Contacts of the strand formed by residues 337 - 339 (chain H) in PDB entry 2QC8
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 PHE 337 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254H THR 4.0 0.7 - - - +
255H ASN* 3.2 1.9 - - - -
256H PHE* 2.9 71.0 + + + -
261H MET* 4.2 9.0 - - - -
270H ILE* 3.8 28.0 - - + -
273H ALA* 3.9 22.7 - - + -
274H ILE* 4.1 11.9 - - + -
277H LEU* 3.5 34.1 - - + -
323H ILE* 3.5 22.2 - - + -
324H ARG 4.0 8.7 - - - +
325H ILE* 4.4 3.1 - - + -
326H PRO* 4.5 1.8 - - - -
336H TYR* 1.3 78.8 - - - +
338H GLU* 1.3 61.0 + - - +
339H ASP* 4.8 4.7 - - + -
355H LEU* 4.8 5.2 - - + -
359H CYS* 4.6 0.7 - - - -
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Residues in contact with GLU 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H HIS* 2.7 21.2 + - + -
254H THR 3.8 2.0 - - - +
255H ASN* 3.1 21.8 - - - +
323H ILE* 3.3 5.2 - - - -
324H ARG* 2.7 78.2 + - + +
326H PRO* 4.9 4.9 - - + -
337H PHE* 1.3 72.5 - - - +
339H ASP* 1.3 59.1 + - - +
340H ARG* 3.2 20.3 + - + +
402H MN 2.1 37.9 + - - -
501H ADP 3.7 2.0 - - - -
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Residues in contact with ASP 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H HIS* 3.5 1.0 - - - -
254H THR* 2.9 44.0 + - - +
277H LEU* 5.0 0.3 - - - +
288H TYR* 2.5 33.9 + - - +
323H ILE* 3.5 19.1 - - + +
337H PHE* 4.0 6.6 + - + -
338H GLU* 1.3 71.0 - - - +
340H ARG* 1.3 57.2 + - - +
341H ARG* 3.0 42.4 + - - +
342H PRO* 3.2 10.5 - - + +
355H LEU* 4.2 13.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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