Contacts of the strand formed by residues 395 - 399 (chain B) in PDB entry 2DB3
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 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ILE* 4.2 8.7 - - + -
303B ILE* 3.6 37.9 - - + -
306B LYS* 3.8 31.0 - - + -
307B LEU* 4.3 13.5 - - + -
320B GLN 3.3 1.2 + - - -
321B VAL* 3.4 30.4 - - + -
322B VAL 2.9 25.3 + - - -
393B THR* 3.2 7.3 - - - +
394B ARG* 1.3 103.1 - - + +
396B VAL* 1.3 63.0 + - - +
397B VAL* 4.1 2.0 - - + -
427B GLN* 3.1 44.2 - - + +
429B LEU* 4.3 5.8 - - + -
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.3 17.5 - - + +
324B VAL* 5.7 1.6 - - + -
393B THR* 3.6 17.3 - - + -
395B PHE* 1.3 79.2 - - - +
397B VAL* 1.3 64.2 + - - +
398B LEU* 4.3 11.4 - - + -
416B ILE* 5.4 4.0 - - + -
417B MET* 3.5 33.4 - - + -
422B MET* 4.1 17.9 - - + -
426B HIS* 3.9 20.0 - - + +
427B GLN 3.0 8.3 + - - +
428B THR* 3.4 5.4 - - + +
429B LEU* 3.0 25.5 + - - +
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Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PHE* 3.9 32.1 - - + -
303B ILE* 3.6 31.2 - - + -
322B VAL 2.7 10.9 + - - +
323B ILE* 3.4 35.2 - - + -
324B VAL* 2.9 28.6 + - - +
395B PHE* 4.9 1.8 - - + -
396B VAL* 1.3 78.8 - - - +
398B LEU* 1.3 75.8 + - - +
429B LEU* 3.5 15.9 - - + +
431B PHE* 4.7 3.1 - - + -
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B VAL* 4.2 9.9 - - + -
396B VAL* 4.3 17.9 - - + -
397B VAL* 1.3 83.1 - - - +
399B ASP* 1.3 62.0 + - - +
401B ALA* 3.5 16.1 - - + +
404B MET* 4.3 8.7 - - + -
405B LEU* 4.2 17.9 - - + -
413B MET* 3.9 39.0 - - + -
417B MET* 4.6 6.7 - - - -
428B THR* 5.2 4.5 - - + -
429B LEU 2.8 11.7 + - - +
430B MET* 3.6 29.9 - - + -
431B PHE* 3.1 23.9 + - - +
446B PHE* 5.4 1.3 - - + -
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Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LYS* 5.3 3.5 - - - +
296B THR* 4.7 1.2 + - - -
299B PHE* 4.1 21.7 - - + -
323B ILE* 4.9 1.6 - - + -
324B VAL 3.2 18.1 + - - +
325B SER* 5.2 1.8 - - - -
326B PRO* 4.0 2.3 - - - +
330B LEU* 4.2 7.4 - - + +
334B ILE* 3.2 32.2 - - + +
397B VAL* 3.8 4.3 - - - +
398B LEU* 1.3 71.2 - - - +
400B GLU* 1.3 90.0 + - + +
401B ALA 3.0 1.9 + - - -
404B MET* 3.3 12.5 - - - +
431B PHE* 4.0 16.5 - - - +
432B SER* 5.4 0.2 - - - -
2802B MG 3.6 23.5 - - - -
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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