Contacts of the strand formed by residues 407 - 412 (chain B) in PDB entry 3BEQ
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 SER 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B LYS* 3.2 17.8 + - - +
351B GLY* 3.3 26.7 - - - -
352B PHE* 3.5 12.6 - - - -
363B GLY 4.9 1.2 + - - -
374B PHE* 3.4 38.8 - - - -
405B GLY 4.6 0.3 + - - -
406B TYR* 1.3 76.5 - - - +
408B GLY* 1.3 58.6 + - - +
423B TRP* 3.1 24.2 - - - -
424B VAL* 4.3 2.7 - - - -
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Residues in contact with GLY 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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228B SER* 4.7 0.9 - - - -
279B SER* 3.5 12.8 - - - -
350B LYS* 4.3 0.9 - - - -
352B PHE* 3.7 10.2 - - - -
407B SER* 1.3 76.4 - - - +
409B SER* 1.3 64.0 + - - -
422B PHE* 3.2 6.4 - - - +
423B TRP* 3.0 50.4 + - - -
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Residues in contact with SER 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE 4.6 0.3 - - - +
228B SER* 4.6 6.5 + - - -
229B GLU* 3.9 11.1 - - - +
279B SER* 3.6 25.6 + - - -
280B CYS 3.8 12.5 + - - -
281B TYR* 4.4 7.2 - - - +
352B PHE* 3.7 16.0 - - - +
353B SER 5.7 0.4 - - - -
354B PHE* 3.6 28.5 - - - -
408B GLY* 1.3 74.7 - - - -
410B PHE* 1.3 65.5 + - - +
421B CYS 3.6 5.8 - - - -
422B PHE* 4.4 0.4 - - - +
423B TRP* 4.0 6.3 + - - -
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Residues in contact with PHE 410 (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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100B TYR* 4.2 16.8 - + - -
122B ILE* 3.2 69.8 - - + +
124B CYS* 4.0 13.2 - - - -
229B GLU* 3.0 14.8 - - - +
354B PHE* 4.4 0.5 - - - -
409B SER* 1.3 72.4 - - - +
411B VAL* 1.3 75.1 + - - +
412B GLN* 4.5 6.1 - - + -
420B PRO* 4.1 0.2 - - - +
421B CYS* 2.9 67.1 + - + +
422B PHE* 3.7 21.3 - - - -
423B TRP* 3.9 11.7 - + - -
445B SER* 4.0 2.0 - - - -
446B PHE 4.5 0.4 - - - -
447B CYS* 4.3 2.0 - - - -
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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
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91B LEU* 5.0 1.3 - - + -
124B CYS* 4.0 12.1 - - - +
229B GLU* 2.9 16.7 + - - +
281B TYR* 3.8 26.7 - - + -
282B PRO* 3.8 18.6 - - + +
354B PHE* 4.7 3.6 - - + -
410B PHE* 1.3 87.2 - - - +
412B GLN* 1.3 95.0 + - - +
418B MET* 4.0 19.5 - - + -
419B ARG 3.2 13.2 - - - +
420B PRO* 4.5 6.1 - - + -
421B CYS* 5.0 0.2 - - - -
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Residues in contact with GLN 412 (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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100B TYR* 3.2 36.9 + - - -
124B CYS* 4.1 6.5 - - - -
129B CYS* 3.4 15.4 - - - -
410B PHE* 4.5 2.1 - - + -
411B VAL* 1.3 78.1 - - - +
412B HIS* 1.3 84.5 + - - +
413B THR* 3.6 19.9 - - + +
417B CYS 4.4 0.7 - - - +
418B MET* 4.0 2.0 - - - +
419B ARG* 3.0 61.4 + - + +
421B CYS* 4.0 16.2 - - - -
447B CYS* 4.1 2.8 - - - -
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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