Contacts of the helix formed by residues 414 - 433 (chain A) in PDB entry 1YNU
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 PRO 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLU* 4.8 5.8 - - - +
49A GLN* 5.5 1.3 - - - +
337A ARG* 4.5 1.3 - - - +
413A LEU* 1.3 92.2 - - + +
415A GLU* 1.3 66.9 + - - +
416A ARG* 3.9 33.7 - - + +
417A THR* 2.9 35.8 + - + +
418A LEU* 3.0 10.6 + - - +
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A GLN* 4.4 14.8 - - - +
337A ARG* 3.5 34.6 + - - +
340A LYS* 3.9 33.3 + - + +
414A PRO* 1.3 70.8 - - - +
416A ARG* 1.3 64.3 + - - +
418A LEU* 3.0 17.6 + - + +
419A ASP* 3.1 18.3 + - - +
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Residues in contact with ARG 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU* 2.7 43.4 + - - -
414A PRO* 3.9 22.6 - - + +
415A GLU* 1.3 80.1 - - - +
417A THR* 1.3 65.5 + - - +
419A ASP* 3.3 14.5 + - - +
420A LEU* 3.1 20.8 + - - +
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Residues in contact with THR 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.6 40.6 + - + -
33A GLU* 5.3 3.5 + - - +
41A ILE* 4.1 21.3 - - + +
413A LEU* 4.2 8.5 - - + -
414A PRO* 2.9 34.7 + - + +
416A ARG* 1.3 80.5 + - - +
418A LEU* 1.3 66.5 + - - +
420A LEU* 3.1 7.3 + - - +
421A ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A MET* 3.2 33.7 - - + -
337A ARG* 3.4 38.4 - - + +
340A LYS* 4.4 18.8 - - + +
341A LEU* 4.2 18.8 - - + +
410A PHE* 4.2 12.8 - - + +
413A LEU* 4.1 15.2 - - + +
414A PRO 3.0 9.8 + - - +
415A GLU* 3.0 14.6 + - - +
417A THR* 1.3 78.2 - - - +
419A ASP* 1.3 60.1 + - - +
421A ALA* 3.3 6.2 + - - +
422A MET* 3.1 30.0 + - + +
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Residues in contact with ASP 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A LYS* 2.7 42.4 + - - +
415A GLU* 3.1 16.7 + - - +
416A ARG* 3.5 15.2 - - - +
417A THR 3.2 0.2 - - - -
418A LEU* 1.3 73.7 - - - +
420A LEU* 1.3 67.1 + - - +
422A MET* 3.1 12.0 + - - +
423A GLN* 3.0 36.3 + - - +
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.4 42.0 - - + +
37A THR* 4.7 5.4 - - - +
41A ILE* 4.2 11.4 - - + -
416A ARG 3.1 12.7 + - - +
417A THR* 3.1 10.9 + - - +
419A ASP* 1.3 77.1 - - - +
421A ALA* 1.3 63.8 + - - +
423A GLN* 3.1 23.2 + - + +
424A ARG* 3.0 42.3 + - + +
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.8 15.2 - - + +
43A MET* 3.8 21.5 - - + -
390A LEU* 3.5 27.9 - - + +
417A THR 3.0 11.8 + - - +
418A LEU* 3.5 10.3 - - - +
420A LEU* 1.3 76.6 - - - +
422A MET* 1.3 64.0 + - + +
424A ARG* 3.3 4.6 + - - +
425A LEU* 3.0 27.7 + - - +
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Residues in contact with MET 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A MET* 4.4 9.0 - - + -
340A LYS 5.0 3.4 - - - +
341A LEU* 3.8 31.2 - - + +
344A GLY* 3.7 35.0 - - - +
345A LEU* 4.0 7.4 - - + -
347A LYS* 3.5 23.1 + - - +
390A LEU* 5.4 1.8 - - + -
408A VAL* 5.7 0.9 - - + -
418A LEU* 3.2 18.2 - - + +
419A ASP* 3.1 12.0 + - - +
421A ALA* 1.3 91.7 - - + +
423A GLN* 1.3 57.2 - - + +
425A LEU* 3.2 20.3 + - + +
426A LYS 2.8 23.7 + - - -
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Residues in contact with GLN 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A LYS* 4.9 5.4 - - - +
419A ASP* 3.0 32.8 + - - +
420A LEU* 3.1 21.2 + - + +
422A MET* 1.3 74.1 - - + +
424A ARG* 1.3 67.8 + - + +
426A LYS* 3.1 7.2 + - - +
427A ALA* 2.9 26.2 + - - +
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Residues in contact with ARG 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 4.7 1.4 - - - -
