Contacts of the strand formed by residues 386 - 390 (chain B) in PDB entry 2N5T
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 LEU 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B TYR* 4.9 5.4 - - + +
320B VAL* 5.9 0.4 - - + -
321B ALA* 3.9 23.6 - - + +
329B VAL* 3.4 15.9 - - + +
331B VAL* 3.9 23.3 - - + -
377B ILE* 3.6 19.3 - - + +
380B ALA* 3.5 15.7 - - + +
381B SER* 3.4 36.1 - - - +
384B GLY 3.1 12.0 + - - +
385B LYS* 1.3 86.3 - - - +
387B ARG* 1.3 66.9 + - - +
421B ASP* 4.9 3.4 + - - +
424B ILE* 3.4 22.1 - - + +
425B GLU 4.5 1.7 + - - -
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Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 5.8 2.0 + - - -
328B ALA* 3.0 32.3 - - - +
329B VAL 2.8 11.5 + - - +
330B ILE* 4.2 19.1 - - + +
331B VAL* 2.8 34.5 + - - +
377B ILE* 4.7 0.2 - - - +
385B LYS* 2.7 32.1 - - - +
386B LEU* 1.3 80.1 - - - +
388B ILE* 1.3 60.9 + - - +
424B ILE* 4.4 0.9 - - - -
425B GLU* 3.4 36.2 + - + +
448B PHE* 3.6 32.5 - - + -
498B TRP* 4.2 15.4 - - - +
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B VAL 3.5 3.8 - - - +
333B THR* 4.0 11.7 - - + -
374B LEU* 3.8 31.2 - - + -
377B ILE* 3.6 25.6 - - + -
378B LEU* 3.9 29.8 - - + -
387B ARG* 1.3 72.3 - - - +
389B MET* 1.3 66.4 + - - +
390B PHE* 4.1 17.3 - - + -
406B ILE* 4.4 16.4 - - + -
424B ILE* 3.9 9.4 - - + -
425B GLU 2.9 9.7 + - - +
426B ILE* 3.3 11.3 - - + -
427B GLY 2.8 25.1 + - - -
448B PHE* 3.5 3.4 - - - -
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Residues in contact with MET 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLY 4.1 6.5 - - - +
294B LEU* 3.3 34.5 - - + -
330B ILE* 3.7 24.5 - - + -
331B VAL 3.0 7.6 + - - +
332B ARG* 3.2 9.3 - - + -
333B THR* 2.8 31.4 + - - +
388B ILE* 1.3 78.2 - - - +
390B PHE* 1.3 64.9 + - - +
427B GLY 3.4 6.1 - - - +
428B VAL* 3.8 17.9 - - - +
429B MET* 3.4 18.8 - - + +
448B PHE* 3.8 16.2 - - + -
450B SER* 3.4 30.7 - - - -
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Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG* 4.3 0.2 - - - -
333B THR* 3.2 31.9 - - + -
360B ILE* 3.5 13.9 - - + -
370B LEU* 4.5 3.1 - - + -
374B LEU* 4.2 12.6 - - + -
388B ILE* 4.1 7.0 - - + -
389B MET* 1.3 73.3 - - - +
391B PRO* 1.3 63.6 - - + +
393B ILE* 3.7 21.4 - - + +
399B VAL* 5.5 4.0 - - + -
402B LEU* 3.5 35.9 - - + -
403B ARG* 5.0 2.2 - - + -
406B ILE* 3.7 34.8 - - + -
426B ILE* 4.1 12.1 - - + -
427B GLY 3.3 16.1 + - - +
428B VAL* 3.7 7.7 - - + -
429B MET* 2.7 36.0 + - - +
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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
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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