Contacts of the helix formed by residues 383 - 401 (chain D) in PDB entry 5FLZ
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 VAL 383 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D LEU* 5.7 7.9 - - + -
267D PHE* 3.7 50.9 - - + +
306D VAL* 3.6 36.6 - - + -
380D MET 3.1 20.2 - - - +
381D SER* 3.1 1.8 - - - -
382D THR* 1.4 76.1 - - + +
384D VAL* 1.3 63.0 + - + +
385D ASN 3.0 1.3 + - - -
386D VAL* 3.1 25.1 + - + +
387D PHE* 3.7 18.6 + - + -
434D MET* 6.3 0.7 - - + -
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Residues in contact with VAL 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D LEU* 5.9 0.7 - - + -
314D THR* 6.3 1.1 - - + -
381D SER 3.4 17.0 - - - +
382D THR* 3.0 5.3 + - - +
383D VAL* 1.3 76.8 - - + +
385D ASN* 1.3 60.4 + - + +
387D PHE* 3.0 29.7 + - + +
388D GLU* 3.0 24.6 + - - +
431D GLN* 3.9 23.6 - - + -
434D MET* 3.6 31.9 - - + -
435D GLU* 3.5 28.5 - - - +
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Residues in contact with ASN 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ARG* 5.4 2.4 - - - +
307D SER* 3.3 22.6 + - - +
310D MET* 6.3 0.8 - - - +
382D THR* 3.1 14.6 + - - +
383D VAL 3.0 0.2 - - - -
384D VAL* 1.3 83.3 - - + +
386D VAL* 1.4 55.3 + - - +
388D GLU* 3.1 26.9 + - - +
389D ASN* 3.0 48.7 + - - +
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Residues in contact with VAL 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PHE* 4.4 16.2 - - + -
176D ARG* 3.4 50.5 - - - +
191D LEU* 5.9 1.8 - - + -
267D PHE* 6.0 3.8 - - + -
306D VAL* 3.2 30.1 - - + +
307D SER* 4.2 1.3 - - - +
383D VAL* 3.2 14.6 - - + +
385D ASN* 1.4 67.7 - - - +
387D PHE* 1.4 72.5 + - + +
389D ASN* 3.4 13.2 + - + +
390D ALA* 3.0 23.6 + - + +
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Residues in contact with PHE 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D LEU* 4.0 19.7 - - + -
195D ILE* 3.5 33.0 - - + -
267D PHE* 3.7 36.8 - + - -
383D VAL* 4.2 16.4 - - + -
384D VAL* 3.0 26.3 + - + +
386D VAL* 1.4 83.0 - - + +
388D GLU* 1.4 53.9 + - - +
390D ALA* 3.2 7.4 + - - +
391D CYS* 2.9 29.1 + - - +
427D ARG* 3.7 21.6 + - + +
430D VAL* 5.0 5.8 - - + -
431D GLN* 3.7 22.7 - - + +
434D MET* 4.8 19.7 - - + -
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Residues in contact with GLU 388 (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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384D VAL* 3.0 21.8 + - - +
385D ASN* 3.1 32.2 + - - +
387D PHE* 1.4 73.2 - - - +
389D ASN* 1.4 57.3 + - - +
391D CYS* 3.2 8.0 - - - +
392D ASN* 2.9 36.6 + - - +
428D GLU* 5.5 1.1 - - - +
431D GLN* 3.2 30.0 - - - +
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Residues in contact with ASN 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ARG* 3.7 42.2 + - - +
385D ASN* 3.0 41.2 + - - +
386D VAL* 3.5 11.5 - - - +
388D GLU* 1.4 75.2 - - - +
390D ALA* 1.4 57.9 - - - +
392D ASN* 3.0 18.9 + - - +
393D THR* 2.9 33.9 + - - +
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Residues in contact with ALA 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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183D GLN* 5.7 5.8 - - - +
184D SER* 3.4 9.4 + - - +
187D THR* 5.7 5.8 - - + -
188D ILE* 4.3 8.3 - - + +
191D LEU* 5.0 9.9 - - + -
386D VAL* 3.0 11.5 + - + +
387D PHE* 3.4 9.2 - - - +
389D ASN* 1.4 77.2 - - - +
391D CYS* 1.4 58.6 + - - +
393D THR* 3.5 4.2 + - - -
394D PHE* 2.9 29.1 + - - +
427D ARG* 3.3 19.2 + - - +
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Residues in contact with CYS 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D PHE 2.9 12.3 + - - +
388D GLU* 3.2 15.3 - - - +
390D ALA* 1.4 75.7 - - - +
392D ASN* 1.4 55.6 + - - +
394D PHE* 3.2 8.4 + - - +
395D ASP* 2.9 48.1 + - - +
424D ALA* 4.9 5.2 - - - -
427D ARG* 3.5 28.4 - - - +
428D GLU* 3.9 24.5 - - - +
431D GLN* 4.9 0.2 - - - +
