Contacts of the helix formed by residues 369 - 376 (chain B) in PDB entry 6T2C
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 369 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B ARG* 4.9 2.5 - - - +
354B GLY* 3.8 7.0 - - - +
367B GLN* 5.4 1.1 - - - +
368B ILE* 1.3 89.0 - - - +
370B ALA* 1.3 64.1 + - - +
371B GLU* 3.6 6.9 + - - +
372B ASN* 2.3 43.9 + - - +
373B LEU* 4.2 3.5 - - - +
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Residues in contact with ALA 370 (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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350B ARG* 5.9 2.2 - - + -
351B LEU* 4.4 21.9 - - + +
352B GLY 3.3 28.9 + - - +
353B ARG 4.7 0.4 - - - -
354B GLY* 4.0 7.1 - - - +
369B SER* 1.3 75.1 - - - +
371B GLU* 1.3 63.3 + - - +
372B ASN 3.1 2.0 - - - -
373B LEU* 3.1 31.5 + - + +
396B MET* 5.5 1.2 - - - +
399B GLY* 4.8 11.5 - - - +
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Residues in contact with GLU 371 (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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369B SER* 3.4 4.2 + - - +
370B ALA* 1.3 77.7 - - - +
372B ASN* 1.3 63.7 + - - +
373B LEU 3.3 0.8 + - - -
374B SER* 4.5 3.2 + - - -
375B ASP* 3.9 13.9 - - - +
398B GLU* 5.0 9.3 - - - +
399B GLY* 4.3 23.7 - - - +
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Residues in contact with ASN 372 (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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376A PHE* 4.7 19.0 - - + -
377A GLU* 5.6 2.0 + - - -
368B ILE* 4.9 5.1 - - + +
369B SER* 2.3 41.9 + - - +
370B ALA 3.1 1.4 - - - -
371B GLU* 1.3 79.0 - - - +
373B LEU* 1.3 64.0 + - - +
374B SER 3.3 2.2 - - - -
375B ASP* 3.4 15.6 + - - +
376B ILE* 3.3 34.2 + - + +
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Residues in contact with LEU 373 (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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36B THR* 4.0 26.2 - - + -
40B MET* 4.5 8.5 - - - -
351B LEU* 4.3 17.5 - - + -
354B GLY* 5.5 0.7 - - - -
355B TYR* 4.4 12.1 - - + -
368B ILE* 4.3 20.9 - - + -
369B SER 4.2 3.6 - - - +
370B ALA* 3.1 27.9 + - + +
371B GLU 3.3 0.2 - - - -
372B ASN* 1.3 79.7 - - - +
374B SER* 1.3 51.6 + - - +
375B ASP 3.4 0.2 + - - -
376B ILE* 4.2 5.3 + - - +
381B PHE* 4.3 6.1 - - + -
389B ILE* 3.8 31.9 - - + +
393B ARG* 2.6 31.4 + - - -
396B MET* 4.1 14.1 - - + -
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Residues in contact with SER 374 (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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370B ALA 4.9 0.2 + - - -
371B GLU 4.5 4.1 + - - -
372B ASN 3.3 0.2 - - - -
373B LEU* 1.3 79.2 - - - +
375B ASP* 1.3 83.6 + - - +
393B ARG* 2.9 32.8 + - - +
396B MET* 3.8 35.9 - - - +
399B GLY 6.0 0.3 + - - -
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Residues in contact with ASP 375 (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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371B GLU 3.9 12.7 - - - +
372B ASN* 3.4 10.8 + - - +
373B LEU 3.3 0.2 - - - -
374B SER* 1.3 109.8 + - - +
376B ILE* 1.3 58.7 + - - +
393B ARG* 4.5 2.0 - - - +
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Residues in contact with ILE 376 (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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376A PHE* 4.0 30.7 - - + -
357B PHE* 4.7 2.7 - - + -
368B ILE* 3.8 27.4 - - + -
372B ASN* 3.3 21.1 - - + +
373B LEU* 4.2 8.9 + - - +
374B SER 3.8 1.4 - - - -
375B ASP* 1.3 76.3 - - - +
377B ASN* 1.3 79.5 + - - +
378B LEU* 3.7 9.1 + - + +
380B TYR* 4.7 11.2 - - + -
381B PHE* 3.8 19.7 - - + -
393B ARG* 3.9 15.4 + - - -
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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