Contacts of the helix formed by residues 383 - 393 (chain B) in PDB entry 6RUT
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 GLY 383 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B TRP* 3.6 30.9 - - - -
380B ASN* 3.2 9.6 + - - +
381B HIS 3.3 1.8 - - - -
382B HIS* 1.3 78.6 - - - +
384B ILE* 1.3 65.3 + - - -
385B TRP 3.3 1.2 + - - -
386B ASP* 3.3 5.9 + - - +
387B TYR* 3.2 17.7 + - - +
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Residues in contact with ILE 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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293B ASN* 4.9 3.4 - - - +
295B PHE* 3.1 28.5 - - + +
296B ALA* 3.4 18.2 - - + +
379B TRP* 3.5 19.3 - - + -
382B HIS 3.8 0.8 + - - -
383B GLY* 1.3 70.5 - - - -
385B TRP* 1.4 62.6 + - - +
387B TYR* 3.2 2.4 + - + -
388B ASN* 2.9 61.0 + - - +
424B LYS 4.3 1.1 - - - +
425B VAL* 4.1 15.7 - - + -
426B GLY 5.3 0.7 - - - +
433B ASP* 3.9 19.3 - - + +
434B GLY* 3.8 29.1 - - - +
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Residues in contact with TRP 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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295B PHE* 3.5 62.1 - + + +
382B HIS* 3.2 55.7 + + + +
383B GLY 3.3 0.6 + - - -
384B ILE* 1.4 79.3 - - - +
386B ASP* 1.3 81.2 + - + +
388B ASN* 3.7 3.9 - - - +
389B ALA* 2.9 32.7 + - + +
565B ARG* 3.5 24.0 - - - -
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Residues in contact with ASP 386 (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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380B ASN* 3.4 23.2 + - - +
382B HIS* 3.7 26.9 - - + -
383B GLY 3.3 3.9 + - - +
384B ILE 3.3 0.2 - - - -
385B TRP* 1.3 92.9 - - + +
387B TYR* 1.4 66.9 + - - +
390B ARG* 2.9 51.8 + - - +
398B GLY 5.1 1.0 + - - -
565B ARG* 2.7 33.5 + - - +
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Residues in contact with TYR 387 (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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298B LYS* 5.8 1.3 - - - -
378B LYS 4.0 1.1 - - - -
379B TRP* 3.8 35.0 - + + -
383B GLY 3.2 8.5 + - - +
384B ILE* 3.2 9.0 + - - +
386B ASP* 1.4 75.0 + - - +
388B ASN* 1.3 72.6 + - - +
391B ASN* 2.8 56.0 + - - +
397B THR* 3.4 34.1 - - + +
418B ASN* 2.7 38.1 + - + +
419B THR* 4.2 2.8 + - - +
421B PRO* 3.6 13.2 - - + -
425B VAL* 3.5 36.6 - - + +
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Residues in contact with ASN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PHE 4.4 4.0 + - - -
296B ALA 3.7 23.0 + - - -
297B LYS 4.5 1.9 + - - +
298B LYS* 3.6 38.8 + - + +
384B ILE* 2.9 43.3 + - - +
385B TRP* 3.7 4.5 - - - +
387B TYR* 1.3 87.1 - - - +
389B ALA* 1.3 63.3 + - - +
391B ASN* 3.7 3.2 - - - +
392B LEU* 3.1 31.3 + - + +
425B VAL* 5.3 0.9 - - - +
426B GLY 5.5 1.9 + - - -
433B ASP* 5.7 0.4 + - - -
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Residues in contact with ALA 389 (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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385B TRP* 2.9 23.8 + - + +
386B ASP 4.1 0.2 - - - +
387B TYR 3.5 0.2 - - - -
388B ASN* 1.3 73.8 - - - +
390B ARG* 1.4 56.1 + - - +
392B LEU* 4.1 3.4 - - - +
393B LEU* 3.1 40.2 + - + +
565B ARG* 3.4 28.0 - - - +
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Residues in contact with ARG 390 (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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380B ASN* 4.5 5.3 - - - +
386B ASP* 2.9 44.3 + - - +
389B ALA* 1.4 73.2 - - - +
391B ASN* 1.4 65.5 + - - +
393B LEU* 3.3 4.3 + - - -
394B LEU 3.2 4.3 + - - -
395B GLN* 2.9 48.9 + - + +
396B THR* 3.0 39.3 + - - +
397B THR* 3.9 12.8 - - + +
398B GLY 3.5 23.9 + - - +
404B ARG* 4.5 7.3 - - - +
562B THR 5.9 0.6 + - - -
565B ARG* 3.5 23.8 - - - +
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Residues in contact with ASN 391 (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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298B LYS* 4.6 10.4 + - - +
302B HIS* 4.0 25.6 + - - -
310B LYS* 6.0 0.4 - - - +
311B LEU* 4.7 6.8 - - - +
387B TYR* 2.8 49.9 + - + +
388B ASN* 3.7 5.4 - - - +
390B ARG* 1.4 70.7 - - - +
392B LEU* 1.4 57.7 + - + +
394B LEU* 3.0 23.0 + - - +
395B GLN 4.1 0.5 + - - +
397B THR* 3.9 2.1 - - + +
418B ASN* 2.9 37.7 - - - +
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Residues in contact with LEU 392 (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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245B PRO* 3.6 38.4 - - + +
298B LYS* 3.6 42.8 - - + +
300B LEU* 4.0 17.5 - - + +
301B LYS* 3.5 36.3 - - - +
302B HIS* 3.6 19.5 + - + +
388B ASN 3.1 15.3 + - - +
389B ALA* 4.2 3.8 - - - +
391B ASN* 1.4 72.7 - - - +
393B LEU* 1.3 58.2 + - + +
394B LEU* 3.0 20.2 + - - +
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Residues in contact with LEU 393 (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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245B PRO* 4.6 2.5 - - + -
389B ALA* 3.1 24.1 + - + +
390B ARG 3.3 4.5 + - - +
392B LEU* 1.3 77.2 - - + +
394B LEU* 1.4 66.7 + - - +
395B GLN* 3.3 17.9 + - - +
565B ARG* 3.6 31.2 - - + +
566B LEU* 3.4 32.0 - - + +
568B TYR* 3.8 28.3 - - + +
571B LEU* 4.0 26.9 - - + +
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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