Contacts of the helix formed by residues 395 - 415 (chain A) in PDB entry 1Y8B
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 GLY 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 4.3 8.5 - - - -
394A HIS* 1.3 82.3 - - - +
396A PRO* 1.3 71.3 - - - +
397A GLN* 3.3 4.3 - - - -
398A GLU* 2.9 30.2 + - - +
399A VAL* 3.3 11.3 + - - +
431A THR* 5.5 0.4 - - - +
437A SER* 5.7 2.2 - - - -
438A CYS* 6.5 0.7 - - - -
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Residues in contact with PRO 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 4.8 2.0 - - + -
92A VAL* 3.7 44.4 - - + -
93A PRO* 5.1 11.9 - - + +
395A GLY* 1.3 84.5 - - - +
397A GLN* 1.3 82.3 - - - +
398A GLU 3.2 0.7 + - - -
399A VAL* 3.4 9.3 + - + +
400A ALA* 3.3 19.6 + - - +
437A SER* 5.4 10.7 - - - +
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Residues in contact with GLN 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 4.6 11.8 + - - -
395A GLY* 4.7 0.3 - - - -
396A PRO* 1.3 97.8 - - - +
398A GLU* 1.3 78.2 + - - +
400A ALA* 3.7 7.7 - - - +
401A PHE* 2.8 40.9 + - + +
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 3.6 10.8 - - - +
53A LEU* 3.1 44.0 - - - +
56A GLU* 4.1 6.4 - - - +
90A TYR* 4.9 1.0 + - - -
392A LYS 3.9 13.3 - - - +
393A MET* 4.5 2.0 - - - -
394A HIS* 3.6 16.6 - - + +
395A GLY* 2.9 38.8 + - - +
397A GLN* 1.3 97.9 - - - +
399A VAL* 1.3 61.5 + - - +
401A PHE* 3.3 6.3 + - - +
402A ALA* 3.0 21.3 + - - +
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A MET* 4.0 17.3 - - + -
395A GLY 3.3 13.2 + - - +
396A PRO* 3.9 7.2 - - + +
398A GLU* 1.3 75.3 - - - +
400A ALA* 1.3 60.2 + - - +
402A ALA* 2.9 7.0 + - - +
403A ASN* 2.4 36.9 + - - +
437A SER 4.2 9.6 - - - +
438A CYS* 3.9 23.8 - - - +
440A ALA* 4.4 5.6 - - + +
441A GLN* 3.2 42.8 - - + +
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PRO 3.3 10.2 + - - +
397A GLN* 3.7 11.2 - - - +
398A GLU 3.3 0.4 - - - -
399A VAL* 1.3 81.7 - - - +
401A PHE* 1.3 64.5 + - - +
402A ALA 2.9 1.2 + - - -
403A ASN* 3.1 19.6 + - - +
404A LYS* 3.1 12.9 + - - +
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Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 4.8 13.5 - - - -
46A LEU* 6.3 1.1 - - + -
49A GLU* 4.8 26.7 - - + +
397A GLN* 2.8 31.5 + - + +
398A GLU* 3.6 8.7 - - - +
400A ALA* 1.3 74.2 - - + +
402A ALA* 1.3 61.5 + - - +
404A LYS* 3.5 11.7 + - + +
405A LEU* 3.2 40.6 + - + +
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Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 6.1 2.5 - - - -
392A LYS* 6.0 2.5 - - + -
393A MET* 5.2 5.8 - - + -
398A GLU 3.0 11.8 + - - +
399A VAL* 2.9 12.2 + - - +
400A ALA 2.9 0.6 + - - -
401A PHE* 1.3 73.7 - - - +
403A ASN* 1.3 51.5 + - - +
404A LYS 2.6 13.1 + - - -
405A LEU* 2.7 3.6 + - - -
406A PHE* 2.4 69.8 + - + +
441A GLN* 3.9 7.6 - - - +
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Residues in contact with ASN 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A VAL* 2.4 34.3 + - - +
400A ALA* 3.2 11.0 + - - +
402A ALA* 1.3 71.8 - - - +
404A LYS* 1.3 57.4 + - - +
406A PHE* 4.1 7.1 - - - +
407A THR* 2.9 26.3 + - - -
440A ALA 5.2 0.4 + - - -
441A GLN* 2.4 45.6 + - - +
443A ARG* 3.1 32.9 - - - +
444A ASN* 5.9 0.4 - - - +
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Residues in contact with LYS 404 (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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400A ALA 3.1 10.7 + - - +
401A PHE* 3.5 18.6 - - + +
402A ALA 2.6 5.3 + - - -
403A ASN* 1.3 77.2 - - - +
405A LEU* 1.3 69.5 + - + +
407A THR* 3.8 7.3 + - - -
408A ARG* 3.5 17.1 - - + +
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.4 21.1 - - + -
45A ASP* 3.4 38.4 - - + +
46A LEU* 3.8 37.9 - - + -
49A GLU* 6.3 0.4 - - + -
401A PHE* 3.2 28.6 + - + +
402A ALA* 2.7 9.0 + - - +
404A LYS* 1.3 78.8 - - + +
406A PHE* 1.3 59.8 + - + +
407A THR 2.9 2.2 - - - -
408A ARG* 2.5 36.4 + - + +
409A ILE* 3.0 12.7 + - + +
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Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 5.9 7.4 - - + -
392A LYS* 4.5 27.1 - - + -
393A MET* 5.3 2.2 - - - -
402A ALA* 2.4 60.8 + - + +
403A ASN* 4.1 5.8 - - - -
405A LEU* 1.3 69.5 - - + +
407A THR* 1.3 57.3 + - - +
409A ILE* 3.9 7.9 - - + -
410A GLU 3.2 6.9 + - - -
422A MET* 3.6 32.8 - - + -
441A GLN* 4.1 21.5 - - + +
444A ASN* 5.0 3.1 - - - +
