Contacts of the helix formed by residues 384 - 398 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450C TYR* 2.6 39.0 + - - -
487C SER* 3.6 18.2 + - - -
489C LEU* 5.3 6.5 - - + +
490C VAL* 3.6 20.0 - - + +
382D SER* 3.1 1.6 - - - +
383D TYR* 1.3 87.2 - - - +
385D VAL* 1.3 66.7 + - + +
386D CYS 3.4 0.4 - - - -
387D SER* 2.6 21.4 + - - -
388D ILE* 3.0 24.1 + - + +
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Residues in contact with VAL 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C LEU* 4.8 14.4 - - + -
371D MET* 4.8 15.0 - - + -
382D SER* 3.5 19.8 + - - +
384D ASP* 1.3 79.7 - - + +
386D CYS* 1.3 63.1 + - - +
387D SER 3.3 0.5 + - - -
388D ILE* 3.7 4.7 + - - +
389D LEU* 3.3 37.1 + - + +
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Residues in contact with CYS 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.3 16.4 - - + -
368D GLY 4.8 2.3 - - - +
371D MET* 3.7 39.8 - - + +
372D LYS* 4.6 7.0 - - + +
380D LEU* 5.9 2.5 - - + -
382D SER 3.2 22.4 + - - +
383D TYR* 3.8 25.8 - - - -
385D VAL* 1.3 78.7 - - - +
387D SER* 1.3 60.7 + - - +
389D LEU* 4.4 4.3 - - - +
390D LEU* 3.3 31.5 + - - +
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Residues in contact with SER 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ILE* 3.7 37.4 - - - +
446C VAL* 4.0 9.8 + - - +
83D PHE* 4.9 7.0 - - - -
87D ASN* 5.9 3.1 - - - -
383D TYR 3.4 13.6 + - - -
384D ASP* 2.6 28.6 + - - -
386D CYS* 1.3 81.8 - - - +
388D ILE* 1.3 68.3 + - - +
389D LEU 3.3 0.9 - - - -
390D LEU* 3.5 2.0 + - - -
391D GLY 3.2 17.2 + - - -
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Residues in contact with ILE 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C VAL* 4.1 23.3 - - + +
489C LEU* 3.7 35.2 - - + +
490C VAL* 5.0 8.5 - - + -
493C PHE* 4.0 31.4 - - + -
384D ASP* 3.0 18.4 + - - +
385D VAL* 4.5 3.6 - - - +
386D CYS 3.7 0.2 - - - -
387D SER* 1.3 85.4 + - - +
389D LEU* 1.3 61.1 + - + +
391D GLY* 4.0 0.2 - - - -
392D THR* 2.7 46.6 + - - +
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Residues in contact with LEU 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D LEU* 4.1 38.9 - - + +
367D SER* 4.0 22.2 - - - +
368D GLY* 4.1 21.8 - - - +
371D MET* 5.5 4.9 - - + -
385D VAL* 3.3 32.5 + - + +
386D CYS* 4.6 3.6 - - - +
387D SER 3.3 0.6 - - - -
388D ILE* 1.3 82.6 - - + +
390D LEU* 1.3 61.9 + - - +
393D SER* 3.2 23.2 + - - -
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Residues in contact with LEU 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ILE* 5.6 3.4 - - + -
76D VAL* 5.4 4.0 - - + +
79D GLN* 4.9 10.5 - - + +
80D LEU* 4.5 12.6 - - + -
83D PHE* 4.3 27.1 - - + -
365D THR* 4.5 8.3 - - + +
368D GLY* 4.1 8.7 - - - +
369D THR* 3.8 33.7 - - + +
372D LYS* 4.5 21.3 - - + -
386D CYS 3.3 21.0 + - - +
387D SER* 3.5 4.8 + - - +
388D ILE 3.3 0.4 - - - -
389D LEU* 1.3 74.9 - - - +
391D GLY* 1.3 62.2 + - - +
393D SER* 2.5 23.7 + - - +
394D THR* 3.0 14.4 + - - -
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Residues in contact with GLY 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C PHE 5.1 0.4 - - - -
442C CYS* 3.6 28.5 - - - +
445C ILE* 5.2 4.2 - - - +
446C VAL* 5.0 2.0 - - - -
80D LEU* 4.5 9.4 - - - -
387D SER 3.2 15.7 + - - -
388D ILE 4.0 0.7 - - - -
