Contacts of the helix formed by residues 384 - 400 (chain D) in PDB entry 6F0X
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 SER 384 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D PRO 4.4 0.7 - - - -
182D GLY 3.1 24.5 - - - -
183D THR* 5.2 2.2 - - - -
321D PRO* 5.8 0.7 - - - -
322D PRO* 5.4 0.4 - - - -
383D LEU* 1.3 77.0 - - - +
385D GLY* 1.3 52.1 - - - +
386D ARG* 3.9 2.4 + - - +
387D VAL* 2.9 18.3 + - - +
388D LEU* 2.7 34.1 + - - +
425D ARG* 3.5 3.4 - - - +
311E ASP* 2.8 36.4 + - - -
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Residues in contact with GLY 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D GLY 4.3 2.6 + - - -
183D THR* 5.3 2.4 - - - +
322D PRO* 4.6 10.8 - - - +
330D ILE* 5.4 3.4 - - - -
383D LEU 4.2 1.0 + - - -
384D SER* 1.3 71.0 - - - +
386D ARG* 1.3 63.3 + - - +
388D LEU* 3.2 21.4 - - - +
389D ARG* 2.8 28.9 + - - +
901D AGS 3.8 26.1 + - - -
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Residues in contact with ARG 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D GLY* 3.0 21.5 + - - +
384D SER* 4.0 7.8 - - - +
385D GLY* 1.3 76.9 - - - +
387D VAL* 1.3 63.8 + - + +
389D ARG* 3.4 2.4 + - - +
390D LYS* 3.0 47.4 + - + +
901D AGS 1.6 125.0 + - - +
172E ASN* 4.1 10.2 - - - +
285E ASP* 5.0 1.6 + - - -
288E LYS* 4.6 6.1 - - - +
311E ASP 4.3 8.7 - - - +
312E ARG* 3.6 26.0 - - - +
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Residues in contact with VAL 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D LEU* 5.3 10.8 - - + -
384D SER* 2.9 26.9 + - - +
386D ARG* 1.3 76.8 - - + +
388D LEU* 1.3 63.3 + - - +
390D LYS* 3.0 14.8 + - + +
391D LEU* 2.9 34.1 + - + +
394D LEU* 5.6 2.0 - - + -
421D GLN* 3.7 32.5 - - + +
425D ARG* 5.2 3.4 - - - +
310E VAL 5.6 0.7 - - - +
311E ASP* 3.3 27.8 - - - +
313E ALA 4.7 11.0 - - - +
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Residues in contact with LEU 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D PRO* 4.9 11.4 - - + -
327D ILE* 4.5 26.5 - - + -
330D ILE* 5.3 9.4 - - + -
331D TYR* 3.3 33.9 - - + +
380D SER* 4.3 8.5 - - - +
381D GLU* 6.1 0.7 - - - -
383D LEU* 4.1 27.4 - - + -
384D SER 2.7 18.8 + - - +
385D GLY* 2.9 26.1 + - - +
387D VAL* 1.3 71.2 - - - +
389D ARG* 1.3 59.5 + - + +
391D LEU* 2.8 39.1 + - + +
392D PRO* 3.3 4.7 - - - +
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Residues in contact with ARG 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D SER* 3.3 40.1 + - - +
330D ILE* 3.4 32.8 + - + +
333D SER* 3.0 30.5 + - - -
334D CYS* 4.2 9.2 - - - -
385D GLY 2.8 15.7 + - - +
386D ARG 4.2 1.6 - - - +
388D LEU* 1.3 73.8 - - - +
390D LYS* 1.3 59.6 + - - +
391D LEU 3.2 0.2 - - - -
392D PRO* 3.6 10.6 - - - +
901D AGS 3.2 39.5 + - + +
167E ASN 4.4 4.7 - - - -
168E LEU* 2.4 41.2 + - - +
169E ILE* 3.6 14.9 - - - +
170E THR* 3.2 23.8 - - - +
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Residues in contact with LYS 390 (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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386D ARG* 3.0 37.5 + - + +
387D VAL* 3.4 15.3 - - + +
388D LEU 3.0 0.4 - - - -
389D ARG* 1.3 76.9 - - - +
391D LEU* 1.3 69.0 + - - +
392D PRO* 3.6 0.4 - - - -
393D PHE* 3.1 18.4 - - - +
394D LEU* 3.1 20.0 + - + +
170E THR* 3.1 17.7 - - - +
171E TRP* 3.7 5.6 - - + -
172E ASN* 3.0 48.2 + - - +
174E VAL* 5.8 0.6 - - - +
311E ASP 5.4 0.4 + - - -
312E ARG* 4.7 13.3 + - - +
313E ALA 4.9 1.9 - - - +
314E ASP* 2.8 38.0 + - - +
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Residues in contact with LEU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D TYR* 3.3 27.1 - - + +
383D LEU* 5.0 5.6 - - + -
387D VAL* 2.9 24.3 + - + +
388D LEU* 2.8 28.5 + - + +
390D LYS* 1.3 75.5 - - - +
392D PRO* 1.3 57.7 - - + +
394D LEU* 2.4 34.6 + - + +
395D ALA* 2.8 10.8 + - - -
414D LEU* 4.2 12.3 - - + -
417D ALA* 4.6 12.3 - - + +
418D VAL* 4.3 20.4 - - + -
421D GLN* 3.6 33.9 - - + +
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Residues in contact with PRO 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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331D TYR* 5.3 5.8 - - + -
334D CYS* 4.4 23.3 - - + -
335D LEU* 6.4 0.7 - - + -
338D LEU* 4.4 12.8 - - + -
388D LEU 3.3 8.1 - - - +
389D ARG* 3.6 11.9 - - - +
