Contacts of the strand formed by residues 367 - 374 (chain C) in PDB entry 1TTT
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 ASN 367 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320C VAL 3.0 9.9 - - - +
321C TYR* 3.3 36.7 - - - +
365C GLY 3.5 9.1 + - - -
366C ASP* 1.3 74.9 - - - +
368C VAL* 1.3 63.8 + - - +
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Residues in contact with VAL 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C SER* 4.0 1.2 + - - -
320C VAL 2.8 22.3 + - - +
322C ILE* 3.9 9.6 - - + -
355C LEU* 4.2 1.1 - - + -
356C PRO* 4.3 2.7 - - + -
359C VAL* 4.1 17.5 - - + -
362C VAL* 3.1 51.4 - - + -
366C ASP* 3.6 2.9 - - + +
367C ASN* 1.3 76.5 - - - +
369C THR* 1.3 80.3 + - - +
370C PHE* 3.1 30.7 - - + -
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Residues in contact with THR 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C GLU* 5.0 10.8 - - + -
318C ALA 3.2 16.8 - - - +
319C SER* 3.7 14.4 - - - -
320C VAL 4.0 0.9 - - - +
356C PRO* 2.9 27.8 - - + +
368C VAL* 1.3 85.5 + - - +
370C PHE* 1.3 77.3 + - - +
401C THR* 6.1 1.8 - - + -
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Residues in contact with PHE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C GLU* 3.4 5.8 - - - +
318C ALA* 2.9 29.3 + - - +
320C VAL* 3.5 33.2 - - + -
322C ILE* 4.6 7.6 - - + -
334C PHE* 4.7 6.3 - + - -
342C PHE* 5.4 0.7 - + - -
353C VAL* 3.2 32.8 - - + -
354C ARG 3.2 15.5 - - - +
355C LEU* 3.8 8.1 - - + -
356C PRO* 3.3 12.3 - - + -
362C VAL* 4.7 0.7 - - + -
368C VAL* 3.1 39.9 - - + -
369C THR* 1.3 85.9 - - - +
371C THR* 1.3 69.3 + - - +
372C VAL* 4.4 13.4 - - + +
388C ILE* 5.0 7.9 - - + -
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Residues in contact with THR 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C LYS* 4.2 21.5 - - - +
316C PHE 3.4 7.0 - - - +
317C GLU* 4.4 8.5 + - - +
352C VAL 3.6 2.6 - - - +
353C VAL* 3.6 1.7 - - - -
354C ARG* 3.2 41.3 + - + -
370C PHE* 1.3 81.8 + - - +
372C VAL* 1.3 85.0 + - - +
373C GLU* 4.8 3.8 - - - +
404C LEU* 4.3 13.3 - - + +
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Residues in contact with VAL 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C THR 3.9 1.3 - - - -
315C LYS* 3.0 4.7 - - - +
316C PHE* 2.8 64.6 + - + +
318C ALA* 5.3 3.1 - - + -
342C PHE* 3.3 50.0 - - + -
351C GLY* 4.1 5.4 - - - -
352C VAL 3.6 7.6 - - - +
353C VAL* 5.2 0.7 - - - -
370C PHE* 4.4 14.8 - - + +
371C THR* 1.3 85.7 - - - +
373C GLU* 1.3 70.5 + - - +
374C LEU* 4.3 2.5 - - + +
386C PHE* 5.6 0.2 - - + -
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Residues in contact with GLU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C THR* 3.1 6.5 - - - +
315C LYS* 3.4 41.0 + - + +
351C GLY* 3.5 0.3 - - - -
352C VAL* 3.0 31.7 + - + +
354C ARG* 2.6 45.8 + - - +
371C THR* 4.8 1.2 - - - +
372C VAL* 1.3 77.7 - - - +
374C LEU* 1.3 64.7 + - - +
375C ILE* 4.7 1.9 - - - +
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Residues in contact with LEU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C HIS 4.1 8.7 - - - +
314C THR* 2.5 33.0 + - - +
316C PHE* 3.6 26.5 - - + -
342C PHE* 4.6 6.5 - - + -
344C PHE* 4.2 12.6 - - + -
349C VAL* 3.4 41.3 - - + +
350C THR 3.7 5.2 - - - +
351C GLY* 4.1 4.0 - - - -
372C VAL* 4.5 0.9 - - + -
373C GLU* 1.3 75.2 - - - +
375C ILE* 1.3 62.5 + - - +
376C LYS 3.2 15.2 + - - +
378C VAL* 4.2 13.7 - - + -
380C LEU* 4.0 16.8 - - + -
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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