Contacts of the strand formed by residues 379 - 382 (chain B) in PDB entry 2YA4
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 VAL 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B VAL* 3.2 4.2 - - - -
365B ILE* 2.8 52.2 + - + +
367B ARG* 5.3 4.5 - - + -
377B ASP* 4.0 9.0 - - + +
378B ARG* 1.3 75.5 - - - +
380B THR* 1.3 67.1 + - - +
381B ILE 3.7 0.5 + - - -
530B GLY 4.3 1.6 - - - +
531B LYS* 3.7 27.8 - - - +
532B THR* 5.1 0.4 - - - -
533B TRP* 3.8 26.0 - - + +
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Residues in contact with THR 380 (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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350B GLU* 4.9 3.9 + - - +
362B GLY* 4.7 1.6 - - - -
363B MET 3.6 11.2 - - - +
364B VAL* 3.7 17.1 - - + +
378B ARG* 4.1 4.5 + - - +
379B VAL* 1.3 80.6 - - - +
381B ILE* 1.3 63.9 + - - +
382B THR 3.7 13.0 - - - +
383B ASN* 3.9 11.2 - - + +
486B ALA* 3.6 34.5 + - + +
533B TRP* 5.3 0.7 - - - +
1782B EDO 6.0 0.4 - - - -
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Residues in contact with ILE 381 (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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363B MET* 2.7 17.0 + - + +
365B ILE* 3.8 28.3 - - + -
379B VAL 4.6 3.1 - - - +
380B THR* 1.3 74.1 - - - +
382B THR* 1.3 64.7 + - - +
403B MET* 3.9 11.7 - - + -
416B SER* 3.8 25.8 - - - +
418B TYR* 4.4 6.5 - - + +
486B ALA* 4.1 1.5 - - - -
487B TYR* 3.5 24.9 - - - -
524B SER* 3.4 35.0 - - - +
533B TRP* 3.8 40.6 - - + +
534B SER 4.8 0.3 - - - +
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Residues in contact with THR 382 (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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361B ILE 4.4 0.5 - - - +
362B GLY* 3.4 1.6 - - - -
363B MET* 2.9 32.3 + - - +
380B THR* 3.5 3.5 - - - +
381B ILE* 1.3 89.6 + - - +
383B ASN* 1.3 65.5 + - - +
384B LEU* 4.5 7.2 - - + +
400B ASN* 3.3 24.9 - - - +
418B TYR* 2.7 32.6 + - - +
486B ALA 3.4 7.4 - - - +
487B TYR* 5.1 0.9 - - + -
522B TRP* 4.4 7.0 - - + -
524B SER* 3.6 2.6 + - - -
536B PRO* 3.7 19.5 - - + +
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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