Contacts of the strand formed by residues 272 - 274 (chain K) in PDB entry 1FQV
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 272 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245K VAL 3.0 3.8 + - - -
246K ARG* 2.5 49.6 + - + -
247K LEU 3.2 20.5 + - - -
270K LEU* 3.4 8.7 - - - +
271K ASP* 1.3 84.1 - - - +
273K LEU* 1.3 59.8 + - - +
274K ASN 4.3 0.2 - - - -
297K ILE* 3.7 0.4 - - - -
299K GLN* 3.3 44.4 + - + +
407K THR 4.2 2.9 - - - +
408K ILE* 4.0 0.8 - - + -
409K ALA* 2.8 31.4 + - + +
410K ARG 4.7 0.2 + - - -
422K TRP* 5.3 0.2 + - - -
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Residues in contact with LEU 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K LEU* 3.4 26.7 - - + +
249K LEU* 5.5 0.4 - - + +
264K LEU* 3.8 27.4 - - + -
270K LEU* 3.8 16.8 - - + -
272K GLU* 1.3 74.6 - - - +
274K ASN* 1.3 63.3 + - - +
275K LEU* 4.1 26.5 - - + -
293K VAL* 3.8 22.4 - - + -
297K ILE* 3.6 15.5 - - + -
299K GLN 2.7 8.9 + - - +
300K LEU* 3.2 17.8 - - + +
301K ASN 2.8 24.6 + - - -
408K ILE* 3.6 3.8 - - - +
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Residues in contact with ASN 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226K GLU* 5.2 0.2 - - - +
247K LEU 3.0 7.7 + - - +
248K ASN* 3.6 23.1 + - - +
249K LEU* 2.8 26.0 + - - +
250K SER* 3.2 10.8 + - - -
273K LEU* 1.3 75.0 - - - +
275K LEU* 1.3 56.4 + - - +
276K SER* 2.8 36.0 + - - +
301K ASN* 3.3 13.7 + - - +
406K THR* 3.7 20.3 - - - +
408K ILE* 3.2 28.7 - - + +
409K ALA* 3.8 2.7 - - + +
410K ARG* 4.9 0.9 + - - -
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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