Contacts of the helix formed by residues 376 - 383 (chain B) in PDB entry 5J1T
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 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 4.4 8.0 - - + +
174A LYS* 4.3 15.0 - - + -
344B LYS* 4.4 16.4 - - - +
373B GLY 3.2 17.7 + - - +
374B SER 3.1 1.4 - - - -
375B THR* 1.3 78.1 + - - +
377B ILE* 1.3 59.8 + - - +
378B PHE 3.0 0.4 - - - -
379B TYR* 3.0 50.6 + - + +
380B LYS 4.2 0.7 + - - -
435B PHE 4.0 20.6 - - - +
436B ASN 4.3 8.1 - - - +
437B HIS 4.2 15.7 - - - +
438B MET* 3.8 27.4 - - + -
442B LYS* 4.3 13.2 - - + -
446B LEU* 5.4 0.4 - - + -
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR 4.9 1.3 - - - +
139A PRO* 4.0 24.5 - - + -
140A HIS* 4.3 7.9 - - + -
344B LYS* 3.9 14.6 - - + +
347B VAL* 3.8 25.4 - - + -
348B ASP* 3.8 39.5 - - + +
374B SER 3.1 18.5 + - - +
375B THR 3.0 1.4 - - - -
376B LEU* 1.3 78.3 - - - +
378B PHE* 1.3 75.2 + - + +
380B LYS* 3.0 31.6 + - + +
381B TYR* 3.4 17.1 - - + -
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Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B VAL* 3.9 20.4 - - + -
351B LEU* 4.2 15.3 - - + -
364B VAL* 4.1 21.5 - - + -
367B PHE* 3.5 29.8 - + + -
370B PHE* 4.7 9.2 - + - -
374B SER 5.2 0.2 - - - -
375B THR* 2.9 25.1 + - - +
377B ILE* 1.3 90.3 - - + +
379B TYR* 1.4 64.7 + - - +
381B TYR* 3.8 4.7 - - + +
382B CYS* 2.9 46.8 + - - +
394B LEU* 4.2 13.5 - - + -
396B LEU* 4.2 14.8 - - + -
446B LEU* 3.7 16.8 - - + -
449B ARG* 5.9 0.2 - - - -
450B ILE* 4.4 2.5 - - + -
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Residues in contact with TYR 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 3.5 25.1 + - + +
171A GLN* 3.8 26.5 - - - -
174A LYS* 3.1 21.4 + - - -
208A ASN* 3.8 0.7 + - - -
376B LEU* 3.0 46.5 + - + +
378B PHE* 1.4 78.8 - - - +
380B LYS* 1.3 61.8 + - - +
383B ASP* 3.3 27.0 + - - +
442B LYS 2.7 21.6 + - - -
445B GLY* 3.2 11.4 + - - -
446B LEU* 3.5 27.1 - - + +
449B ARG* 3.6 42.6 - - - +
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR 3.4 25.4 + - - +
136A LEU* 3.9 24.0 + - + +
139A PRO* 5.1 6.0 - - + +
348B ASP* 2.8 36.8 + - - +
377B ILE* 3.0 23.2 + - + +
379B TYR* 1.3 79.6 - - - +
381B TYR* 1.3 77.5 + - + +
386B ASN 4.3 2.3 - - - +
387B ALA* 3.5 5.0 - - - -
388B ALA* 2.9 32.9 + - + -
101C ASN* 6.0 0.2 - - - -
107C TYR* 3.0 47.0 + - - -
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Residues in contact with TYR 381 (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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293B PRO* 3.2 22.3 - - - +
348B ASP* 2.7 43.2 + - - -
351B LEU* 3.7 34.5 - - + -
352B SER* 3.4 11.8 + - - -
355B PHE* 4.3 13.5 - + - -
377B ILE* 3.4 24.7 - - + +
378B PHE* 3.2 7.9 + - + +
379B TYR 3.2 0.4 - - - -
380B LYS* 1.3 96.2 - - + +
382B CYS* 1.3 61.4 + - - +
383B ASP 3.7 0.7 - - - -
387B ALA* 3.6 5.9 - - - +
388B ALA* 4.2 8.3 - - + +
389B PHE* 3.8 35.6 - + + +
392B VAL* 6.3 0.2 - - + -
394B LEU* 4.1 21.8 - - + +
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Residues in contact with CYS 382 (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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292B GLU* 4.5 5.7 - - - +
293B PRO* 4.4 7.7 - - - +
295B THR* 3.7 23.1 + - - +
378B PHE* 2.9 33.3 + - - +
381B TYR* 1.3 85.2 - - - +
383B ASP* 1.3 68.6 + - - +
384B HIS* 3.5 1.9 + - - -
394B LEU* 4.5 7.6 - - - -
396B LEU* 5.6 0.4 - - - -
449B ARG* 3.5 39.0 - - + +
450B ILE* 4.0 17.5 - - + -
452B HIS* 5.1 0.5 + - - -
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Residues in contact with ASP 383 (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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133A VAL* 5.9 4.9 - - + +
170A ASP* 5.5 2.0 - - - +
171A GLN* 5.0 0.9 + - - -
292B GLU* 3.8 6.6 - - - +
293B PRO* 4.2 0.2 - - - +
379B TYR* 3.3 18.1 + - - +
381B TYR 3.7 1.2 - - - -
382B CYS* 1.3 80.9 - - - +
384B HIS* 1.3 66.3 + - - +
385B GLU* 2.9 17.7 + - - +
386B ASN* 2.9 32.9 + - + +
387B ALA* 3.4 29.2 - - - +
449B ARG* 2.8 42.1 + - - +
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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