Contacts of the helix formed by residues 411 - 425 (chain A) in PDB entry 3I5Y
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 THR 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A LYS 3.5 5.5 + - - +
410A ILE* 1.3 78.1 - - - +
412A GLN* 1.3 65.6 + - - +
413A ASN* 4.0 6.8 + - - +
414A LYS* 3.1 26.8 + - + +
415A ARG 3.1 16.8 + - - -
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Residues in contact with GLN 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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190A ARG* 3.0 40.2 + - - +
191A ASP* 3.6 19.0 + - - -
194A LEU* 3.9 13.3 - - + +
219A VAL* 5.7 0.2 - - - -
220A GLY 3.9 10.1 - - - +
221A GLY* 3.4 33.0 - - - +
222A THR* 4.4 9.4 - - + -
410A ILE 3.6 0.8 + - - -
411A THR* 1.3 71.1 - - - +
413A ASN* 1.3 66.3 + - - +
415A ARG* 3.4 15.6 + - - +
416A THR* 3.1 42.6 + - - +
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Residues in contact with ASN 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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221A GLY 5.5 2.2 - - - +
411A THR* 3.3 7.2 + - - +
412A GLN* 1.3 80.3 - - - +
414A LYS* 1.3 61.7 + - + +
416A THR* 3.5 5.4 + - - -
417A SER* 3.2 25.6 + - - -
9B U 5.1 10.2 + - - +
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Residues in contact with LYS 414 (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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410A ILE* 3.6 20.0 - - + -
411A THR* 3.1 19.3 + - + +
413A ASN* 1.3 78.9 - - + +
415A ARG* 1.3 66.3 + - - +
417A SER* 3.0 8.5 + - - +
418A LEU* 2.9 34.3 + - + +
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Residues in contact with ARG 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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190A ARG* 3.6 16.3 - - - +
191A ASP* 2.7 38.9 + - - +
406A PHE* 4.3 11.0 - - + -
407A HIS 3.8 8.8 + - - +
408A GLY* 3.9 16.3 + - - -
410A ILE* 3.1 38.6 + - + +
411A THR 3.1 7.1 + - - +
412A GLN* 3.4 31.9 + - - +
414A LYS* 1.3 77.5 - - - +
416A THR* 1.3 57.9 + - - +
418A LEU* 3.6 9.2 - - - +
419A VAL* 3.0 33.1 + - - +
435A VAL* 3.6 14.7 - - - +
6B U 2.9 38.9 + - - -
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Residues in contact with THR 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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191A ASP* 4.9 2.5 - - - -
194A LEU* 3.6 20.4 - - + +
412A GLN* 3.1 29.9 + - - +
413A ASN* 3.7 5.8 - - - -
415A ARG* 1.3 78.0 - - - +
417A SER* 1.3 59.2 + - - +
419A VAL* 3.4 7.1 + - - +
420A LYS* 3.0 28.6 + - + +
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Residues in contact with SER 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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413A ASN 3.2 12.8 + - - -
414A LYS* 3.0 21.8 + - - +
416A THR* 1.3 79.7 - - - +
418A LEU* 1.3 55.8 + - - +
420A LYS* 3.1 13.8 + - - +
421A ARG* 2.9 27.0 + - - +
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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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404A LEU* 4.1 19.1 - - + +
405A GLU 3.5 23.8 - - - +
406A PHE* 3.9 20.2 - - + -
410A ILE* 4.4 7.6 - - + -
414A LYS* 2.9 31.6 + - + +
415A ARG* 3.6 8.3 - - - +
417A SER* 1.3 74.9 + - - +
419A VAL* 1.3 66.2 + - + +
421A ARG* 3.8 7.3 - - - +
422A PHE* 3.0 30.7 + - - +
430A LEU* 3.6 29.2 - - + -
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Residues in contact with VAL 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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191A ASP* 4.4 8.5 - - + +
195A GLN* 6.2 0.2 - - + -
406A PHE* 4.1 27.1 - - + -
415A ARG 3.0 24.5 + - - +
416A THR* 3.6 6.7 - - - +
418A LEU* 1.3 79.0 - - + +
420A LYS* 1.3 64.1 + - - +
423A LYS* 3.1 49.2 + - + +
440A MET* 3.8 18.8 - - + -
442A PHE* 3.8 17.9 - - + -
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Residues in contact with LYS 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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416A THR* 3.0 15.5 + - + +
417A SER* 3.2 14.4 - - - +
419A VAL* 1.3 79.8 - - - +
421A ARG* 1.3 60.6 + - - +
423A LYS* 3.7 9.6 - - - +
424A LYS* 3.4 43.3 + - + +
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Residues in contact with ARG 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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402A PRO* 3.4 34.9 - - - +
404A LEU* 4.5 22.9 - - + +
417A SER 2.9 15.4 + - - +
418A LEU* 3.8 7.4 - - - +
419A VAL 3.3 0.2 - - - -
420A LYS* 1.3 75.2 - - - +
422A PHE* 1.3 61.4 + - - +
424A LYS* 3.0 12.3 + - - +
425A ASP* 2.7 55.2 + - - +
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Residues in contact with PHE 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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375A LYS* 2.7 67.2 + - + -
376A ALA 3.5 20.6 - - - -
377A ILE* 3.8 22.7 - - + -
404A LEU* 3.8 22.9 - - + -
418A LEU 3.0 17.7 + - - +
421A ARG* 1.3 74.7 - - - +
423A LYS* 1.3 56.1 + - - +
425A ASP* 4.0 5.9 + - + +
427A SER 5.1 2.9 - - - -
428A GLY* 3.5 29.8 - - - -
430A LEU* 3.8 24.2 - - + -
442A PHE* 3.5 32.5 - + + -
445A VAL* 4.2 1.8 - - + -
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Residues in contact with LYS 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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195A GLN* 2.8 36.6 + - - +
198A ALA* 6.2 2.9 - - - -
199A GLU* 5.2 4.0 + - - -
202A LYS* 5.8 3.7 - - - +
375A LYS* 3.7 3.6 + - - -
419A VAL* 3.1 43.3 + - + +
420A LYS* 3.7 10.1 - - - +
422A PHE* 1.3 79.8 - - - +
424A LYS* 1.3 61.4 + - + +
440A MET* 4.6 1.8 - - - -
441A ASP* 2.8 37.1 + - - +
442A PHE* 3.7 6.9 - - + -
443A PRO* 3.4 29.7 - - + +
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Residues in contact with LYS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LYS* 3.4 34.2 + - + +
421A ARG* 3.0 12.6 + - - +
423A LYS* 1.3 81.9 - - + +
425A ASP* 1.3 70.1 + - - +
426A GLU* 3.6 1.9 + - - +
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Residues in contact with ASP 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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375A LYS* 3.1 29.8 + - - +
402A PRO* 4.4 3.5 - - - +
404A LEU* 5.4 1.7 - - - +
421A ARG* 2.7 63.8 + - - +
422A PHE* 4.0 8.7 + - + +
423A LYS 3.6 0.6 - - - -
424A LYS* 1.3 78.3 - - - +
426A GLU* 1.3 69.3 + - - +
427A SER 3.3 19.7 - - - +
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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
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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