Contacts of the strand formed by residues 375 - 379 (chain B) in PDB entry 3CUQ
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 375 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A LYS* 4.3 12.1 - - + +
338B THR* 3.6 22.4 - - - +
339B SER* 4.4 4.8 + - - +
354B LYS* 4.5 18.8 - - + +
358B LEU* 5.4 2.0 - - + -
368B ARG* 3.9 41.5 - - + +
369B ASP 3.8 4.7 - - - +
370B ASP* 4.4 19.5 - - + +
374B GLY* 1.3 70.2 - - - -
376B ARG* 1.3 71.8 + - - +
377B PHE* 4.0 28.6 - - + -
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Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER* 3.3 28.6 + - - +
337B LEU 3.8 8.3 - - - +
338B THR* 4.2 10.8 - - + -
341B GLU* 4.3 20.2 + - - -
368B ARG* 3.4 4.3 - - - -
369B ASP* 2.8 58.0 + - + +
373B GLU* 2.9 37.3 + - - +
374B GLY 4.6 4.7 - - - +
375B LEU* 1.3 76.8 - - - +
377B PHE* 1.3 62.6 + - - +
378B TYR* 4.0 11.5 + - + -
23C VAL* 4.3 22.6 - - + +
67D ARG* 5.2 1.2 - - - +
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Residues in contact with PHE 377 (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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331B VAL* 3.5 8.2 - - + +
336B SER* 3.2 7.3 - - - -
337B LEU 3.0 36.0 + - - +
339B SER* 4.2 13.5 - - - -
354B LYS* 5.5 1.8 - - + -
357B LEU* 3.5 46.4 - - + -
358B LEU* 4.2 16.8 - - + -
361B GLU* 4.1 24.9 - - + -
366B LEU* 4.2 25.1 - - + -
367B CYS 3.5 12.8 - - - +
368B ARG* 4.4 8.5 - - + -
375B LEU* 4.0 33.4 - - + -
376B ARG* 1.3 75.7 - - - +
378B TYR* 1.3 60.9 + - - +
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Residues in contact with TYR 378 (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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331B VAL* 4.0 3.8 - - - -
335B GLY 4.0 9.4 - - - -
336B SER* 3.4 32.6 + - - -
366B LEU* 3.1 6.8 - - - -
367B CYS* 2.8 31.8 + - - -
369B ASP* 3.7 26.4 + - + -
376B ARG* 4.0 13.0 + - + -
377B PHE* 1.3 75.6 - - - +
379B PRO* 1.3 74.0 - - + +
13D PHE* 3.8 21.5 - + + -
14D PRO* 3.5 24.7 - - + +
15D PRO* 3.5 26.9 - - + -
67D ARG* 5.5 0.7 + - - -
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Residues in contact with PRO 379 (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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328B LEU* 4.2 13.9 - - + -
331B VAL* 3.7 8.9 - - + -
332B SER* 3.7 26.9 - - - +
335B GLY 3.5 19.1 - - - +
365B HIS 3.9 6.5 - - - +
366B LEU* 4.4 0.2 - - + -
367B CYS* 3.3 8.1 - - - -
378B TYR* 1.3 91.7 - - + +
380B ASN* 1.3 60.2 + - - +
381B LEU* 2.8 26.3 + - + +
13D PHE* 3.6 9.0 - - + -
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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
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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