Contacts of the strand formed by residues 395 - 399 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ILE* 4.4 7.9 - - + -
303A ILE* 3.8 33.9 - - + -
306A LYS* 3.9 31.2 - - + -
307A LEU* 4.8 6.5 - - + -
320A GLN 3.2 11.3 + - - -
321A VAL* 3.3 28.8 - - + +
322A VAL 2.9 25.8 + - - +
393A THR* 3.4 4.4 - - - +
394A ARG* 1.3 103.8 - - + +
396A VAL* 1.3 62.0 + - - +
397A VAL* 4.0 1.1 - - + -
427A GLN* 3.1 43.1 - - + -
429A LEU* 4.7 5.2 - - + -
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Residues in contact with VAL 396 (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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322A VAL* 3.5 13.7 - - + +
324A VAL* 5.9 1.3 - - + -
393A THR* 3.7 19.7 - - + -
395A PHE* 1.3 75.2 - - - +
397A VAL* 1.3 61.5 + - - +
398A LEU* 4.5 14.4 - - + -
416A ILE* 5.9 3.8 - - + -
417A MET* 4.4 25.1 - - + -
422A MET* 4.0 17.9 - - + -
426A HIS* 4.0 19.7 - - + +
427A GLN 2.9 10.5 + - - +
428A THR* 3.3 11.3 - - + +
429A LEU* 2.8 26.7 + - - +
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 3.9 36.3 - - + -
303A ILE* 3.5 32.1 - - + -
321A VAL* 4.8 2.9 - - + -
322A VAL 2.9 8.2 + - - +
323A ILE* 3.4 21.9 - - + -
324A VAL* 2.9 26.5 + - - +
396A VAL* 1.3 80.9 - - - +
398A LEU* 1.3 74.2 + - - +
399A ASP 3.9 0.2 + - - -
429A LEU* 3.3 23.6 - - + +
431A PHE* 4.6 2.5 - - + -
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Residues in contact with LEU 398 (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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324A VAL* 4.0 16.6 - - + -
396A VAL* 4.5 13.9 - - + +
397A VAL* 1.3 81.0 - - - +
399A ASP* 1.3 63.0 + - - +
401A ALA* 3.3 17.0 - - + +
404A MET* 4.4 7.4 - - + -
405A LEU* 4.1 26.5 - - + -
413A MET* 3.7 28.5 - - + -
416A ILE* 6.5 0.2 - - + -
417A MET* 3.9 24.9 - - + -
428A THR* 5.5 1.6 - - + -
429A LEU 2.8 11.8 + - - +
430A MET* 3.6 17.9 - - + -
431A PHE 3.2 23.2 + - - -
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Residues in contact with ASP 399 (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 LYS* 5.5 2.3 - - - +
296A THR* 5.1 1.7 + - - -
299A PHE* 4.3 20.2 - - + -
323A ILE* 4.9 1.6 - - + -
324A VAL 3.1 18.2 + - - +
325A SER* 5.2 0.7 - - - -
326A PRO* 4.0 1.9 - - - +
330A LEU* 4.2 7.9 - - + +
334A ILE* 3.4 31.7 - - + +
397A VAL* 3.8 3.9 + - - +
398A LEU* 1.3 71.0 - - - +
400A GLU* 1.3 89.9 + - + +
401A ALA 2.9 1.4 + - - -
404A MET* 3.5 11.3 - - - +
431A PHE* 3.9 16.9 - - - +
432A SER* 5.4 0.7 - - - -
2801A MG 3.4 24.9 - - - -
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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