Contacts of the strand formed by residues 412 - 418 (chain B) in PDB entry 4U7D
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 412 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ASN 3.0 6.9 + - - +
286B LEU* 3.5 14.8 - - + -
287B TYR* 2.7 32.4 + - - +
383B VAL 3.8 11.9 - - - +
384B ARG* 3.1 22.4 - - - +
405B ALA* 4.3 2.9 - - + -
406B GLY* 3.8 18.6 - - - +
410B MET 3.3 0.4 + - - +
411B LYS* 1.3 75.9 - - - +
413B ASP* 1.3 62.3 + - - +
474B MET* 5.2 0.4 - - - +
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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
----------------------------------------------------------
287B TYR* 3.2 29.0 - - + +
311B ARG* 3.4 16.5 + - - -
312B TYR* 2.5 44.5 + - + +
384B ARG 2.7 12.1 + - - +
385B PHE* 3.2 4.3 - - + +
386B VAL 2.9 26.0 + - - +
405B ALA* 4.6 0.9 - - - +
412B ALA* 1.3 75.5 - - - +
414B CYS* 1.3 63.6 + - - +
415B ILE* 4.1 7.1 - - + +
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Residues in contact with CYS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.2 14.6 - - - -
287B TYR 2.6 16.1 + - - +
288B TYR* 3.6 29.4 - - + -
289B GLU 3.0 26.7 + - - +
386B VAL* 3.4 8.3 - - - +
398B TYR* 3.7 13.2 + - - +
402B SER* 3.7 29.2 - - - -
405B ALA* 4.2 10.3 - - - -
413B ASP* 1.3 77.2 - - - +
415B ILE* 1.3 59.5 + - - +
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Residues in contact with ILE 415 (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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287B TYR* 5.5 2.2 - - + +
289B GLU* 3.4 16.8 - - + +
291B ARG* 3.8 39.5 - - + +
307B LEU* 4.6 15.5 - - + -
311B ARG* 4.2 13.5 - - - +
312B TYR* 3.5 26.7 - - + +
385B PHE* 6.1 0.7 - - + -
386B VAL 3.0 10.1 + - - -
387B ILE* 3.3 17.9 - - + +
388B HIS* 2.7 30.8 + - - -
398B TYR* 4.6 1.6 - - - -
413B ASP* 4.5 3.8 - - + -
414B CYS* 1.3 81.5 - - - +
416B LEU* 1.3 56.9 + - - +
417B TYR* 4.0 15.3 - - + -
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Residues in contact with LEU 416 (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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289B GLU 2.9 14.0 + - - +
290B VAL* 3.3 8.3 - - + -
291B ARG 2.9 27.9 + - - +
388B HIS* 3.8 16.8 - - + -
391B MET* 4.0 16.8 - - + +
398B TYR* 3.9 33.2 - - + +
414B CYS 4.1 0.6 + - - -
415B ILE* 1.3 73.4 - - - +
417B TYR* 1.3 77.6 + - - +
418B TYR* 3.6 4.4 + - + +
443B MET* 4.2 12.8 - - - -
446B TYR* 4.2 13.9 - - + -
447B CYS* 3.9 31.2 - - - -
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Residues in contact with TYR 417 (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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291B ARG* 3.4 43.4 + - + -
292B GLN 3.5 20.6 - - - -
293B LYS* 3.8 13.1 - - + +
294B PRO* 5.0 1.1 - - + -
300B PHE* 3.4 46.2 - + + -
303B ASP* 4.9 13.3 - - + +
304B ILE* 4.9 7.5 - - + +
307B LEU* 3.6 23.0 - - + +
387B ILE* 4.0 23.3 - - + -
388B HIS 2.9 20.4 + - - +
389B HIS 3.8 7.2 - - - +
390B SER* 4.1 6.8 - - - -
391B MET 4.1 1.4 + - - -
415B ILE* 4.0 10.9 - - + +
416B LEU* 1.3 77.7 - - - +
418B TYR* 1.3 62.2 + - - +
419B GLY 3.6 2.6 + - - -
422B ASP* 4.4 0.2 - - - +
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Residues in contact with TYR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 4.0 14.6 - - + -
291B ARG 3.0 14.7 + - - +
292B GLN* 3.2 20.8 + - - +
293B LYS* 2.9 23.9 + - - +
391B MET* 3.5 29.2 - - + -
416B LEU* 3.6 4.8 + - - -
417B TYR* 1.3 69.5 - - - +
419B GLY* 1.3 69.7 + - - +
420B PHE* 4.4 7.5 - - - -
423B ILE* 4.3 8.2 - - + +
444B VAL* 4.0 5.3 - - + +
447B CYS* 3.6 38.4 - - + -
448B GLN* 2.6 34.5 + - + +
543B GLU 5.0 0.5 + - - -
544B LYS* 4.9 10.0 - - + -
547B ALA* 3.6 15.4 - - - +
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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