Contacts of the helix formed by residues 378 - 385 (chain B) in PDB entry 3HS5
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 ALA 378 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B TYR* 4.3 0.2 - - - -
149B THR* 3.3 17.7 - - + +
151B ALA 4.7 2.9 - - - +
376B ARG 3.3 3.9 + - - +
377B ILE* 1.3 79.4 - - - +
379B SER* 1.3 65.7 + - - +
380B GLU* 3.8 12.6 - - - +
381B PHE* 3.1 18.3 + - + +
382B ASN* 3.2 10.2 + - - +
529B PHE* 3.5 37.8 - - + -
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Residues in contact with SER 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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148B TYR* 3.7 24.3 - - - +
149B THR 2.8 18.2 + - - -
150B ARG* 3.8 14.8 - - - -
218B PRO 5.0 0.9 + - - -
219B GLY* 5.5 1.8 - - - -
378B ALA* 1.3 72.1 - - - +
380B GLU* 1.3 57.3 + - - +
382B ASN* 3.3 8.8 + - - +
383B THR* 2.9 23.4 + - - -
458B MET* 3.5 23.8 - - - +
460B TYR* 2.6 28.9 + - - -
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Residues in contact with GLU 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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150B ARG* 3.4 22.2 - - - -
151B ALA* 3.0 25.6 + - - +
152B LEU 3.2 13.7 + - - -
378B ALA* 3.8 2.8 - - - +
379B SER* 1.3 77.2 + - - +
381B PHE* 1.3 58.4 + - - +
383B THR* 3.3 4.3 + - - -
384B LEU* 2.9 37.0 + - + +
460B TYR* 3.5 17.7 - - + -
466B TYR* 2.5 51.1 + - + +
503B LEU* 4.6 9.5 - - + +
525B LEU* 5.6 1.3 - - + -
529B PHE* 4.5 12.3 - - + -
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Residues in contact with PHE 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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1B ACD 3.3 59.5 - - + -
209B PHE* 4.0 0.9 - + - -
210B PHE* 3.5 19.7 - + - -
377B ILE* 4.8 5.6 - - + -
378B ALA* 3.1 16.4 + - + +
380B GLU* 1.3 75.4 - - - +
382B ASN* 1.3 64.3 + - - +
384B LEU* 3.4 15.3 - - + +
385B TYR* 3.2 49.5 + + - +
526B GLY 3.8 10.8 - - - -
529B PHE* 3.4 45.0 - + + -
530B SER* 4.0 8.3 - - - -
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Residues in contact with ASN 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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148B TYR* 3.4 23.8 + - + -
210B PHE* 3.4 29.5 - - + -
212B THR* 3.5 5.7 + - - -
218B PRO 5.3 1.2 + - - -
378B ALA 3.2 7.0 + - - +
379B SER* 3.3 13.4 + - - +
381B PHE* 1.3 79.5 - - - +
383B THR* 1.3 55.3 + - - +
385B TYR* 3.1 10.7 + - - +
386B HIS* 2.7 43.4 + - - -
619B COH 2.9 34.3 + - - +
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Residues in contact with THR 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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379B SER 2.9 5.3 + - - -
380B GLU 3.3 6.0 + - - -
382B ASN* 1.3 77.4 - - - +
384B LEU* 1.3 62.8 + - - +
385B TYR 3.2 1.0 + - - -
386B HIS* 3.3 28.3 + - + +
451B SER* 5.1 2.7 - - - +
455B SER* 3.9 14.8 + - - +
458B MET* 4.4 6.2 - - - +
460B TYR* 2.7 38.2 + - + -
503B LEU* 5.0 5.6 - - + -
504B TYR* 3.7 38.0 - - + +
507B LEU* 5.5 0.2 - - + -
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Residues in contact with LEU 384 (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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1B ACD 4.5 5.6 - - + -
380B GLU 2.9 21.8 + - - +
381B PHE* 3.4 28.0 - - + +
383B THR* 1.3 73.4 - - - +
385B TYR* 1.3 64.3 + - + +
386B HIS 3.2 1.9 + - - -
387B TRP* 2.9 24.4 + - - +
503B LEU* 5.7 1.6 - - + -
504B TYR* 5.4 0.7 - - - -
507B LEU* 3.7 28.3 - - + -
522B MET* 3.2 25.6 - - - +
525B LEU* 3.8 33.4 - - + -
526B GLY* 3.9 21.8 - - - +
529B PHE* 4.0 9.9 - - + -
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Residues in contact with TYR 385 (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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1B ACD 3.0 43.9 - - + +
206B THR* 3.4 25.3 - - + +
210B PHE* 3.5 23.3 - + + -
348B TYR* 2.7 22.4 + - - -
381B PHE* 3.2 35.9 + + - +
382B ASN 3.1 8.5 + - - +
384B LEU* 1.3 79.7 - - + +
386B HIS* 1.3 57.2 + - - +
387B TRP* 2.9 47.0 + + - +
619B COH 3.5 31.1 - - + +
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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