Contacts of the strand formed by residues 339 - 345 (chain A) in PDB entry 2XFN
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 ALA 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A ILE* 3.7 16.2 - - + -
299A VAL 3.1 12.3 - - - +
300A TYR* 3.6 17.0 - - + +
301A TYR 4.6 0.4 - - - +
306A TRP* 3.5 9.2 - - - -
329A ASP* 3.4 7.3 - - - +
330A ASP* 2.8 37.3 + - + +
331A THR* 3.3 5.3 + - - -
337A TYR 3.3 8.7 + - - +
338A ALA* 1.3 78.8 - - - +
340A ILE* 1.3 60.9 + - - +
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Residues in contact with ILE 340 (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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297A CYS 3.7 1.2 - - - +
298A ILE* 3.4 4.2 - - - -
299A VAL* 2.9 34.3 + - - +
301A TYR* 4.3 9.9 - - + -
306A TRP* 3.6 50.3 - - + -
313A GLY* 4.1 19.7 - - - +
315A MET* 4.1 11.7 - - + -
327A THR* 3.6 32.8 - - + -
328A LEU 3.7 1.8 - - - +
329A ASP* 4.4 4.0 - - - -
339A ALA* 1.3 73.4 - - - +
341A MET* 1.3 63.3 + - - +
342A GLY 4.0 0.2 + - - -
368A TYR* 3.9 23.1 - - + -
372A LEU* 5.5 2.7 - - + -
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Residues in contact with MET 341 (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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60A TYR* 3.4 22.2 - - + +
296A LYS* 3.6 23.3 - - + -
297A CYS 3.5 3.6 - - - -
298A ILE* 4.2 13.2 - - + -
326A TYR* 5.1 0.7 - - + -
327A THR* 2.9 8.8 - - - -
328A LEU* 2.9 58.0 + - + +
330A ASP* 4.0 21.0 - - + +
340A ILE* 1.3 74.0 - - - +
342A GLY* 1.3 78.9 + - - +
343A PHE* 3.7 40.8 - - + -
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Residues in contact with GLY 342 (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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295A ILE 3.8 0.2 - - - +
296A LYS* 3.8 0.5 - - - -
297A CYS* 2.9 38.7 + - - +
324A VAL* 3.8 7.4 - - - -
326A TYR 3.3 9.4 - - - -
327A THR* 4.0 0.4 - - - -
340A ILE 4.0 0.8 + - - -
341A MET* 1.3 83.3 - - - +
343A PHE* 1.3 60.2 - - - -
368A TYR* 3.7 18.4 + - - -
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Residues in contact with PHE 343 (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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60A TYR* 4.7 11.0 - + - -
171A LEU* 3.8 24.0 - - + -
294A VAL* 3.7 17.7 - - + -
295A ILE 3.6 1.3 - - - -
296A LYS* 3.9 27.4 - - + -
324A VAL* 3.4 19.4 - - - -
325A ALA 3.5 8.5 + - - -
326A TYR* 3.1 19.5 + + + +
328A LEU* 5.8 0.2 - - + -
341A MET* 3.7 35.9 - - + -
342A GLY* 1.3 73.4 - - - -
344A ILE* 1.3 61.9 + - - +
345A LEU* 3.7 22.2 + - + +
398A TYR* 3.8 29.8 - + - -
1500A FAD 4.3 11.4 - + + -
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Residues in contact with ILE 344 (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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294A VAL* 3.3 7.1 - - - +
295A ILE* 2.9 43.8 + - + +
297A CYS* 3.6 25.6 - - - -
323A PRO 3.5 23.1 - - - +
324A VAL* 3.7 14.6 - - + -
343A PHE* 1.3 69.7 - - - +
345A LEU* 1.3 59.8 + - - +
348A LYS* 3.5 32.5 - - + +
349A ALA* 3.6 6.0 - - - +
352A LEU* 4.0 12.3 - - + -
360A ARG* 4.1 23.3 - - + -
364A LEU* 4.2 14.1 - - + -
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Residues in contact with LEU 345 (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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167A LEU 5.2 0.4 - - - +
170A ASN* 3.7 26.9 - - + +
171A LEU* 3.8 33.2 - - + +
174A THR* 3.8 20.9 - - + -
176A GLU* 4.7 0.2 - - - +
293A SER 4.0 0.9 - - - -
294A VAL* 4.2 3.1 - - + -
323A PRO 4.4 1.6 + - - -
325A ALA* 3.9 29.1 - - + +
343A PHE* 3.7 28.4 + - + +
344A ILE* 1.3 76.9 - - - +
346A ALA* 1.3 74.2 + - + +
347A HIS* 3.2 1.9 + - - -
348A LYS* 3.0 23.3 + - + +
349A ALA 4.0 0.7 - - - -
398A TYR* 4.0 7.9 - - - +
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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