Contacts of the helix formed by residues 379 - 397 (chain D) in PDB entry 1YCH
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 ARG 379 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ALA* 5.9 5.3 - - - +
377D VAL 4.3 6.5 - - - +
378D PRO* 1.3 78.4 - - - +
380D GLY* 1.3 68.0 + - - +
381D GLU* 3.3 13.5 - - - +
382D ASP* 2.8 31.1 + - - +
383D LEU* 3.1 14.7 + - - +
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Residues in contact with GLY 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D ARG* 1.3 73.4 - - - +
381D GLU* 1.3 66.2 + - - +
383D LEU* 3.4 7.9 + - - +
384D GLN* 3.1 21.4 + - - +
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Residues in contact with GLU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D ARG* 3.7 14.4 - - - +
380D GLY* 1.3 76.0 + - - +
382D ASP* 1.3 56.0 + - - +
384D GLN* 3.4 8.4 - - - +
385D ARG* 2.7 36.6 + - - +
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Residues in contact with ASP 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D THR 4.9 2.6 - - - +
374D VAL* 3.7 29.6 - - + +
377D VAL 4.1 2.3 - - - +
378D PRO* 3.7 6.1 - - + +
379D ARG* 2.8 46.0 + - - +
381D GLU* 1.3 79.4 - - - +
383D LEU* 1.3 63.1 + - - +
385D ARG* 3.3 6.9 + - - +
386D CYS* 3.1 25.5 + - - -
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Residues in contact with LEU 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LYS* 3.7 34.8 - - + +
269D MET* 4.3 10.1 - - + -
272D ALA* 3.5 12.9 - - + +
378D PRO* 3.4 31.9 - - + +
379D ARG 3.1 15.0 + - - +
380D GLY* 4.0 7.9 - - - +
382D ASP* 1.3 80.0 - - - +
384D GLN* 1.3 57.8 + - - +
386D CYS* 3.3 5.6 + - - +
387D TYR* 2.9 24.9 + - - +
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Residues in contact with GLN 384 (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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118A HIS* 5.8 0.6 + - + -
380D GLY 3.1 15.5 + - - +
381D GLU* 3.1 12.3 + - - +
383D LEU* 1.3 74.4 - - - +
385D ARG* 1.3 60.5 + - - +
387D TYR* 3.1 24.2 + - - +
388D GLU* 2.8 58.6 + - - +
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Residues in contact with ARG 385 (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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118A HIS* 5.3 2.4 - - - +
120A ASP* 5.7 2.6 + - - -
372D PRO* 5.6 5.6 - - + -
381D GLU 2.7 20.4 + - - +
382D ASP* 3.5 7.9 - - - +
384D GLN* 1.3 73.7 - - - +
386D CYS* 1.3 51.5 + - - +
388D GLU* 3.1 41.6 + - - +
389D LEU* 2.8 73.8 + - + +
392D LYS* 4.8 9.3 - - - +
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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
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269D MET* 3.7 36.6 - - - -
272D ALA* 3.7 13.7 - - + -
273D LEU* 3.7 21.8 - - + +
372D PRO* 4.0 21.8 - - - -
374D VAL* 5.8 1.8 - - - -
382D ASP 3.1 18.2 + - - -
383D LEU* 3.4 10.1 - - - +
385D ARG* 1.3 74.9 - - - +
387D TYR* 1.3 58.5 + - - +
389D LEU* 3.1 10.5 + - - +
390D GLY 2.9 24.9 + - - -
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Residues in contact with TYR 387 (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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98A PRO* 5.2 2.9 - - - +
272D ALA* 3.8 12.5 - - + +
275D ASP* 3.7 31.9 - - + -
276D GLY* 3.3 17.1 - - - -
279D ALA* 3.2 24.2 - - + +
383D LEU 2.9 15.1 + - - +
384D GLN* 3.3 31.9 - - - +
386D CYS* 1.3 75.6 - - - +
388D GLU* 1.3 69.8 + - + +
390D GLY 3.3 1.2 + - - -
391D ARG* 3.0 41.2 + - + +
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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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118A HIS* 2.3 68.9 + - - +
120A ASP* 3.6 12.2 - - - +
384D GLN* 2.8 43.0 + - - +
385D ARG* 3.1 37.6 + - - +
387D TYR* 1.3 79.3 - - + +
389D LEU* 1.3 57.5 + - - +
391D ARG* 3.0 25.7 - - - +
392D LYS* 3.0 9.0 + - - +
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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
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273D LEU* 4.2 7.6 - - + -
340D LEU* 4.4 5.4 - - + -
367D ILE* 4.7 10.1 - - + -
