Contacts of the strand formed by residues 414 - 421 (chain A) in PDB entry 2YA6
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 ILE 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LEU* 3.6 21.1 - - + -
339A THR* 3.9 8.5 - - + -
345A ILE* 3.7 25.1 - - + -
405A LEU* 4.6 2.9 - - + -
406A VAL 3.5 4.3 - - - +
407A GLN* 3.5 33.9 - - + +
412A LYS 3.7 2.0 - - - +
413A ARG* 1.3 72.1 - - - +
415A PHE* 1.3 65.7 + - - +
525A TYR* 3.0 6.9 - - - +
526A SER* 2.8 42.6 + - - +
529A ASP* 3.7 27.8 - - - +
530A GLY 3.8 2.0 - - - +
533A TRP* 3.6 22.6 - - + -
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Residues in contact with PHE 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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404A VAL 3.5 0.9 - - - +
405A LEU* 3.3 11.0 - - - +
406A VAL* 2.8 52.2 + - + +
408A ASP* 4.1 15.3 - - + -
413A ARG* 3.4 46.7 - - + -
414A ILE* 1.3 73.8 - - - +
416A SER* 1.3 60.4 + - - +
417A ILE* 4.1 8.3 - - + -
523A MET* 3.8 36.3 - - + -
524A SER 3.5 2.5 - - - +
525A TYR* 4.0 6.5 - + + -
533A TRP* 4.3 0.9 - - - -
570A ILE* 4.1 9.6 - - + -
597A HIS 3.3 23.3 - - - -
598A GLY* 3.7 17.7 - - - -
601A TRP* 4.6 6.5 - + - -
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Residues in contact with SER 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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363A MET* 5.3 0.2 - - - +
381A ILE* 3.8 26.1 - - - +
403A MET* 3.5 20.6 - - - +
404A VAL 3.4 4.7 - - - -
405A LEU* 3.9 8.3 - - - -
415A PHE* 1.3 72.6 - - - +
417A ILE* 1.3 61.0 + - - +
418A TYR* 3.4 21.0 - - - -
523A MET* 3.3 4.2 - - - +
524A SER 2.8 34.2 + - - +
533A TRP* 3.9 8.7 - - - -
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Residues in contact with ILE 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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403A MET* 3.1 3.1 - - - -
404A VAL* 2.8 36.5 + - + +
415A PHE* 4.6 7.0 - - + -
416A SER* 1.3 75.5 + - - +
418A TYR* 1.3 63.9 + - - +
521A LEU* 4.0 17.7 - - + -
522A TRP 3.4 10.8 - - - +
523A MET* 3.7 16.8 - - + -
539A ILE* 4.2 11.9 - - + -
553A VAL* 3.7 22.8 - - + +
572A ILE* 3.8 26.5 - - + -
592A ILE* 4.6 2.2 - - + -
601A TRP* 3.7 39.9 - - + -
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Residues in contact with TYR 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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363A MET* 3.2 35.0 - - + -
381A ILE* 4.4 3.1 - - + -
382A THR* 2.7 20.4 + - - -
400A ASN* 3.5 33.2 - - + -
401A ILE 4.2 0.2 - - - +
402A ASP 3.1 18.4 - - - +
416A SER* 3.4 35.0 - - - -
417A ILE* 1.3 74.6 - - - +
419A ASP* 1.3 63.9 - - - +
521A LEU* 3.7 3.7 - - - -
522A TRP* 2.8 53.8 + + + +
524A SER* 2.7 31.0 + - - -
536A PRO* 3.7 11.4 - - - +
553A VAL* 4.3 2.2 - - - -
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Residues in contact with ASP 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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400A ASN* 3.1 27.5 + - - -
401A ILE* 3.0 30.5 + - + +
402A ASP* 3.9 6.2 - - - +
418A TYR* 1.3 76.0 - - - +
420A MET* 1.3 60.2 + - - +
421A PHE* 4.2 8.7 - - + -
519A SER* 5.9 0.2 - - - +
520A TYR 3.5 8.1 - - - +
521A LEU* 3.6 4.9 - - - +
550A PHE* 3.7 10.9 - - - -
551A LEU 4.8 0.2 - - - -
552A GLY* 3.1 13.2 - - - -
553A VAL* 3.0 27.5 + - - +
1777A DAN 3.4 26.2 - - - +
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Residues in contact with MET 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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384A LEU* 4.0 8.3 - - + -
399A VAL 3.2 6.3 - - - +
400A ASN* 3.5 16.2 - - - +
419A ASP* 1.3 74.5 - - - +
421A PHE* 1.3 89.8 + - - +
422A PRO* 3.9 3.6 - - + -
504A TYR* 3.5 47.3 - - + -
515A ILE* 4.2 2.7 - - + -
520A TYR* 2.8 54.3 + - + +
522A TRP* 3.5 43.7 - - + +
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Residues in contact with PHE 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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398A PRO* 3.6 0.2 - - - +
399A VAL* 2.8 40.4 + - + +
401A ILE* 4.0 27.8 - - + -
419A ASP* 4.2 10.8 - - + -
420A MET* 1.3 86.7 - - - +
422A PRO* 1.3 76.8 - - + +
426A GLY* 3.7 32.3 - - - -
427A ILE* 3.5 19.5 - - - -
430A MET* 4.1 9.9 - - + -
518A ASP 3.6 14.1 - - - -
519A SER* 3.8 21.8 - - - -
550A PHE* 3.8 26.9 - + - -
1777A DAN 4.5 2.5 - - + -
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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