + - - -
303C ILE* 3.2 22.7 + - - +
328C THR* 1.3 72.5 - - - +
330C VAL* 1.3 72.1 + - - +
331C ILE* 3.2 30.9 - - + +
362C LYS* 3.6 19.9 + - + +
390C GLU 4.5 5.0 - - - +
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Residues in contact with VAL 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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303C ILE* 3.5 13.9 - - + +
305C ILE* 4.6 13.2 - - + -
316C ALA 4.2 11.4 - - - +
319C LEU* 3.4 49.6 - - + +
320C GLY 4.5 0.2 - - - +
323C ALA* 3.6 13.7 - - + -
328C THR* 4.3 1.1 + - - +
329C GLU* 1.3 81.6 - - - +
331C ILE* 1.3 65.8 + - - +
360C GLY 4.2 12.8 + - - +
361C VAL* 3.6 13.2 - - + -
362C LYS* 3.0 24.9 + - - +
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Residues in contact with ILE 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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302C SER* 3.9 9.0 - - - +
303C ILE 2.9 7.3 + - - +
304C THR* 3.2 22.0 - - + +
305C ILE* 2.7 34.2 + - - +
329C GLU* 3.2 36.1 - - + +
330C VAL* 1.3 80.0 - - - +
332C GLN* 1.3 61.4 + - - +
333C LEU* 4.2 1.3 - - + -
361C VAL* 4.6 0.7 - - - -
362C LYS* 3.4 28.9 - - + +
364C MET* 3.8 26.7 - - + -
389C VAL* 3.8 24.2 - - + -
390C GLU 5.0 2.2 - - - +
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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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305C ILE* 3.4 18.6 - - + +
307C GLY 2.9 26.5 + - - +
308C GLY* 3.5 7.9 - - - -
312C GLY 3.5 0.4 - - - -
313C SER 3.4 19.0 - - - +
316C ALA* 3.6 22.1 - - + +
331C ILE* 1.3 74.0 - - - +
333C LEU* 1.3 62.1 + - - +
334C PHE* 3.8 8.3 - - + -
339C ASN* 3.1 29.0 + - - +
356C VAL* 3.9 8.1 - - - +
361C VAL* 3.8 15.3 - - + +
362C LYS 3.0 7.4 + - - +
363C VAL* 3.3 7.1 - - + +
364C MET* 2.8 26.9 + - - +
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Residues in contact with LEU 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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304C THR* 3.7 25.4 - - + -
305C ILE 2.9 7.9 + - - +
306C ILE* 3.3 18.3 - - + +
307C GLY 2.9 23.4 + - - -
331C ILE* 5.0 0.7 - - + -
332C GLN* 1.3 75.0 - - - +
334C PHE* 1.3 63.6 + - - +
364C MET* 3.5 23.8 - - + +
367C ALA* 3.6 20.6 - - + +
369C VAL* 3.8 26.7 - - + -
381C ILE* 4.4 9.4 - - + -
383C LEU* 4.0 9.2 - - + -
389C VAL* 4.2 22.9 - - + -
700C NAD 6.1 0.7 - - + -
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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