390D LEU* 1.3 76.2 - - - +
392D THR* 1.3 54.0 + - - +
394D THR* 3.1 2.4 + - - -
395D LEU* 2.7 35.5 + - - +
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Residues in contact with THR 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C CYS* 4.0 2.2 - - - -
493C PHE* 3.8 17.6 - - + -
364D LEU* 4.2 19.7 - - + -
388D ILE* 2.7 34.7 + - - +
391D GLY* 1.3 72.3 - - - +
393D SER* 1.3 65.3 + - - +
395D LEU* 3.8 14.2 - - + +
396D LEU* 3.2 31.6 + - + +
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Residues in contact with SER 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 4.4 6.5 - - - +
361D SER* 4.4 16.3 - - - +
364D LEU* 4.5 6.1 - - - +
365D THR* 3.3 28.2 + - - -
389D LEU 3.2 15.2 + - - -
390D LEU* 2.5 28.6 + - - +
392D THR* 1.3 76.6 - - - +
394D THR* 1.3 56.2 + - - +
396D LEU* 2.8 5.2 + - - -
397D VAL* 2.5 42.1 + - - +
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Residues in contact with THR 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C GLY* 4.7 1.6 - - - +
441C PHE* 4.2 18.4 - - + -
76D VAL* 3.7 15.8 - - + +
77D THR* 4.4 10.3 - - - +
80D LEU* 3.3 26.7 - - + +
390D LEU 3.0 15.9 + - - -
391D GLY 3.1 4.4 + - - -
393D SER* 1.3 83.0 + - - +
395D LEU* 1.3 60.9 + - - +
397D VAL* 4.2 8.1 - - + +
398D TRP* 3.2 46.3 + - + +
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Residues in contact with LEU 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ILE 5.1 0.2 - - - +
438C GLY* 3.6 32.4 + - - +
439C TYR* 3.7 43.3 - - + +
442C CYS* 3.8 22.0 - - + +
493C PHE* 5.5 3.1 - - + -
497C TYR* 5.0 2.9 - - + -
391D GLY 2.7 21.4 + - - +
392D THR* 3.8 14.6 - - + +
394D THR* 1.3 73.3 - - - +
396D LEU* 1.3 58.2 + - + +
398D TRP* 4.7 1.6 - - - +
399D VAL* 3.4 27.0 + - + +
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Residues in contact with LEU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D LEU* 3.3 62.3 - - + +
358D LEU* 5.5 0.2 - - - +
360D THR* 4.4 14.4 - - + -
361D SER* 3.7 21.5 - - - +
364D LEU* 6.4 1.8 - - + -
392D THR* 3.2 24.2 + - + +
393D SER* 2.8 2.5 + - - +
395D LEU* 1.3 77.0 - - + +
397D VAL* 1.3 64.1 + - - +
398D TRP 3.5 0.2 - - - -
399D VAL* 3.3 20.8 - - + +
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Residues in contact with VAL 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLN* 5.0 5.5 - - - +
72D LYS* 4.7 26.5 - - + +
73D ILE* 3.7 28.0 - - + +
76D VAL* 5.0 12.6 - - + -
77D THR* 6.1 0.4 - - - +
358D LEU* 5.4 7.8 - - + +
361D SER* 3.8 23.8 - - - +
362D ASP* 6.1 0.2 - - - +
365D THR* 5.0 3.8 - - - +
393D SER* 2.5 37.4 + - - +
394D THR* 4.2 8.3 - - - +
396D LEU* 1.3 71.0 - - - +
398D TRP* 1.3 64.5 + - + +
400D GLY* 2.9 22.5 + - - -
401D VAL 4.1 1.6 + - - -
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Residues in contact with TRP 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C VAL* 3.3 52.6 - - + +
437C LEU* 4.9 22.7 - - + -
438C GLY* 4.4 12.1 - - - -
441C PHE* 4.4 22.6 - + - -
73D ILE* 4.1 26.8 + - + +
77D THR* 3.1 29.9 + - + -
394D THR* 3.2 38.7 + - + +
395D LEU 4.7 0.4 - - - +
397D VAL* 1.3 85.7 - - + +
399D VAL* 1.3 61.7 + - + +
400D GLY 3.3 0.7 + - - -
401D VAL* 3.3 21.4 + - + +
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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