Contacts of the strand formed by residues 415 - 420 (chain B) in PDB entry 6IY6
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 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B ASP* 3.1 5.4 - - - +
393B LYS 2.9 26.2 + - - -
394B TYR* 3.2 16.3 + - - +
399B ARG* 3.3 22.7 + - - -
403B THR* 3.9 5.2 - - - -
413B SER* 2.5 30.7 + - - -
414B ASN* 1.3 73.7 - - - +
416B TYR* 1.3 62.4 + - - +
428B GLY 3.7 0.2 - - - -
429B ALA* 3.6 21.3 - - - +
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Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B TYR* 3.8 22.4 - + - -
302B VAL* 3.8 7.3 - - - +
303B MET* 3.6 47.8 - - + -
306B ILE* 3.8 13.8 - - + +
390B ILE* 4.1 4.5 - - + -
391B LEU 3.1 12.8 - - - +
392B ASP* 4.0 2.2 - - - +
394B TYR* 4.2 2.9 - - - -
399B ARG* 4.0 0.4 - - - +
415B SER* 1.3 79.9 - - - +
417B ASP* 1.3 68.7 + - - +
418B MET* 4.4 7.4 - - + -
426B LEU* 3.8 17.3 - - + -
428B GLY* 2.9 40.0 + - - +
429B ALA* 3.5 17.9 + - - -
467B ALA* 3.9 2.5 - - + +
468B GLY 2.7 32.9 + - - -
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Residues in contact with ASP 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLU* 4.2 0.7 - - - +
390B ILE* 3.4 5.7 - - - +
391B LEU 2.8 33.1 + - - +
394B TYR* 2.8 32.2 + - + +
399B ARG* 3.0 25.3 + - - -
416B TYR* 1.3 77.7 - - - +
418B MET* 1.3 61.2 + - - +
419B PHE* 3.6 15.3 - - + -
424B GLU* 3.0 25.1 - - + +
426B LEU 3.3 14.1 - - - +
427B SER* 3.6 4.7 + - - -
605B PO4 3.6 6.1 + - - -
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Residues in contact with MET 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B MET* 3.5 36.6 - - + +
306B ILE* 3.7 27.6 - - + -
307B ALA* 3.9 6.3 - - - +
310B MET* 4.9 1.8 - - - -
388B PHE* 3.9 32.5 - - + -
389B TYR 3.5 6.3 - - - +
390B ILE* 3.9 26.5 - - + -
416B TYR* 4.4 8.1 - - + -
417B ASP* 1.3 77.3 - - - +
419B PHE* 1.3 60.8 + - - +
424B GLU* 3.9 1.9 - - - -
425B ILE* 3.1 30.7 + - + +
426B LEU* 3.2 27.7 + - + +
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Residues in contact with PHE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B LEU* 4.7 2.0 - - + -
373B GLU* 3.6 38.6 - - + -
387B ASP 3.1 11.8 - - - +
388B PHE* 3.2 18.9 - - - -
389B TYR* 3.1 53.0 + + + -
391B LEU* 3.7 23.1 - - + -
394B TYR* 3.6 18.4 - - - -
417B ASP* 3.6 22.0 - - + -
418B MET* 1.3 76.3 - - - +
420B MET* 1.3 61.4 + - - +
422B GLY* 4.2 10.1 - - - -
423B GLU 3.5 11.0 - - - +
424B GLU* 3.4 24.9 - - + -
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Residues in contact with MET 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B PHE* 3.4 32.5 - - + -
337B PHE* 3.5 24.9 - - + -
387B ASP 3.2 4.0 - - - -
388B PHE* 3.9 8.1 - - + -
419B PHE* 1.3 71.9 - - - +
421B ARG* 1.3 70.2 + - - +
422B GLY 3.1 0.4 - - - -
423B GLU 3.0 18.5 + - - +
425B ILE* 3.7 39.8 - - + +
476B VAL* 3.7 34.1 - - + +
479B LEU* 3.4 19.8 - - + +
480B PHE* 3.8 13.2 - - + +
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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