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Residues in contact with ASN 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D GLU* 2.9 19.6 + - - +
389D ASN* 3.0 24.3 + - - +
391D CYS* 1.4 73.4 - - - +
393D THR* 1.3 67.2 + - - +
395D ASP* 3.5 6.6 + - - +
396D LYS* 3.2 23.4 + - - +
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Residues in contact with THR 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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178D SER* 3.5 20.5 + - - +
181D VAL* 3.7 15.3 - - + +
183D GLN* 3.5 17.1 + - - +
184D SER* 3.4 26.9 - - - -
389D ASN* 2.9 18.0 + - - +
390D ALA* 3.9 2.4 - - - -
392D ASN* 1.3 80.0 - - - +
394D PHE* 1.3 59.3 + - - +
396D LYS* 3.2 7.9 + - + +
397D VAL* 3.1 24.8 + - + +
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Residues in contact with PHE 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D SER* 3.3 9.1 + - - +
188D ILE* 3.6 24.9 - - + -
390D ALA 2.9 19.0 + - - +
391D CYS* 3.4 13.9 - - - +
393D THR* 1.3 71.9 - - - +
395D ASP* 1.3 93.4 + - - +
397D VAL* 3.2 20.9 - - + +
398D PHE* 3.2 31.3 + + - +
420D GLN* 4.0 29.6 - - + -
421D ASP* 4.2 16.4 - - - -
424D ALA* 3.7 25.1 - - + -
427D ARG* 3.7 18.8 - - - +
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Residues in contact with ASP 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D CYS* 2.9 32.2 + - - +
392D ASN* 3.9 6.4 - - - +
394D PHE* 1.3 99.5 - - - +
396D LYS* 1.3 55.1 + - - +
398D PHE* 3.5 5.5 + - - +
399D ALA* 2.9 31.0 + - - +
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Residues in contact with LYS 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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181D VAL* 5.1 9.6 - - + -
392D ASN 3.2 15.0 + - - +
393D THR* 3.2 15.5 + - + +
395D ASP* 1.3 77.0 - - - +
397D VAL* 1.3 61.3 + - + +
399D ALA* 3.4 9.5 - - + +
400D LYS* 3.3 30.9 + - + +
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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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181D VAL* 3.3 37.7 - - + +
182D VAL* 4.3 4.7 - - + +
184D SER* 4.5 3.1 - - - -
185D TYR* 3.2 44.9 + - + -
393D THR* 3.4 13.7 - - + +
394D PHE* 3.2 24.0 - - + +
396D LYS* 1.3 73.7 - - + +
398D PHE* 1.4 62.2 + - + +
400D LYS* 3.1 35.6 + - - +
401D GLY 3.3 8.8 + - - -
402D ALA* 3.9 0.7 + - + -
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Residues in contact with PHE 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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185D TYR* 4.6 4.7 - - - -
394D PHE* 3.2 30.9 + + + +
395D ASP* 3.9 6.3 - - - +
397D VAL* 1.4 80.6 - - + +
399D ALA* 1.4 62.6 + - - +
401D GLY* 3.3 13.7 + - - -
404D LEU* 5.8 1.7 - - + +
416D MET* 3.4 41.4 - - + +
417D GLN* 4.0 32.8 - - + +
420D GLN* 4.1 14.6 - - - -
421D ASP* 3.7 26.7 - - - -
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Residues in contact with ALA 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 ASP 2.9 19.5 + - - +
396D LYS* 3.4 11.2 - - + +
397D VAL 3.2 0.2 - - - -
398D PHE* 1.4 78.2 - - - +
400D LYS* 1.3 61.5 + - - +
401D GLY 3.4 0.2 + - - -
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Residues in contact with LYS 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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181D VAL* 3.5 37.8 - - - +
182D VAL* 5.7 0.2 - - - -
396D LYS* 3.3 14.2 + - + +
397D VAL* 3.1 30.8 + - - +
399D ALA* 1.3 75.0 - - - +
401D GLY* 1.4 62.5 + - - +
402D ALA* 4.1 22.2 - - + +
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Residues in contact with GLY 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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397D VAL 3.3 5.6 + - - -
398D PHE 3.3 13.0 + - - -
400D LYS* 1.4 81.1 - - - +
402D ALA* 1.4 62.8 + - - +
403D PHE 3.5 2.3 + - - -
404D LEU* 3.9 31.2 + - - +
416D MET* 6.2 0.2 - - - -
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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