368D ALA* 4.5 21.3 - - + -
372D PRO* 2.9 43.5 - - + -
385D ARG* 2.8 45.8 + - + +
386D CYS* 3.1 8.9 + - - +
388D GLU* 1.3 73.3 - - - +
390D GLY* 1.3 64.0 + - - +
391D ARG 3.0 1.8 - - - -
392D LYS* 3.1 18.9 + - + +
393D ILE* 3.0 28.3 + - - +
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Residues in contact with GLY 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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273D LEU* 3.7 28.9 - - - +
276D GLY 3.6 6.1 - - - -
277D LEU* 3.3 19.1 - - - +
386D CYS 2.9 12.2 + - - -
387D TYR 3.3 3.1 + - - -
389D LEU* 1.3 76.7 - - - +
391D ARG* 1.3 56.6 + - - +
393D ILE* 4.5 2.9 - - - -
394D ALA* 3.0 25.1 + - - +
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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
----------------------------------------------------------
94A MET* 3.7 19.6 + - - +
95A GLU* 5.1 2.6 - - - +
98A PRO* 3.5 40.8 + - - +
119A ILE* 5.2 4.6 - - - +
120A ASP* 2.9 40.3 + - + +
121A PHE* 4.7 1.2 - - - +
276D GLY 3.7 17.9 - - - -
279D ALA* 4.1 5.1 - - - +
280D GLY* 4.4 7.2 - - - +
387D TYR* 3.0 41.0 + - + +
388D GLU* 3.0 19.3 - - - +
390D GLY* 1.3 76.8 - - - +
392D LYS* 1.3 61.7 + - - +
394D ALA* 3.5 4.0 + - - +
395D ALA* 3.1 21.0 + - - +
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Residues in contact with LYS 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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120A ASP* 3.6 27.6 - - - +
367D ILE* 4.3 30.4 + - + -
368D ALA* 5.8 1.6 - - - +
385D ARG* 4.8 8.0 - - - +
388D GLU 3.0 10.7 + - - +
389D LEU* 3.3 25.8 - - + +
391D ARG* 1.3 75.7 - - - +
393D ILE* 1.3 66.8 + - + +
395D ALA* 3.0 15.5 + - + +
396D ARG* 3.1 12.4 + - + +
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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
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273D LEU* 5.1 0.2 - - + -
277D LEU* 3.6 20.4 - - + -
306D ALA* 3.7 13.5 - - + -
308D LEU* 3.5 33.0 - - + -
338D VAL* 4.5 6.1 - - + -
339D GLY* 5.1 2.5 - - - +
340D LEU* 4.2 9.0 - - + -
367D ILE* 3.7 36.1 - - + -
389D LEU 3.0 21.4 + - - +
390D GLY* 4.7 2.9 - - - -
392D LYS* 1.3 75.2 - - - +
394D ALA* 1.3 63.1 + - - +
396D ARG* 3.0 7.1 + - - +
397D ILE* 2.9 40.4 + - + +
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Residues in contact with ALA 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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122A ASN* 5.6 0.5 - - - +
277D LEU* 3.8 15.0 - - - +
280D GLY* 3.6 39.0 - - - +
282D CYS* 4.1 17.1 - - - -
390D GLY 3.0 18.3 + - - +
391D ARG 3.7 3.4 - - - +
392D LYS 3.2 0.2 - - - -
393D ILE* 1.3 77.6 - - - +
395D ALA* 1.3 63.3 + - - +
397D ILE* 3.4 2.9 + - - +
398D ALA* 3.1 20.4 + - - +
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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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120A ASP* 4.7 2.0 - - + +
121A PHE* 3.6 32.1 - - - +
122A ASN* 3.8 16.7 + - - +
123A TYR* 5.9 3.6 - - + -
391D ARG 3.1 13.1 + - - +
392D LYS* 3.0 14.6 + - + +
394D ALA* 1.3 77.7 - - - +
396D ARG* 1.3 61.7 + - - +
398D ALA* 3.2 18.9 - - - +
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Residues in contact with ARG 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 VAL* 4.0 22.2 - - + +
365D GLU* 2.6 44.6 + - - -
367D ILE* 3.5 35.4 - - + +
392D LYS 3.1 10.0 + - - +
393D ILE 3.0 7.4 + - - +
395D ALA* 1.3 75.3 - - - +
397D ILE* 1.3 56.0 + - + +
398D ALA* 2.8 18.4 + - - +
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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
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253D ALA* 3.5 27.4 - - - -
254D LYS 4.0 5.6 - - - +
255D ALA* 4.3 6.7 - - + -
277D LEU* 4.7 0.4 - - + -
282D CYS* 3.8 16.4 - - - -
305D ARG* 3.2 40.7 + - + +
306D ALA* 3.1 39.7 - - + +
338D VAL* 5.2 6.3 - - + -
393D ILE* 2.9 27.0 + - + +
394D ALA 3.7 4.5 - - - +
396D ARG* 1.3 73.2 - - + +
398D ALA* 1.3 64.5 + - - +
399D ASP* 3.0 3.7 + - - +
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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