Contacts of the strand formed by residues 367 - 374 (chain T) in PDB entry 6O81
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 ILE 367 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297T ARG 4.7 11.7 + - - +
298T PRO* 5.2 2.5 - - + -
311T CYS* 4.2 16.8 - - + -
365T PRO 4.3 0.2 + - - -
366T GLU* 1.3 70.2 - - - +
368T PHE* 1.3 61.0 + - - +
369T THR 4.0 0.5 + - - -
432T PRO* 3.8 23.6 - - + -
433T VAL 3.7 6.7 - - - -
434T CYS* 4.1 5.1 - - + +
463T VAL 3.9 0.2 - - - +
464T THR* 3.5 0.5 - - - -
465T ILE* 2.9 47.3 + - + +
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Residues in contact with PHE 368 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365T PRO* 4.7 1.6 - - + -
366T GLU* 3.3 33.4 - - + -
367T ILE* 1.3 73.4 - - - +
369T THR* 1.3 61.2 + - - +
370T GLU 4.8 5.8 - - - +
371T LEU* 5.3 6.7 - - + -
429T LEU* 4.8 3.3 - - - +
431T ASN 4.3 2.1 - - - +
432T PRO* 3.7 6.8 - - - +
433T VAL* 2.9 39.5 + - + +
434T CYS* 4.5 2.9 - - - -
435T THR 4.9 0.9 - - - -
436T GLU 3.2 36.8 - - - -
437T VAL* 4.9 8.3 - - + -
462T GLY* 4.8 9.6 - - - -
463T VAL 3.4 12.3 - - - +
464T THR* 3.7 31.9 - - - -
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Residues in contact with THR 369 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367T ILE 4.0 0.8 + - - -
368T PHE* 1.3 73.9 - - - +
370T GLU* 1.3 62.4 + - - +
428T VAL* 3.6 4.0 - - - +
429T LEU* 2.9 35.9 + - - +
431T ASN 5.5 0.7 - - - -
432T PRO* 5.5 3.1 - - - -
463T VAL* 3.0 13.9 + - - -
465T ILE* 6.2 3.6 - - - -
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Residues in contact with GLU 370 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368T PHE* 5.2 1.6 - - - -
369T THR* 1.3 81.7 - - - +
371T LEU* 1.3 60.3 + - - +
372T GLU 4.2 0.3 + - - -
426T LYS* 5.9 4.3 - - + -
427T ILE 3.5 9.4 - - - +
428T VAL* 4.3 11.0 - - + -
462T GLY* 3.3 2.6 - - - -
463T VAL* 2.9 39.1 + - + +
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Residues in contact with LEU 371 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368T PHE* 5.3 10.1 - - + -
369T THR 4.3 0.2 - - - -
370T GLU* 1.3 72.3 - - - +
372T GLU* 1.3 60.4 + - - +
373T ILE* 3.7 5.2 + - + +
425T GLY 3.6 2.1 - - - +
426T LYS* 3.5 2.2 - - - -
427T ILE* 2.9 36.6 + - + +
429T LEU* 6.2 0.2 - - - +
459T ILE* 5.5 9.4 - - + -
461T ARG 3.5 9.0 - - - +
462T GLY* 4.3 2.7 - - - -
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Residues in contact with GLU 372 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370T GLU 4.2 1.2 + - - -
371T LEU* 1.3 69.3 - - - +
373T ILE* 1.3 61.3 + - - +
424T LEU* 5.8 6.1 - - + -
425T GLY 3.4 7.4 - - - +
426T LYS* 3.8 17.3 - - + +
459T ILE* 3.9 0.6 - - - -
460T ARG* 2.8 26.5 + - + +
461T ARG* 2.9 32.6 + - + +
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Residues in contact with ILE 373 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371T LEU* 3.7 6.4 + - + +
372T GLU* 1.3 76.0 - - - +
374T SER* 1.3 64.2 + - - +
424T LEU* 3.4 6.7 - - - +
425T GLY* 2.9 33.9 + - - +
441T ILE* 5.4 8.1 - - + +
457T GLY* 5.1 2.7 - - - -
458T GLN 3.3 18.2 - - - +
459T ILE* 4.0 10.5 - - + -
460T ARG* 3.9 4.3 - - - +
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Residues in contact with SER 374 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373T ILE* 1.3 75.4 - - - +
375T TYR* 1.3 63.5 + - - +
376T PHE* 3.2 7.0 + - - +
423T ASP 3.3 11.0 - - - -
424T LEU* 5.5 0.4 - - - -
456T TRP 3.6 0.7 - - - +
457T GLY* 3.3 19.8 - - - -
458T GLN* 3.0 23.9 + - - -
460T ARG* 5.2 2.4 - - - +
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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