Contacts of the strand formed by residues 409 - 414 (chain F) in PDB entry 6T8B
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 VAL 409 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A ARG* 3.5 29.8 - - - +
369F GLU* 3.6 1.4 - - - -
370F ILE* 2.8 53.2 + - + +
372F PRO* 3.5 17.6 - - + +
378F VAL* 3.8 22.2 - - + -
381F ILE* 4.7 7.0 - - + -
399F VAL* 3.8 27.4 - - + -
400F VAL 3.9 7.2 - - - +
401F GLU 4.5 1.1 - - - +
408F THR* 1.3 76.8 - - - +
410F GLY* 1.3 62.9 + - - +
411F ILE* 4.9 0.4 - - + -
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Residues in contact with GLY 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F ARG* 4.2 17.7 - - - -
368F PHE 4.3 1.6 - - - -
369F GLU* 4.3 2.5 - - - -
398F ARG 3.6 0.2 - - - +
399F VAL 3.4 0.5 - - - -
400F VAL* 2.5 57.1 + - - +
403F ILE* 4.1 8.8 - - - +
409F VAL* 1.3 73.4 - - - +
411F ILE* 1.3 61.8 + - - -
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Residues in contact with ILE 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F LEU* 4.2 13.7 - - + -
347F LEU* 3.9 19.1 - - + -
366F THR 3.5 0.7 - - - +
367F ARG* 3.3 0.7 - - - -
368F PHE* 2.6 45.4 + - - +
370F ILE* 3.5 30.1 - - + -
381F ILE* 4.4 9.9 - - + -
388F LEU* 3.9 15.9 - - + -
397F VAL* 4.3 14.6 - - + -
398F ARG 3.6 3.8 - - - +
399F VAL* 4.3 16.2 - - + -
409F VAL* 3.9 0.6 + - + -
410F GLY* 1.3 74.2 - - - +
412F GLU* 1.3 60.3 + - - +
413F ILE* 3.8 27.3 + - + -
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Residues in contact with GLU 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365F ILE* 3.7 30.5 - - + +
366F THR 3.7 5.8 - - - -
367F ARG* 2.9 45.3 + - + +
396F SER 4.7 0.2 - - - +
397F VAL* 3.9 0.7 - - - -
398F ARG* 2.8 36.2 + - - +
400F VAL* 3.2 19.9 - - + +
411F ILE* 1.3 74.0 - - - +
413F ILE* 1.3 63.1 + - - +
414F PRO* 3.7 5.5 - - - +
447F ILE* 3.3 6.6 - - - +
690F ARG* 3.1 39.6 + - - +
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Residues in contact with ILE 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F MET* 4.0 12.3 - - + -
343F LEU* 4.1 11.0 - - + -
365F ILE* 4.3 0.4 - - - -
366F THR* 3.0 31.5 + - - +
368F PHE* 3.4 39.3 - - + -
392F LEU* 3.8 24.7 - - + -
394F VAL* 3.7 20.4 - - + -
397F VAL* 3.6 17.3 - - + -
411F ILE* 3.8 11.0 - - + -
412F GLU* 1.3 71.6 - - - +
414F PRO* 1.3 83.9 - - + +
415F ASN 3.7 0.2 + - - -
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Residues in contact with PRO 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364F VAL 3.6 8.7 - - - +
365F ILE* 4.0 7.0 - - + -
394F VAL* 4.2 21.1 - - + +
395F ILE* 4.5 10.3 - - + +
396F SER 3.9 20.6 - - - +
397F VAL* 4.3 5.8 - - + -
412F GLU 3.7 7.2 - - - +
413F ILE* 1.3 102.1 - - + +
415F ASN* 1.3 69.6 + - - +
416F GLU* 5.4 0.7 - - - +
673F LEU* 3.9 31.0 - - + -
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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