Contacts of the helix formed by residues 367 - 382 (chain B) in PDB entry 3H3T
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 PHE 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365B HIS* 2.9 12.3 + - + -
366B ARG* 1.3 109.6 - - + +
368B VAL* 1.3 64.7 + - - +
369B GLN 3.2 3.2 + - - -
370B LYS* 3.3 21.5 + - + +
371B VAL* 2.9 21.9 + - + +
458B LEU* 4.1 11.2 - - + -
464B ILE* 3.9 19.7 - - + -
483B LEU* 3.4 28.5 - - + -
507B VAL* 3.5 35.4 - - + -
508B ASP 4.5 8.5 - - - -
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Residues in contact with VAL 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B HIS* 3.1 24.3 + - - -
366B ARG 3.5 1.2 - - - -
367B PHE* 1.3 77.3 - - - +
369B GLN* 1.3 55.9 + - - +
371B VAL* 3.2 5.6 + - - +
372B GLU* 3.0 31.1 + - - +
487B ARG* 5.6 0.2 + - - -
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Residues in contact with GLN 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ARG 5.1 1.5 + - - +
367B PHE 3.2 0.8 - - - -
368B VAL* 1.3 73.3 - - - +
370B LYS* 1.3 66.0 + - - +
372B GLU* 3.4 6.1 + - - +
373B GLU* 3.1 23.4 + - - +
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Residues in contact with LYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B PHE* 3.3 23.2 + - + +
369B GLN* 1.3 78.1 - - - +
371B VAL* 1.3 61.3 + - - +
373B GLU* 3.2 20.9 + - - +
374B MET* 3.0 53.7 + - + +
505B PHE* 3.5 32.3 - - + -
506B SER 5.6 2.5 - - - -
507B VAL* 5.8 0.2 - - + -
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B HIS* 4.4 8.3 - - + +
367B PHE 2.9 19.1 + - - +
368B VAL* 3.5 9.2 - - - +
370B LYS* 1.3 76.5 - - - +
372B GLU* 1.3 63.1 + - - +
374B MET* 3.4 1.2 + - - +
375B VAL* 3.0 27.9 + - + +
483B LEU* 3.9 20.9 - - + -
485B VAL* 3.9 28.7 - - + -
487B ARG* 3.8 22.9 - - - +
505B PHE* 3.7 25.8 - - + -
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Residues in contact with GLU 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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368B VAL 3.0 16.3 + - - +
369B GLN* 3.9 5.8 - - - +
370B LYS 3.3 0.2 - - - -
371B VAL* 1.3 77.8 - - - +
373B GLU* 1.3 56.5 + - - +
375B VAL* 3.8 9.1 - - - +
376B GLN* 2.8 37.5 + - - +
487B ARG* 3.2 35.1 + - - +
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Residues in contact with GLU 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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369B GLN 3.1 17.5 + - - +
370B LYS* 3.2 29.2 + - - +
372B GLU* 1.3 77.4 - - - +
374B MET* 1.3 58.9 + - + +
376B GLN* 3.9 4.4 - - - +
377B ASN* 2.9 51.4 + - - +
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Residues in contact with MET 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LYS* 3.0 48.1 + - + +
371B VAL 3.8 3.6 - - - +
373B GLU* 1.3 78.4 - - - +
375B VAL* 1.3 60.0 + - - +
377B ASN* 3.3 8.4 + - + +
378B HIS* 2.8 45.8 + - + +
503B CYS* 4.7 5.2 - - + -
505B PHE* 4.0 32.3 - - + -
524B ASN* 2.8 45.1 - - - +
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Residues in contact with VAL 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 VAL* 3.0 33.4 + - + +
372B GLU* 3.8 15.7 - - - +
374B MET* 1.3 75.3 - - - +
376B GLN* 1.3 59.6 + - - +
378B HIS* 3.9 1.2 - - - +
379B MET* 3.0 36.8 + - + +
485B VAL* 5.1 1.6 - - + -
487B ARG* 4.8 15.3 - - + +
489B ILE* 3.7 28.9 - - + -
501B ILE* 4.5 15.0 - - + +
503B CYS* 3.7 26.2 - - - -
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Residues in contact with GLN 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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372B GLU* 2.8 24.3 + - - +
373B GLU* 3.9 4.5 - - - +
375B VAL* 1.3 75.3 - - - +
377B ASN* 1.3 68.8 + - - +
379B MET* 3.1 10.1 + - - +
380B THR* 2.8 47.1 + - - +
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Residues in contact with ASN 377 (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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373B GLU* 2.9 43.3 + - - +
374B MET* 3.8 11.0 - - + +
376B GLN* 1.3 82.5 - - - +
378B HIS* 1.3 59.8 + - + +
380B THR* 4.5 1.5 + - - -
381B TYR* 2.8 53.8 + - + +
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Residues in contact with HIS 378 (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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374B MET* 2.8 37.7 + - + +
375B VAL 3.9 3.4 - - - +
377B ASN* 1.3 76.7 - - + +
379B MET* 1.3 61.2 + - - +
382B SER* 2.7 55.8 + - - +
383B LEU* 3.8 1.9 + - - +
501B ILE* 4.1 14.8 - - + -
503B CYS* 4.3 6.7 - - - +
524B ASN* 2.9 36.4 + - - -
525B VAL 4.4 2.2 + - - -
526B ALA* 3.6 20.4 - - + +
528B ILE* 4.4 4.0 - - + +
554B VAL* 3.5 24.8 - - + +
556B ASN* 5.1 5.4 - - - -
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Residues in contact with MET 379 (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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375B VAL* 3.0 31.9 + - + +
376B GLN* 3.1 12.3 + - - +
378B HIS* 1.3 76.3 - - - +
380B THR* 1.3 62.1 + - - +
383B LEU* 3.8 38.4 - - + +
489B ILE* 4.0 37.5 - - + -
499B THR* 4.1 20.0 - - + +
501B ILE* 4.5 9.6 - - - -
528B ILE* 4.3 20.9 - - - -
530B GLN* 5.4 0.4 - - - +
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Residues in contact with THR 380 (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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466A TYR* 6.2 2.0 - - + -
515A ASN* 3.5 24.9 - - - +
376B GLN* 2.8 37.0 + - - +
377B ASN* 3.8 4.0 - - - -
379B MET* 1.3 80.7 - - - +
381B TYR* 1.3 77.4 + - + +
383B LEU* 4.9 1.0 + - - +
384B GLN* 2.8 25.1 + - - +
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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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514A LEU 4.9 1.7 + - - -
515A ASN* 3.5 27.5 - - - -
516A ASN* 3.7 40.9 + - + +
517A ARG* 3.7 36.2 + - + +
377B ASN* 2.8 47.9 + - + +
380B THR* 1.3 91.3 - - + +
382B SER* 1.3 63.6 + - - +
383B LEU 3.2 4.5 + - - -
384B GLN* 3.3 20.9 + - - +
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Residues in contact with SER 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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517A ARG* 5.2 2.7 - - - +
377B ASN 4.7 0.3 + - - -
378B HIS* 2.7 50.1 + - - -
381B TYR* 1.3 73.5 - - - +
383B LEU* 1.3 51.2 + - - +
384B GLN 3.2 1.6 - - - -
419B LYS* 2.4 33.1 + - - +
528B ILE* 3.8 19.5 - - - -
552B THR* 3.5 7.2 - - - +
554B VAL* 3.7 18.2 - - - +
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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