Contacts of the helix formed by residues 384 - 398 (chain B) in PDB entry 6E7P
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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450A TYR* 2.6 38.4 + - - -
487A SER* 3.6 15.2 + - - -
489A LEU* 5.3 6.5 - - + +
490A VAL* 3.6 22.3 - - + +
382B SER 3.1 1.2 - - - -
383B TYR* 1.3 85.1 - - - +
385B VAL* 1.3 66.8 + - + +
386B CYS 3.4 0.7 - - - -
387B SER* 2.6 21.4 + - - -
388B ILE* 3.0 24.4 + - + +
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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
----------------------------------------------------------
489A LEU* 4.8 15.3 - - + -
371B MET* 4.8 16.2 - - + -
382B SER* 3.5 19.4 + - - +
384B ASP* 1.3 79.6 - - + +
386B CYS* 1.3 61.5 + - - +
387B SER 3.3 0.7 + - - -
388B ILE* 4.4 4.7 - - - +
389B LEU* 3.3 36.7 + - + +
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Residues in contact with CYS 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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83B PHE* 4.3 17.0 - - - -
368B GLY 4.8 2.2 - - - +
371B MET* 3.7 39.8 - - + +
372B LYS* 4.6 6.7 - - + +
380B LEU* 5.9 2.0 - - + -
382B SER 3.2 22.2 + - - +
383B TYR* 3.8 25.6 - - - -
385B VAL* 1.3 78.8 - - - +
387B SER* 1.3 60.7 + - - +
389B LEU* 4.4 4.9 - - - +
390B LEU* 3.3 31.0 + - - +
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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
----------------------------------------------------------
445A ILE* 3.7 37.1 - - - +
446A VAL* 4.0 9.7 + - - +
83B PHE* 4.9 6.5 - - - -
87B ASN* 5.9 2.5 - - - -
383B TYR 3.4 13.4 + - - -
384B ASP* 2.6 28.8 + - - -
386B CYS* 1.3 81.5 - - - +
388B ILE* 1.3 67.6 + - - +
389B LEU 3.3 1.6 - - - -
390B LEU* 3.5 2.0 + - - +
391B GLY* 3.2 18.5 + - - -
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Residues in contact with ILE 388 (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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446A VAL* 4.1 23.6 - - + -
489A LEU* 3.8 34.8 - - + +
490A VAL* 5.0 8.3 - - + -
493A PHE* 4.0 31.2 - - + -
384B ASP* 3.0 18.2 + - + +
385B VAL* 3.7 3.8 + - - +
387B SER* 1.3 84.7 + - - +
389B LEU* 1.3 62.0 + - + +
392B THR* 2.7 46.6 + - - +
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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
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364B LEU* 4.1 39.6 - - + +
367B SER* 4.0 22.9 - - - +
368B GLY* 4.1 21.5 - - - +
371B MET* 5.5 5.2 - - + -
385B VAL* 3.3 31.6 + - + +
386B CYS* 4.6 2.7 - - - +
387B SER 3.3 0.4 - - - -
388B ILE* 1.3 83.2 - - + +
390B LEU* 1.3 61.6 + - - +
393B SER* 3.2 23.4 + - - -
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Residues in contact with LEU 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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445A ILE* 5.6 2.7 - - + -
76B VAL* 5.4 3.7 - - + +
79B GLN* 4.9 10.8 - - + +
80B LEU* 4.0 13.8 - - + +
83B PHE* 4.3 27.4 - - + -
365B THR* 4.5 8.3 - - + +
368B GLY* 4.1 8.7 - - - +
369B THR* 3.8 33.0 - - + +
372B LYS* 4.5 20.9 - - + -
386B CYS 3.3 21.5 + - - +
387B SER* 3.5 4.4 + - - +
388B ILE 3.3 0.2 - - - -
389B LEU* 1.3 75.1 - - - +
391B GLY* 1.3 62.3 + - - +
393B SER* 2.5 24.2 + - - +
394B THR* 3.0 14.0 + - - -
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Residues in contact with GLY 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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441A PHE 5.0 0.4 - - - -
442A CYS* 3.6 29.3 - - - +
445A ILE* 5.2 4.0 - - - +
446A VAL* 5.1 1.3 - - - -