391D LEU* 1.3 92.6 - - + +
393D PHE* 1.3 63.9 + - - +
395D ALA* 3.7 0.9 - - + +
396D HIS* 2.9 26.5 + - - +
410D PHE* 3.6 23.6 - - + -
414D LEU* 3.7 21.5 - - + -
159E PHE* 5.4 1.3 - - - -
169E ILE* 4.9 7.0 - - + -
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Residues in contact with PHE 393 (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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390D LYS* 3.1 11.9 - - - +
392D PRO* 1.3 79.5 - - - +
394D LEU* 1.3 76.2 + - + +
396D HIS* 3.3 2.4 + - - +
397D ALA* 3.0 25.5 + - + +
152E TYR* 3.7 26.9 - + - -
155E THR* 5.5 0.7 - - + -
156E THR* 3.7 26.5 - - - -
159E PHE* 3.8 40.6 - + + -
169E ILE* 4.4 17.5 - - + +
171E TRP* 3.3 67.5 - + + -
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Residues in contact with LEU 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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387D VAL* 5.1 1.8 - - + +
390D LYS* 3.1 31.4 - - + +
391D LEU* 2.4 21.0 + - + +
393D PHE* 1.3 94.5 - - + +
395D ALA* 1.3 55.9 + - - +
397D ALA* 3.1 3.4 + - - -
398D LEU* 2.8 46.0 + - + +
417D ALA* 5.2 5.2 - - + -
421D GLN* 4.1 16.2 - - - +
152E TYR* 4.0 15.7 - - + -
313E ALA 5.5 0.2 - - - +
314E ASP* 3.1 36.3 - - + +
315E ILE* 4.0 7.9 - - + -
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Residues in contact with ALA 395 (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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391D LEU 2.8 5.6 + - - +
392D PRO 3.7 6.7 - - - +
394D LEU* 1.3 76.3 - - - +
396D HIS* 1.3 58.1 + - - +
399D TYR* 2.8 43.2 + - - +
400D VAL* 3.8 3.0 + - - +
410D PHE* 4.6 5.4 - - + +
413D ALA* 4.3 3.1 - - + +
414D LEU* 3.7 44.9 - - + +
417D ALA* 4.1 11.8 - - + +
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Residues in contact with HIS 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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338D LEU* 6.4 1.6 - - + -
343D ILE* 4.8 8.0 - - + +
344D ILE* 5.4 1.8 - - + -
392D PRO 2.9 17.4 + - - +
393D PHE 3.9 2.9 - - - +
395D ALA* 1.3 77.9 - - - +
397D ALA* 1.3 60.0 + - - +
398D LEU 3.6 0.2 + - - -
400D VAL* 3.3 48.7 + - + +
401D GLN* 3.8 4.7 + - - -
402D ALA 3.3 19.7 + - - -
403D PRO* 4.2 5.6 + - + +
405D VAL* 3.7 16.5 - - + +
410D PHE* 4.2 12.7 - + + -
155E THR* 3.2 23.7 + - + +
158E LEU* 4.1 17.7 - - + -
159E PHE* 4.1 18.7 - + + -
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Residues in contact with ALA 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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393D PHE* 3.0 20.6 + - + +
394D LEU* 3.1 8.0 + - - +
396D HIS* 1.3 79.2 - - - +
398D LEU* 1.3 61.7 + - + +
400D VAL 4.9 0.4 - - - -
401D GLN* 4.6 0.9 - - - +
151E ASP* 2.9 34.7 - - - +
152E TYR* 3.9 26.7 - - + +
155E THR* 3.5 26.5 + - - +
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Residues in contact with LEU 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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394D LEU* 2.8 28.4 + - + +
395D ALA 3.2 0.2 + - - -
397D ALA* 1.3 84.4 - - + +
399D TYR* 1.3 86.3 + - + +
400D VAL 3.9 0.2 - - - -
401D GLN* 5.7 0.9 - - - -
417D ALA* 5.7 1.8 - - + -
420D LYS* 3.6 24.7 - - + +
421D GLN* 6.3 0.9 - - - +
148E HIS* 3.6 57.3 - - + +
151E ASP* 4.5 4.7 - - - -
152E TYR* 5.2 0.9 - - + -
315E ILE* 3.8 31.4 - - + -
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Residues in contact with TYR 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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395D ALA* 2.8 19.6 + - - +
398D LEU* 1.3 104.3 - - + +
400D VAL* 1.3 65.5 + - - +
401D GLN* 5.6 0.9 - - - -
413D ALA* 3.6 30.0 - - + +
416D LEU* 4.5 26.4 + - + -
417D ALA* 4.0 20.1 - - + -
420D LYS* 3.4 29.8 + - + +
148E HIS* 6.0 3.6 - + - -
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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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395D ALA 4.1 2.2 - - - +
396D HIS* 3.3 47.4 + - + +
398D LEU 3.9 0.2 - - - -
399D TYR* 1.3 86.1 - - + +
401D GLN* 1.3 71.1 + - - +
402D ALA* 3.2 39.3 + - + +
405D VAL* 3.8 23.1 - - + -
410D PHE* 4.7 10.8 - - + -
413D ALA* 5.5 5.4 - - + -
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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