Contacts of the strand formed by residues 286 - 292 (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 LEU 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B ARG* 3.0 40.5 + - + +
284B PRO 3.2 0.6 - - - -
285B ASN* 1.3 87.7 - - - +
287B TYR* 1.3 60.0 + - - +
288B TYR* 3.5 30.3 + - + +
402B SER 4.3 9.9 - - - +
403B GLY* 4.5 2.7 - - - -
405B ALA* 3.5 30.7 - - + +
406B GLY 4.9 0.2 - - - +
412B ALA* 3.5 22.2 - - + -
414B CYS* 4.2 15.7 - - - -
455B ARG* 2.8 32.5 + - - +
474B MET* 3.2 6.1 - - - +
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Residues in contact with TYR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN 3.8 0.6 + - - -
286B LEU* 1.3 71.0 - - - +
288B TYR* 1.3 62.0 + - - +
289B GLU* 3.2 43.0 + - + -
311B ARG* 5.5 6.1 - - - -
412B ALA 2.7 10.4 + - - +
413B ASP* 3.2 31.0 - - + +
414B CYS* 2.6 34.2 + - - +
415B ILE* 5.6 2.2 - - + -
473B LYS 4.4 3.1 - - - -
474B MET* 3.5 27.8 - - + +
475B CYS 3.9 15.9 - - - -
476B ASP* 3.4 19.5 - - - -
479B CYS* 4.3 17.4 - - - +
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Residues in contact with TYR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 5.2 3.3 - + - -
282B ASN* 5.7 0.2 - - - -
283B ARG* 4.8 6.0 + - - +
286B LEU* 3.5 24.5 - - + +
287B TYR* 1.3 72.5 - - - +
289B GLU* 1.3 60.7 + - - +
398B TYR* 4.4 12.6 - + - -
399B TYR* 4.5 11.3 + - - -
402B SER* 4.1 15.4 + - - -
403B GLY* 5.7 0.7 - - - -
414B CYS* 3.6 31.4 - - + -
446B TYR* 4.1 7.2 - - - +
454B ARG* 3.9 22.8 - - + +
455B ARG* 3.7 45.5 - - + -
458B MET* 4.1 30.9 - - + +
474B MET 3.2 7.9 + - - -
475B CYS* 3.1 5.1 - - + +
476B ASP* 2.9 27.7 + - - +
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Residues in contact with GLU 289 (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 36.2 + - + -
288B TYR* 1.3 75.1 - - - +
290B VAL* 1.3 76.4 + - - +
291B ARG* 2.7 43.0 + - + -
311B ARG* 5.0 1.2 + - - -
398B TYR* 4.6 1.6 + - - -
414B CYS 3.0 11.6 + - - +
415B ILE* 4.5 12.2 - - + +
416B LEU* 2.9 24.9 + - - +
446B TYR* 5.0 1.3 + - - -
454B ARG* 5.0 0.2 - - - -
476B ASP* 3.5 19.8 - - + +
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Residues in contact with VAL 290 (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* 1.3 77.5 - - - +
291B ARG* 1.3 70.1 + - - +
416B LEU* 3.3 19.7 - - + +
418B TYR* 4.0 18.4 - - + -
446B TYR* 3.3 37.0 - - + -
447B CYS* 4.0 20.2 - - + +
454B ARG* 3.7 22.1 + - - +
476B ASP* 2.9 16.6 + - - +
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Residues in contact with ARG 291 (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* 2.7 32.7 + - + +
290B VAL* 1.3 80.6 - - - +
292B GLN* 1.3 63.0 + - - +
303B ASP* 6.3 0.4 - - - +
307B LEU* 4.3 18.6 - - - +
311B ARG* 3.8 29.7 - - - +
415B ILE* 3.8 14.2 - - + +
416B LEU 2.9 7.3 + - - +
417B TYR* 3.4 43.3 + - + -
418B TYR* 3.0 28.5 + - - +
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Residues in contact with GLN 292 (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* 1.3 75.2 - - - +
293B LYS* 1.3 92.8 + - - +
294B PRO* 3.7 6.1 - - + +
417B TYR* 3.5 12.5 - - - -
418B TYR* 3.2 25.4 + - - +
419B GLY* 4.5 4.6 - - - -
420B PHE 5.3 0.4 - - - +
540B GLU* 4.1 29.2 - - + +
543B GLU* 4.7 8.5 + - - +
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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