Contacts of the helix formed by residues 386 - 401 (chain D) in PDB entry 6N0M
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 THR 386 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D MET* 3.6 7.4 - - - -
374D THR* 3.2 7.6 + - - +
376D ASN* 5.1 0.4 + - - -
377D THR 3.6 7.9 - - - +
378D ILE* 3.4 36.8 - - + -
384D VAL 3.6 9.1 + - - +
385D ASP* 1.3 76.0 + - - +
387D SER* 1.3 65.7 + - - +
388D VAL 3.1 3.4 - - - -
389D LEU* 2.9 15.6 + - - +
390D ARG* 2.8 27.4 + - - +
900D K94 2.6 39.5 + - + +
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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
----------------------------------------------------------
371D TYR* 5.2 3.9 - - - -
385D ASP* 2.5 28.1 + - - -
386D THR* 1.3 76.1 + - - +
388D VAL* 1.3 58.7 + - - +
390D ARG* 3.7 25.3 - - - +
391D ARG* 2.9 44.3 + - - +
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Residues in contact with VAL 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D MET* 3.8 47.1 - - + +
268D LEU* 4.6 24.7 - - + +
385D ASP* 5.0 4.5 - - - +
386D THR 3.0 1.2 + - - -
387D SER* 1.3 78.1 - - - +
389D LEU* 1.3 62.8 + - - +
391D ARG* 3.6 24.0 + - - +
392D ALA* 3.1 20.4 + - - +
408D TYR* 3.8 4.9 + - - -
412D GLU* 5.0 2.5 - - - +
416D LEU* 3.6 18.0 - - + +
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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
----------------------------------------------------------
261D LEU* 3.8 20.0 - - + -
265D MET* 4.0 15.5 - - + -
378D ILE* 3.5 30.5 - - + -
386D THR 2.9 8.1 + - - +
388D VAL* 1.3 77.6 - - + +
390D ARG* 1.3 60.2 + - - +
392D ALA* 3.3 1.6 + - - +
393D ILE* 3.1 25.8 + - + +
416D LEU* 4.1 23.6 - - + +
417D LEU* 3.7 23.1 - - + -
444D TRP* 4.2 19.7 - - + -
447D PHE* 5.0 0.4 - - + -
900D K94 4.0 17.9 - - + -
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Residues in contact with ARG 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D TYR* 2.6 43.2 + - + -
372D SER* 4.0 6.0 + - - +
373D LEU 3.7 15.5 - - - -
374D THR* 3.5 22.8 - - - +
385D ASP* 5.4 0.2 + - - -
386D THR* 2.8 26.9 + - - +
387D SER* 3.7 27.5 - - - +
389D LEU* 1.3 75.5 - - - +
391D ARG* 1.3 59.0 + - - +
393D ILE* 3.4 3.5 + - - +
394D TRP* 3.1 27.7 + - - +
454D HIS* 3.9 6.5 - - - -
458D LEU* 4.0 19.6 - - + +
900D K94 3.5 46.3 + - + -
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Residues in contact with ARG 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D TYR* 3.3 29.5 + - - +
387D SER* 2.9 44.3 + - - +
388D VAL* 3.8 30.4 - - - +
390D ARG* 1.3 72.6 - - - +
392D ALA* 1.3 56.1 + - - +
394D TRP* 4.3 0.7 - - - -
395D ASN* 2.7 57.3 + - - +
408D TYR* 3.5 23.1 - - + -
412D GLU* 4.4 9.5 + - - -
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Residues in contact with ALA 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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388D VAL 3.1 12.0 + - - +
389D LEU 3.4 10.3 - - - +
390D ARG 3.2 0.2 - - - -
391D ARG* 1.3 73.8 - - - +
393D ILE* 1.3 57.7 + - - +
395D ASN* 4.2 0.2 - - - +
396D TYR* 2.8 36.9 + - - +
408D TYR* 3.2 21.5 + - - +
413D VAL* 4.2 7.8 - - - +
416D LEU* 3.9 13.9 - - + -
417D LEU* 3.5 23.4 - - + +
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Residues in contact with ILE 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D LEU* 3.1 14.4 + - + +
390D ARG 3.8 6.7 - - - +
391D ARG 3.4 0.2 - - - -
392D ALA* 1.3 75.9 - - - +
394D TRP* 1.3 64.9 + - - +
396D TYR* 3.7 1.4 - - - +
397D ILE* 3.2 35.3 + - + +
417D LEU* 3.8 20.0 - - + -
421D LEU* 4.3 9.0 - - + -
425D ILE* 3.9 17.0 - - + -
444D TRP* 3.8 18.4 - - + -
455D VAL* 4.0 17.9 - - + +
458D LEU* 4.1 22.2 - - + -
900D K94 3.4 29.6 - - - -
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Residues in contact with TRP 394 (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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367D PHE* 4.7 14.4 - + + -
371D TYR* 4.5 40.6 - + + -
390D ARG 3.1 18.1 + - - +
