Contacts of the strand formed by residues 407 - 414 (chain B) in PDB entry 2R7D
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 TRP 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B PHE* 3.5 20.4 - + - -
399B ILE* 4.7 11.9 + - + +
402B GLN* 3.8 16.3 + - + -
405B ARG* 3.3 69.5 + - + +
406B VAL* 1.3 75.9 - - - +
408B ASP* 1.3 64.5 + - - +
409B ALA 3.6 0.3 + - - -
423B ILE* 3.9 24.7 - - + -
425B ASP* 4.5 11.9 - - + -
426B LEU* 3.5 37.9 - - + -
443B GLN* 3.5 6.6 - - - -
444B VAL* 2.9 41.8 + - + +
446B PHE* 3.8 29.9 - + + +
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Residues in contact with ASP 408 (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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406B VAL 5.1 2.8 - - - +
407B TRP* 1.3 72.8 - - - +
409B ALA* 1.3 59.4 + - - +
410B VAL* 5.6 0.4 - - - -
423B ILE* 3.7 10.9 - - - +
424B PRO* 3.5 18.9 - - + +
425B ASP* 4.9 11.2 + - - +
442B LEU 3.8 3.8 - - - -
443B GLN* 3.2 19.6 + - - +
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Residues in contact with ALA 409 (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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407B TRP 3.6 0.2 + - - -
408B ASP* 1.3 74.5 - - - +
410B VAL* 1.3 66.8 + - - +
421B LEU* 4.3 11.0 - - + -
422B LEU 3.1 12.6 - - - +
423B ILE* 3.5 14.4 - - + -
424B PRO* 4.4 0.2 - - - -
441B ALA* 3.1 7.8 - - - +
442B LEU* 2.8 33.9 + - - +
444B VAL* 3.4 30.3 - - + -
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 4.2 34.3 - - + -
306B PRO* 5.1 1.1 - - + -
408B ASP 5.6 0.4 - - - -
409B ALA* 1.3 82.0 - - - +
411B VAL* 1.3 73.9 + - - +
412B VAL* 3.4 3.1 + - + -
421B LEU* 3.4 3.7 - - - -
422B LEU* 2.7 41.0 + - - +
424B PRO* 4.5 8.5 - - + -
439B GLY* 4.0 22.2 - - - +
440B THR 4.3 0.2 - - - -
441B ALA* 4.2 14.4 - - + +
442B LEU* 6.3 0.2 - - - -
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PRO* 3.3 9.0 - - - +
410B VAL* 1.3 73.9 - - - +
412B VAL* 1.3 59.2 + - - +
413B ASP 3.4 23.6 - - - +
419B ALA* 3.8 16.6 - - + -
420B THR 3.7 3.6 - - - +
421B LEU* 4.5 5.2 - - + +
436B ALA* 4.0 16.4 - - + +
437B ALA 3.7 2.7 - - - +
438B PRO* 3.4 23.7 - - + -
439B GLY* 2.6 34.4 + - - +
440B THR* 3.4 28.8 + - - +
442B LEU* 4.2 10.5 - - + -
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 4.3 19.3 - - + -
306B PRO* 3.7 23.8 - - + +
309B TRP* 3.3 53.3 - - + +
310B ALA* 5.0 1.6 + - - +
410B VAL* 3.8 4.7 - - + +
411B VAL* 1.3 76.7 - - - +
413B ASP* 1.3 63.2 + - - +
420B THR* 2.9 29.9 + - + +
422B LEU* 3.5 37.5 - - + -
438B PRO* 5.2 1.5 - - - +
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Residues in contact with ASP 413 (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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309B TRP* 3.9 11.3 + - + +
310B ALA* 6.2 2.2 - - - -
313B LYS* 2.6 32.8 + - - -
411B VAL* 3.4 13.2 - - - +
412B VAL* 1.3 83.3 - - - +
414B ARG* 1.3 84.9 + - - +
419B ALA* 3.3 4.0 - - - -
420B THR* 2.7 44.1 + - - +
438B PRO* 4.9 7.0 - - - -
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Residues in contact with ARG 414 (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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413B ASP* 1.3 97.9 + - - +
415B ARG* 1.3 69.2 + - - +
416B GLY* 3.1 31.0 + - - +
417B ALA* 3.5 8.9 + - - +
418B GLN 3.3 6.5 - - - +
419B ALA* 3.3 17.1 - - - +
420B THR* 4.4 2.9 - - - +
434B THR 2.5 33.9 + - - -
435B PRO* 3.0 21.8 + - - +
436B ALA 3.3 17.3 + - - -
438B PRO* 4.6 17.7 - - + +
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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