37A THR 3.6 18.2 + - - -
38A ASN* 4.3 4.4 + - - +
39A GLY 3.2 17.0 + - - -
41A ILE* 3.0 35.4 - - - +
388A VAL* 3.2 28.2 + - + +
389A HIS* 2.7 42.8 + - - +
390A LEU* 3.9 2.6 - - - +
420A LEU* 3.0 30.8 + - + +
421A ALA 3.7 5.4 - - - +
423A GLN* 1.3 77.1 - - + +
425A LEU* 1.3 57.3 + - - +
427A ALA* 3.8 6.0 - - - +
428A PHE* 3.2 26.7 + - - +
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU* 3.6 30.7 - - + -
348A SER* 4.1 10.3 - - - +
350A ILE* 4.0 17.5 - - + -
365A MET* 4.8 11.0 - - + -
384A ILE* 5.7 6.1 - - + -
388A VAL* 4.0 7.6 - - + +
390A LEU* 4.5 15.0 - - + -
421A ALA 3.0 13.8 + - - +
422A MET* 3.4 20.2 - - + +
423A GLN 3.0 0.2 - - - -
424A ARG* 1.3 76.7 - - - +
426A LYS* 1.3 64.4 + - - +
428A PHE* 3.4 11.8 + - + +
429A VAL* 3.1 35.1 + - + +
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Residues in contact with LYS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A LYS* 2.7 56.0 + - + +
348A SER* 3.2 21.1 + - - +
422A MET 2.8 14.7 + - - +
423A GLN* 3.1 6.0 + - - +
425A LEU* 1.3 73.4 - - - +
427A ALA* 1.3 68.8 + - - +
429A VAL* 2.9 22.4 - - + +
430A GLY* 2.9 12.6 + - - +
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Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A GLN 2.9 15.7 + - - +
424A ARG* 3.8 7.4 - - - +
426A LYS* 1.3 79.8 - - - +
428A PHE* 1.3 58.3 + - - +
430A GLY* 3.1 3.2 + - - -
431A GLU* 2.8 33.7 + - + +
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Residues in contact with PHE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A MET* 5.7 0.9 - - + -
368A LEU* 5.2 2.9 - - + -
380A LEU* 4.1 26.5 - - + -
383A LYS* 4.4 17.0 - - + -
384A ILE* 4.7 4.3 - - + -
387A GLU* 3.9 21.8 - - + -
388A VAL* 3.7 28.3 - - + -
424A ARG 3.2 16.1 + - - +
425A LEU* 3.6 12.8 - - + +
426A LYS 3.3 0.2 - - - -
427A ALA* 1.3 79.0 - - - +
429A VAL* 1.3 70.1 + - + +
431A GLU* 2.9 20.9 + - - +
432A TYR* 3.1 41.7 + + + +
433A TYR* 4.3 22.0 - + - -
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A SER* 3.8 28.9 - - - +
350A ILE* 4.6 4.0 - - + -
368A LEU* 3.9 28.9 - - + -
425A LEU* 3.1 20.1 + - + +
426A LYS* 2.9 33.9 - - + +
428A PHE* 1.3 77.5 - - + +
430A GLY* 1.3 60.7 + - - +
431A GLU 2.9 5.3 + - - -
433A TYR* 2.7 52.3 + - + +
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Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A LYS* 2.9 20.1 + - - -
427A ALA 3.2 5.8 - - - -
429A VAL* 1.3 77.3 - - - +
431A GLU* 1.3 56.8 + - - +
432A TYR 3.7 0.2 - - - -
433A TYR 4.1 11.8 - - - +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ALA* 2.8 18.6 + - + +
428A PHE* 3.1 9.9 - - - +
429A VAL 2.9 0.4 - - - -
430A GLY* 1.3 79.1 - - - +
432A TYR* 1.3 83.5 + - + +
433A TYR 3.8 0.7 - - - -
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Residues in contact with TYR 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A LYS* 4.5 20.0 - - - -
387A GLU* 3.7 25.3 + - - -
428A PHE* 3.1 34.9 + + - +
431A GLU* 1.3 113.2 - - + +
433A TYR* 1.3 91.1 + - + +
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Residues in contact with TYR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A HIS 4.8 2.9 - - - -
368A LEU* 3.2 60.9 + - + +
380A LEU* 4.4 11.1 - - - +
428A PHE* 4.3 14.6 - + - -
429A VAL* 2.7 36.5 + - + +
430A GLY* 4.1 13.2 - - - +
431A GLU 5.0 0.3 - - - -
432A TYR* 1.3 103.8 + - + +
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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
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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