Contacts of the strand formed by residues 336 - 339 (chain A) in PDB entry 2XFR
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 SER 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A GLN* 2.6 40.3 + - - +
290A LEU 2.9 11.8 + - - -
291A ALA* 4.0 7.0 - - - -
292A ILE* 3.1 29.8 + - - +
330A LEU* 4.1 2.1 - - - +
334A ARG 5.2 1.0 + - - -
335A ALA* 1.3 74.1 - - - +
337A ILE* 1.3 66.8 + - - +
338A ASN* 4.1 0.4 - - - -
374A ASN* 3.3 29.2 + - - +
375A VAL* 5.3 0.2 - - - -
376A ALA* 5.5 0.9 - - - -
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ILE* 3.9 3.1 - - - -
294A ILE* 3.9 31.9 - - + -
323A TYR* 5.2 2.5 - - + +
327A ALA* 4.2 10.3 - - + +
330A LEU* 3.5 23.1 - - + -
336A SER* 1.3 75.8 - - - +
338A ASN* 1.3 69.6 + - - +
339A PHE* 4.0 6.5 - - + +
364A VAL* 4.0 23.6 - - + +
367A ALA* 5.8 0.4 - - + -
368A GLY* 4.1 19.3 - - - +
373A LEU* 4.0 18.1 - - + +
374A ASN 3.2 6.7 + - - +
375A VAL* 3.4 11.3 - - + -
376A ALA* 2.8 27.7 + - - +
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Residues in contact with ASN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A MET* 4.1 7.7 - - - +
85A GLN* 5.8 0.4 + - - -
176A GLU* 2.8 31.3 + - - +
291A ALA* 4.8 6.1 - - + -
292A ILE 2.9 15.0 + - - +
293A LYS* 3.5 10.9 - - - +
294A ILE 3.3 21.0 + - - -
336A SER* 5.0 0.2 - - - -
337A ILE* 1.3 72.8 - - - +
339A PHE* 1.3 65.1 + - - +
376A ALA* 3.5 24.5 - - + +
377A CYS* 3.5 11.4 + - - +
378A GLU* 3.0 27.4 + - - +
415A THR* 5.1 3.3 + - - -
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Residues in contact with PHE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LYS* 5.2 1.0 + - - -
294A ILE* 3.4 27.4 - - + -
295A SER 3.4 21.8 - - - -
296A GLY* 3.9 9.2 - - - -
323A TYR* 5.3 0.9 - + - -
337A ILE* 3.9 4.5 - - + -
338A ASN* 1.3 78.4 - - - +
340A THR* 1.3 83.4 + - - +
341A CYS* 5.1 0.7 - - + -
360A LEU* 3.7 31.4 - - + -
361A VAL* 3.9 25.1 - - + -
364A VAL* 3.7 42.6 - - + -
365A LEU* 4.5 6.7 - - + -
376A ALA 2.9 11.5 + - - +
377A CYS* 3.5 16.3 - - - -
378A GLU* 2.9 23.7 + - - +
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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