391D ARG* 3.6 6.5 - - - +
393D ILE* 1.3 79.9 - - - +
395D ASN* 1.3 79.0 + - - +
397D ILE* 3.3 3.6 + - - +
398D HIS* 3.1 41.6 + - - +
405D TYR* 4.0 6.2 + + - -
458D LEU* 3.6 30.5 - - + +
461D GLU* 3.8 15.7 - - + -
462D ALA* 3.5 47.3 - - + +
465D GLN* 3.5 25.2 + - - -
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Residues in contact with ASN 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D TYR* 4.5 1.6 + - - -
391D ARG* 2.7 35.6 + - - +
392D ALA 4.2 0.2 - - - +
394D TRP* 1.3 85.0 - - - +
396D TYR* 1.3 51.7 + - - +
398D HIS* 3.4 4.9 + - - +
399D CYS* 2.8 31.9 + - - +
405D TYR* 3.5 32.0 - - - +
408D TYR* 3.2 44.9 - - + +
410D TYR* 3.6 21.0 + - + +
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Residues in contact with TYR 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D GLU* 4.0 23.0 + - + -
293D GLU 5.3 0.2 + - - -
295D LEU* 3.3 26.0 - - + +
392D ALA 2.8 19.7 + - - +
393D ILE 3.7 2.5 - - - +
395D ASN* 1.3 75.1 - - - +
397D ILE* 1.3 62.4 + - + +
399D CYS* 3.1 9.9 - - + +
400D VAL* 2.9 42.1 + - + +
413D VAL* 3.6 25.3 - - + +
417D LEU* 3.6 18.2 - - + -
422D LYS* 3.4 36.5 + - + -
425D ILE* 3.6 31.4 - - + -
426D LYS* 4.0 13.0 + - + +
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Residues in contact with ILE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393D ILE* 3.2 31.3 + - + +
394D TRP 3.8 4.5 - - - +
396D TYR* 1.3 75.2 - - + +
398D HIS* 1.3 66.5 + - + +
400D VAL* 3.1 15.6 + - + +
401D PHE* 3.1 26.9 + - + -
425D ILE* 3.4 31.4 - - + -
429D ALA* 4.6 8.3 - - + -
459D LEU* 3.2 36.3 - - + +
462D ALA* 3.8 8.1 - - + -
463D ARG* 3.8 34.8 - - + +
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Residues in contact with HIS 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394D TRP* 3.1 21.6 + - - +
395D ASN 3.6 8.1 - - - +
397D ILE* 1.3 80.4 - - + +
399D CYS* 1.3 55.9 + - - +
401D PHE* 3.2 5.1 + - - +
402D GLY 2.9 10.0 + - - -
403D ILE* 2.8 45.3 + - + +
405D TYR* 2.7 40.8 + - + -
462D ALA* 2.8 42.7 + - + -
465D GLN* 3.5 25.5 - - + +
466D ALA* 3.8 16.2 + - + -
469D LEU* 5.4 2.9 - - + -
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Residues in contact with CYS 399 (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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287D PHE* 3.4 38.1 - - + -
290D GLU* 3.8 17.3 - - + -
291D LYS* 3.7 39.4 - - - +
395D ASN 2.8 14.4 + - - +
396D TYR* 3.1 19.5 + - + +
398D HIS* 1.3 73.2 - - - +
400D VAL* 1.3 64.8 + - - +
402D GLY* 2.9 14.7 + - - -
403D ILE 3.9 0.6 + - - -
410D TYR* 4.1 5.4 - - + -
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Residues in contact with VAL 400 (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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290D GLU 6.1 0.7 - - - +
291D LYS* 5.4 4.5 - - - +
323D TYR* 2.9 40.3 + - + +
334D PRO* 3.2 14.6 - - - +
396D TYR* 2.9 48.6 + - + +
397D ILE* 3.1 12.5 + - + +
399D CYS* 1.3 76.0 - - - +
401D PHE* 1.3 63.5 + - + +
426D LYS* 4.2 18.4 - - + -
429D ALA* 6.1 0.7 - - + -
430D CYS* 3.4 30.5 - - - -
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Residues in contact with PHE 401 (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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166D LEU 5.1 1.3 - - - -
167D ALA 4.3 11.9 - - - -
168D HIS 5.0 3.8 - - - -
170D PRO* 3.7 35.0 - - + -
171D TRP* 3.8 13.7 - + - -
323D TYR* 5.2 2.0 - + - -
334D PRO* 4.0 4.0 - - - -
397D ILE* 3.1 26.8 + - + +
398D HIS 3.4 4.3 - - - +
399D CYS 3.1 0.4 - - - -
400D VAL* 1.3 91.4 - - + +
402D GLY* 1.3 51.9 + - - +
403D ILE* 3.8 1.3 - - + -
429D ALA* 3.8 25.6 - - + -
430D CYS* 4.2 12.6 - - - -
463D ARG* 3.8 29.2 - - + -
466D ALA* 3.8 26.9 - - + -
467D ALA* 5.7 0.4 - - + -
470D TYR* 2.5 32.8 + - + -
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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
------------------------------------------------------------
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