Contacts of the helix formed by residues 384 - 395 (chain B) in PDB entry 6R7H
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 ASP 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355B ARG* 3.4 29.5 + - - +
380B ILE* 3.3 24.6 - - - +
381B ASP* 3.0 31.5 + - - +
383B ALA* 1.3 77.7 - - + +
385B VAL* 1.3 62.2 + - - +
386B GLU 3.4 0.7 - - - -
387B SER* 3.6 8.4 + - - +
388B LEU* 3.1 30.3 + - - +
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Residues in contact with VAL 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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371B ILE* 4.5 14.8 - - + +
374B ILE* 3.9 31.6 - - + -
375B SER* 3.9 18.6 - - - -
378B LEU* 6.0 0.4 - - + -
380B ILE* 3.9 20.6 - - + -
381B ASP 3.3 20.6 - - - +
382B VAL* 3.8 10.5 + - + +
383B ALA 3.4 0.8 - - - -
384B ASP* 1.3 77.0 - - - +
386B GLU* 1.3 65.0 + - - +
388B LEU* 3.4 6.7 + - + +
389B LEU* 3.1 33.7 + - + +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 6.0 0.2 - - - +
381A TYR* 2.6 38.8 + - - +
371B ILE* 4.4 21.1 - - - +
382B VAL 4.0 11.5 + - - +
383B ALA 4.2 4.7 + - - +
384B ASP 3.4 0.2 - - - -
385B VAL* 1.3 79.4 - - - +
387B SER* 1.3 61.9 + - - +
389B LEU* 3.8 5.8 + - - +
390B VAL* 3.3 25.8 + - - +
402B ILE* 3.5 12.8 - - - +
404B GLN* 3.6 23.4 - - - +
407B GLN* 5.7 1.9 + - - -
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU 4.6 11.6 - - - +
336A SER* 4.2 14.7 + - - -
337A LYS* 5.2 10.5 + - - +
383B ALA 4.0 11.6 + - - -
384B ASP* 3.6 10.5 + - - -
385B VAL 3.3 0.6 - - - -
386B GLU* 1.3 78.4 - - - +
388B LEU* 1.3 62.3 + - - +
390B VAL* 3.8 6.7 + - - +
391B GLN* 3.7 18.4 + - - +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ARG* 4.2 36.3 - - + +
355B ARG* 3.8 43.3 - - + +
356B THR* 5.0 0.7 - - - +
359B LEU* 5.1 9.4 - - + -
378B LEU* 5.8 4.0 - - + -
380B ILE* 6.1 2.0 - - + -
384B ASP* 3.1 21.0 + - - +
385B VAL* 4.0 6.5 - - + +
387B SER* 1.3 78.3 - - - +
389B LEU* 1.3 60.4 + - + +
390B VAL 3.2 0.2 - - - -
391B GLN* 3.4 11.2 + - + +
392B CYS* 3.0 44.2 + - - -
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 3.9 26.2 - - + -
371B ILE* 4.8 13.0 - - + -
374B ILE* 4.3 13.5 - - + -
385B VAL* 3.1 33.5 + - + +
386B GLU* 4.2 8.5 - - - +
387B SER 3.4 0.4 - - - -
388B LEU* 1.3 78.7 - - + +
390B VAL* 1.3 61.5 + - + +
392B CYS* 4.0 3.4 - - + +
393B ILE* 3.3 31.8 + - + +
398B ILE* 5.1 7.6 - - + -
402B ILE* 3.8 43.5 - - + -
409B LEU* 4.2 13.2 - - + -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER* 3.4 24.9 - - - +
338A TYR* 5.0 3.1 - - - +
376A GLN 5.0 0.4 - - - +
377A TYR* 4.9 15.3 - - + +
380A PRO* 3.7 25.2 - - + +
381A TYR* 3.4 32.3 - - + +
386B GLU* 3.3 18.1 + - - +
387B SER* 4.1 5.2 - - - +
388B LEU 3.2 0.6 - - - -
389B LEU* 1.3 78.8 - - + +
391B GLN* 1.3 62.6 + - - +
393B ILE 3.5 0.9 + - - -
394B LEU* 3.2 33.3 + - + +
402B ILE* 6.1 0.7 - - + -
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Residues in contact with GLN 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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303A ARG* 3.4 33.3 + - - +
334A TYR* 3.6 23.1 + - - +
335A GLU* 3.9 7.9 + - - +
336A SER* 3.8 6.9 + - - +
352B ARG* 3.5 35.4 + - - +
387B SER 3.7 8.5 + - - +
388B LEU* 3.4 14.3 + - + +
390B VAL* 1.3 79.8 - - - +
392B CYS* 1.3 64.4 + - - +
395B ASP* 2.9 39.3 + - - +
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Residues in contact with CYS 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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356B THR* 3.9 35.7 - - - -
359B LEU* 4.8 7.4 - - + -
388B LEU* 3.0 40.1 + - - +
389B LEU* 4.0 7.2 - - + +
390B VAL 3.3 0.4 - - - -
391B GLN* 1.3 80.3 - - - +
393B ILE* 1.3 62.7 + - + +
395B ASP* 3.6 3.4 + - - -
397B THR* 2.4 30.4 + - - +
398B ILE* 3.3 27.9 + - + -
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Residues in contact with ILE 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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379A SER 5.2 1.8 - - - +
380A PRO* 3.7 36.3 - - + +
389B LEU* 3.3 19.6 + - + +
392B CYS* 1.3 77.6 - - - +
394B LEU* 1.3 64.1 + - + +
396B ASN* 3.2 16.8 + - - -
398B ILE* 3.4 33.6 - - + +
399B HIS* 5.3 0.4 - - - +
400B GLY 3.7 24.7 - - - +
402B ILE* 3.8 26.0 - - + -
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ARG* 3.5 43.4 + - - +
304A GLN* 4.9 5.7 + - - +
336A SER* 4.6 0.7 - - - +
338A TYR* 4.3 5.4 - - - +
376A GLN* 3.4 49.6 - - + +
379A SER* 4.0 16.4 - - - -
380A PRO* 3.8 7.0 - - + -
390B VAL* 3.2 31.5 + - + +
391B GLN 4.2 0.2 - - - +
393B ILE* 1.3 77.8 - - + +
395B ASP* 1.3 58.3 + - - +
396B ASN* 3.2 11.7 + - - +
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Residues in contact with ASP 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ARG* 2.9 20.3 + - - -
304A GLN* 3.6 17.3 + - - +
334A TYR* 3.0 23.3 + - - -
391B GLN* 2.9 33.2 + - - +
392B CYS* 4.7 0.4 - - - -
393B ILE 3.2 1.4 - - - -
394B LEU* 1.3 75.5 - - - +
396B ASN* 1.3 71.3 + - - +
397B THR* 3.3 22.3 + - + +
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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