Contacts of the helix formed by residues 413 - 422 (chain D) in PDB entry 5YD6
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 SER 413 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409D LEU 2.7 23.0 + - - -
410D LEU 3.3 6.7 + - - -
411D THR 3.1 0.8 - - - -
412D GLY* 1.3 76.1 - - - +
414D MET* 1.3 58.3 + - - +
415D GLU 3.7 0.7 - - - -
416D ILE* 3.9 3.3 - - - +
417D ILE* 3.0 41.5 + - - +
443D PHE* 4.3 1.8 - - - -
447D PHE* 3.5 24.8 - - - -
464D PHE* 5.7 0.9 - - - +
465D CYS* 3.4 28.6 + - - +
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Residues in contact with MET 414 (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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410D LEU 3.4 12.8 - - - +
411D THR* 3.0 28.1 + - - +
412D GLY 3.4 0.2 - - - -
413D SER* 1.3 75.8 - - - +
415D GLU* 1.3 66.9 + - + +
418D ARG* 2.9 34.3 + - - +
439D PHE* 3.5 15.0 - - + -
443D PHE* 3.5 28.5 - - + -
587D ILE* 3.3 42.8 - - + +
588D ILE* 5.0 6.1 - - - -
591D LEU* 3.9 30.3 - - + -
601D 8SU 5.6 0.2 - - - -
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Residues in contact with GLU 415 (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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411D THR 4.3 2.9 + - - +
412D GLY 5.0 1.6 + - - +
414D MET* 1.3 82.6 - - + +
416D ILE* 1.3 54.7 + - + +
418D ARG* 3.3 39.4 + - - +
419D GLY* 2.7 32.2 + - - -
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Residues in contact with ILE 416 (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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380B THR* 4.1 28.3 - - + +
375D SER* 3.3 37.0 - - - +
412D GLY 3.9 10.7 + - - +
413D SER 3.6 7.3 + - - +
414D MET 3.3 0.6 - - - -
415D GLU* 1.3 77.6 - - + +
417D ILE* 1.3 57.3 + - - +
419D GLY* 3.3 3.5 + - - -
420D TRP* 3.0 26.0 + - - +
450D ARG* 3.6 9.6 - - - +
465D CYS* 3.6 34.8 - - + +
466D ASN* 5.2 4.9 - - + +
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Residues in contact with ILE 417 (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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413D SER* 3.0 27.3 + - - +
414D MET 4.0 2.9 - - - +
416D ILE* 1.3 71.3 - - - +
418D ARG* 1.3 64.5 + - - +
420D TRP* 3.3 13.3 + - + +
421D ALA* 3.1 20.4 + - - +
439D PHE* 3.7 18.6 - - + -
443D PHE* 3.9 17.5 - - + -
446D LEU* 3.9 30.3 - - + -
447D PHE* 3.6 35.7 - - + +
450D ARG* 3.6 25.6 - - - +
465D CYS* 6.3 0.7 - - + -
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Residues in contact with ARG 418 (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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414D MET* 2.9 24.9 + - - +
415D GLU* 3.3 39.4 + - - +
417D ILE* 1.3 77.0 - - - +
419D GLY* 1.3 60.8 + - - +
421D ALA* 3.2 7.0 + - - +
422D GLU* 3.2 43.6 + - - +
427D PHE* 6.2 2.5 - - - -
432D LYS* 5.0 14.9 - - - +
436D ASP* 5.2 5.3 + - - -
439D PHE* 3.7 46.9 - - + -
590D LYS* 5.9 3.4 - - - +
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Residues in contact with GLY 419 (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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375D SER* 5.4 1.3 - - - -
415D GLU 2.7 19.6 + - - -
416D ILE* 3.3 4.7 + - - -
418D ARG* 1.3 72.5 - - - +
420D TRP* 1.3 59.6 + - - +
422D GLU* 3.6 13.2 + - - +
423D LYS* 3.6 29.4 + - - +
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Residues in contact with TRP 420 (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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368D LEU* 4.8 2.4 + - + -
371D ALA* 3.5 40.1 - - + +
372D HIS* 3.6 13.4 - - - +
375D SER* 3.6 22.8 - - - +
416D ILE 3.0 10.3 + - - +
417D ILE* 3.4 19.1 - - + +
418D ARG 3.2 0.2 - - - -
419D GLY* 1.3 74.6 - - - +
421D ALA* 1.3 79.7 + - + +
423D LYS* 3.1 17.5 + - - +
424D ILE* 3.6 23.4 + - + +
446D LEU* 3.4 33.9 - - + -
450D ARG* 4.2 12.7 - - - +
504D SER* 4.9 3.3 + - - +
507D ALA* 3.4 30.7 - - + +
508D ALA* 3.6 24.9 - - + -
511D MET* 3.6 20.2 - - + -
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Residues in contact with ALA 421 (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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417D ILE 3.1 12.7 + - - +
418D ARG* 3.2 14.3 + - + +
420D TRP* 1.3 79.0 - - + +
422D GLU* 1.3 55.4 + - - +
423D LYS 3.1 10.0 + - - -
424D ILE* 3.1 15.6 + - - +
427D PHE* 3.3 34.7 - - + +
439D PHE* 5.0 4.7 - - + -
511D MET* 3.6 31.0 - - + -
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Residues in contact with GLU 422 (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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418D ARG* 3.2 41.3 + - + +
419D GLY* 4.0 12.2 - - - +
420D TRP 3.4 0.4 - - - -
421D ALA* 1.3 75.0 - - - +
423D LYS* 1.3 61.5 + - + +
424D ILE 3.4 4.5 - - - +
427D PHE* 4.1 10.3 - - + -
428D ALA* 4.8 15.9 - - + +
435D GLN* 4.4 19.8 + - - +
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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