80B LEU* 4.5 9.9 - - - -
387B SER 3.2 15.9 + - - -
388B ILE 4.0 0.2 - - - -
390B LEU* 1.3 76.2 - - - +
392B THR* 1.3 53.7 + - - +
394B THR* 3.1 1.7 + - - -
395B LEU* 2.7 36.2 + - - +
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Residues in contact with THR 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A CYS* 4.0 2.6 - - - -
493A PHE* 3.9 16.9 - - + -
364B LEU* 4.2 20.9 - - + -
388B ILE* 2.7 34.3 + - - +
391B GLY* 1.3 72.1 - - - +
393B SER* 1.3 64.4 + - - +
395B LEU* 3.8 14.4 - - + +
396B LEU* 3.2 31.2 + - + +
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Residues in contact with SER 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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76B VAL* 4.4 6.1 - - - +
361B SER* 4.4 16.8 - - - +
364B LEU* 4.5 5.7 - - - +
365B THR* 3.3 28.2 + - - -
389B LEU 3.2 15.4 + - - -
390B LEU* 2.5 28.3 + - - +
392B THR* 1.3 77.0 - - - +
394B THR* 1.3 56.5 + - - +
396B LEU* 2.8 4.4 + - - +
397B VAL* 2.5 42.1 + - - +
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Residues in contact with THR 394 (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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438A GLY* 4.7 1.8 - - - -
441A PHE* 4.1 17.9 - - + -
76B VAL* 3.7 15.7 - - + +
77B THR* 4.4 9.9 - - - +
80B LEU* 3.3 26.9 - - + +
390B LEU 3.0 15.9 + - - -
391B GLY 3.1 4.8 + - - -
393B SER* 1.3 80.3 + - - +
395B LEU* 1.3 63.8 + - - +
397B VAL* 4.2 7.2 - - + +
398B TRP* 3.2 46.9 + - + +
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Residues in contact with LEU 395 (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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435A ILE 5.1 0.4 - - - +
438A GLY* 3.5 32.8 + - - +
439A TYR* 3.7 42.4 - - + +
442A CYS* 3.8 22.2 - - + -
493A PHE* 5.6 2.7 - - + -
497A TYR* 5.0 3.1 - - + -
391B GLY 2.7 21.0 + - - +
392B THR* 3.8 14.8 - - + +
394B THR* 1.3 73.3 - - - +
396B LEU* 1.3 57.1 + - + +
398B TRP* 4.7 1.7 - - - +
399B VAL* 3.4 27.7 + - + +
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Residues in contact with LEU 396 (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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357B LEU* 3.3 59.1 - - + +
360B THR* 4.4 14.1 - - + -
361B SER* 3.7 21.9 - - - +
364B LEU* 6.4 1.1 - - + -
392B THR* 3.2 24.3 + - + +
393B SER 2.8 2.3 + - - +
395B LEU* 1.3 77.0 - - + +
397B VAL* 1.3 64.5 + - - +
398B TRP 3.5 0.2 - - - -
399B VAL* 3.3 20.2 - - + +
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Residues in contact with VAL 397 (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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69B GLN* 5.0 5.5 - - - +
72B LYS* 4.7 26.2 - - + +
73B ILE* 3.7 28.6 - - + +
76B VAL* 5.0 13.2 - - + -
77B THR* 6.1 0.2 - - - +
358B LEU* 5.4 7.1 - - + +
361B SER* 3.8 24.0 - - - +
365B THR* 5.0 3.4 - - - +
393B SER* 2.5 34.5 + - - +
394B THR* 4.2 7.4 - - + +
396B LEU* 1.3 74.3 - - - +
398B TRP* 1.3 64.3 + - + +
400B GLY* 2.9 22.0 + - - -
401B VAL 4.1 1.7 + - - -
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Residues in contact with TRP 398 (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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434A VAL* 3.2 51.0 - - + +
437A LEU* 4.9 22.0 - - + -
438A GLY* 4.5 12.3 - - - -
441A PHE* 4.4 22.1 - + - -
73B ILE* 4.1 26.1 + - + +
77B THR* 3.1 29.3 + - + -
394B THR* 3.2 38.3 + - + +
395B LEU 4.7 0.4 - - - +
397B VAL* 1.3 86.7 - - + +
399B VAL* 1.3 60.6 + - + +
400B GLY 3.3 0.5 + - - -
401B VAL* 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