445A ARG* 2.4 67.9 + - + +
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Residues in contact with THR 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ASN 2.9 20.0 + - - -
404A LYS 3.9 6.7 - - - -
405A LEU 2.9 0.6 - - - -
406A PHE* 1.3 79.2 - - - +
408A ARG* 1.3 66.0 + - - +
410A GLU* 4.0 2.6 - - + +
411A THR* 2.9 28.7 + - - +
443A ARG* 5.7 1.4 - - - +
444A ASN* 4.6 8.7 + - - -
445A ARG* 3.7 7.0 - - - +
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Residues in contact with ARG 408 (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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38A ASN* 4.4 12.2 + - - +
41A GLU* 3.3 26.7 + - - -
42A ILE* 4.5 16.3 - - + +
404A LYS* 3.5 22.7 - - + +
405A LEU* 2.5 25.8 + - + +
407A THR* 1.3 77.7 - - - +
409A ILE* 1.3 64.4 + - - +
410A GLU 3.2 1.9 + - - -
411A THR* 3.4 14.4 + - - -
412A MET* 3.1 15.5 + - - +
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Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.2 21.6 - - + +
364A GLY 5.7 1.8 - - - +
365A VAL* 5.3 11.9 - - + -
405A LEU 3.0 7.8 + - - +
406A PHE* 3.3 15.9 - - + +
408A ARG* 1.3 77.9 - - - +
410A GLU* 1.3 58.0 + - - +
412A MET* 3.0 24.3 - - - +
413A LEU* 2.7 53.7 + - + +
445A ARG* 3.3 20.9 - - - +
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Residues in contact with GLU 410 (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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406A PHE 3.2 2.2 + - - +
407A THR* 4.1 4.7 - - + +
408A ARG 3.2 0.8 - - - -
409A ILE* 1.3 80.1 - - - +
411A THR* 1.3 61.0 + - - +
413A LEU* 4.7 1.1 - - - -
414A GLY* 2.4 47.0 + - - +
416A ALA 5.6 1.3 - - - +
417A PRO 4.0 17.2 - - - +
418A ASN* 4.1 21.8 + - - -
420A LEU* 5.3 12.1 - - + +
444A ASN* 4.4 6.1 + - - +
445A ARG* 2.8 52.1 + - - +
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Residues in contact with THR 411 (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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407A THR* 2.9 18.4 + - - +
408A ARG* 3.4 13.1 + - - -
409A ILE 3.4 0.6 - - - -
410A GLU* 1.3 79.6 - - - +
412A MET* 1.3 60.4 + - - +
414A GLY* 5.1 0.2 - - - -
415A MET* 4.0 9.4 + - - -
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Residues in contact with MET 412 (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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30A LEU* 5.0 13.0 - - + +
34A ALA* 6.4 2.0 - - + -
35A PHE* 3.8 27.4 - - + -
38A ASN* 3.3 50.0 - - + +
39A PHE* 5.0 0.9 - - - +
42A ILE* 3.7 17.9 - - + -
365A VAL* 5.5 0.4 - - + -
372A LEU* 5.8 0.9 - - - +
408A ARG 3.1 14.6 - - - +
409A ILE* 3.0 23.1 - - + +
411A THR* 1.3 79.6 - - - +
413A LEU* 1.3 88.7 + - + -
414A GLY 3.1 5.3 + - - -
415A MET* 3.8 10.4 + - - +
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Residues in contact with LEU 413 (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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30A LEU* 4.4 9.4 - - + -
35A PHE* 4.3 10.1 - - + -
364A GLY 5.6 0.7 - - - +
365A VAL* 4.3 19.5 - - + +
368A GLY* 3.5 35.7 - - - +
369A ALA* 3.8 6.3 - - - +
371A ALA* 5.7 1.9 - - + +
372A LEU* 3.7 18.1 - - + +
375A LEU* 2.8 22.6 - - - +
409A ILE* 2.7 46.9 + - + +
410A GLU* 3.5 2.0 - - - -
412A MET* 1.3 85.0 - - + +
414A GLY* 1.3 57.4 + - - +
415A MET* 4.9 0.2 - - - -
420A LEU* 4.3 11.1 - - + +
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Residues in contact with GLY 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 2.8 22.6 - - - +
410A GLU* 2.4 37.0 + - - -
412A MET 3.1 0.2 - - - -
413A LEU* 1.3 71.6 - - - +
415A MET* 1.3 56.8 + - - +
416A ALA* 2.4 32.3 + - - +
418A ASN* 5.5 2.0 - - - -
420A LEU* 4.8 5.6 - - - -
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Residues in contact with MET 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR 4.2 11.7 - - - +
29A GLY* 4.7 11.9 - - - +
30A LEU* 5.0 2.9 - - - -
31A ASP* 6.1 0.9 - - - +
372A LEU* 4.0 27.4 - - + -
375A LEU* 4.1 23.4 - - + +
376A LYS* 4.3 15.3 - - + +
378A GLN* 5.2 1.0 - - - +
411A THR 4.0 9.4 + - - -
412A MET 3.8 12.4 + - - +
413A LEU 4.9 0.4 - - - -
414A GLY* 1.3 74.6 - - - +
416A ALA* 1.3 59.8 + - - +
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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
------------------------------------------------------------
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