Contacts of the strand formed by residues 415 - 420 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392H ASP* 3.1 5.2 - - - +
393H LYS 2.9 25.8 + - - -
394H TYR* 3.2 17.0 + - - +
399H ARG* 3.3 24.4 + - - -
403H THR* 3.9 5.4 - - - -
413H SER* 2.5 30.8 + - - -
414H ASN* 1.3 73.5 - - - +
416H TYR* 1.3 62.6 + - - +
428H GLY 3.8 0.2 - - - -
429H ALA* 3.6 20.2 - - - +
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Residues in contact with TYR 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H TYR* 3.8 21.8 - + - -
302H VAL* 3.8 7.4 - - - +
303H MET* 3.6 47.3 - - + -
306H ILE* 3.8 13.5 - - + +
390H ILE* 4.1 4.9 - - + -
391H LEU 3.1 13.2 - - - +
392H ASP* 4.0 1.3 - - - +
394H TYR* 4.2 2.5 - - - -
399H ARG* 4.0 0.6 - - - +
415H SER* 1.3 80.1 - - - +
417H ASP* 1.3 68.7 + - - +
418H MET* 4.4 7.2 - - + -
426H LEU* 3.8 17.7 - - + -
428H GLY* 2.9 41.2 + - - +
429H ALA* 3.5 19.0 + - - -
467H ALA* 3.9 1.8 - - + +
468H GLY 2.7 34.1 + - - -
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Residues in contact with ASP 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373H GLU* 4.2 0.9 - - - +
390H ILE* 3.4 5.4 - - - +
391H LEU 2.8 34.0 + - - +
394H TYR* 2.9 33.8 + - + +
399H ARG* 3.0 26.5 + - - -
416H TYR* 1.3 78.2 - - - +
418H MET* 1.3 61.7 + - - +
419H PHE* 3.6 16.8 - - + -
424H GLU* 3.0 26.0 - - + +
426H LEU 3.3 14.1 - - - +
427H SER* 3.6 5.1 + - - -
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Residues in contact with MET 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H MET* 3.5 35.9 - - + +
306H ILE* 3.7 28.3 - - + -
307H ALA* 3.9 6.1 - - - +
310H MET* 4.9 1.8 - - - -
388H PHE* 3.9 32.8 - - + -
389H TYR 3.5 6.1 - - - +
390H ILE* 3.9 26.7 - - + -
416H TYR* 4.4 7.6 - - + -
417H ASP* 1.3 76.5 - - - +
419H PHE* 1.3 61.4 + - - +
424H GLU* 3.9 1.7 - - - -
425H ILE* 3.1 29.6 + - + +
426H LEU* 3.2 29.4 + - + +
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Residues in contact with PHE 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368H LEU* 4.7 1.3 - - + -
373H GLU* 3.6 37.7 - - + -
387H ASP 3.1 11.6 - - - +
388H PHE* 3.2 19.3 - - - -
389H TYR* 3.1 51.6 + + + -
391H LEU* 3.7 23.8 - - + -
394H TYR* 3.6 18.2 - - - -
417H ASP* 3.6 24.2 - - + -
418H MET* 1.3 76.8 - - - +
420H MET* 1.3 62.3 + - - +
422H GLY* 4.2 10.3 - - - -
423H GLU 3.5 10.5 - - - +
424H GLU* 3.4 25.6 - - + -
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Residues in contact with MET 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314H PHE* 3.4 32.1 - - + -
337H PHE* 3.5 25.4 - - + -
387H ASP 3.2 4.9 - - - -
388H PHE* 3.9 7.9 - - + -
419H PHE* 1.3 72.4 - - - +
421H ARG* 1.3 68.6 + - - +
422H GLY 3.1 0.7 - - - -
423H GLU* 3.0 18.5 + - - +
425H ILE* 3.7 40.5 - - + +
476H VAL* 3.6 34.1 - - + +
479H LEU* 3.4 19.4 - - + +
480H PHE* 3.8 13.9 - - + +
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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
------------------------------------------------------------
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