Contacts of the strand formed by residues 551 - 556 (chain B) in PDB entry 1ZJA
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 551 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ALA* 3.9 16.0 - - - -
352B THR* 2.8 33.9 + - - -
462B PHE* 3.9 2.1 - - - -
506B VAL 3.4 6.7 - - - -
507B VAL* 4.0 9.9 - - - -
530B GLU* 3.1 6.2 - - - +
531B SER* 2.7 48.5 + - - +
550B GLN* 1.3 81.3 - - - +
552B GLY* 1.3 59.5 + - - +
554B TYR* 4.7 1.1 - - - -
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Residues in contact with GLY 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B THR* 4.4 2.1 - - - +
505B VAL* 3.5 6.8 - - - +
506B VAL 3.0 31.3 + - - +
529B ILE* 3.2 13.0 - - - -
530B GLU* 4.0 0.7 - - - -
551B SER* 1.3 79.7 - - - +
553B ILE* 1.3 65.9 + - - +
554B TYR* 3.5 21.0 - - - -
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Residues in contact with ILE 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B THR* 3.8 12.1 - - + -
356B THR* 3.6 24.7 - - + -
466B LEU* 3.6 28.9 - - + -
469B ILE* 4.6 11.4 - - + -
476B LEU* 4.4 15.7 - - + -
503B TYR* 4.7 2.9 - - + -
504B LEU 3.4 7.2 - - - +
505B VAL* 4.4 10.8 - - + -
527B THR 3.9 0.3 - - - -
528B LEU* 2.9 46.7 + - + +
529B ILE* 3.0 23.0 + - + +
552B GLY* 1.3 76.9 - - - +
554B TYR* 1.3 68.5 + - - +
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Residues in contact with TYR 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B TYR* 3.1 11.7 - - - +
504B LEU* 2.7 62.0 + - + +
506B VAL* 4.3 8.8 + - + -
524B ILE* 3.9 19.7 - - + -
526B GLU 3.3 10.1 - - - +
527B THR* 3.5 28.5 - - + -
528B LEU* 4.4 1.1 - - - +
530B GLU* 2.6 31.6 + - + -
537B PRO* 3.7 23.1 - - + -
544B LEU* 3.7 25.1 - - + +
546B LEU* 4.9 1.7 - - - +
550B GLN* 3.9 7.1 + - - -
552B GLY* 3.5 30.6 + - - -
553B ILE* 1.3 72.7 - - - +
555B LYS* 1.3 61.8 + - - +
556B VAL* 4.5 0.2 - - - -
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Residues in contact with LYS 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B GLU* 3.2 42.0 + - - +
502B THR 3.7 8.5 - - - +
503B TYR* 3.1 37.7 + - + +
524B ILE* 4.0 0.5 - - - -
525B ALA* 2.7 37.6 + - + +
526B GLU* 2.9 29.9 + - + +
528B LEU* 4.1 6.5 - - + +
554B TYR* 1.3 72.7 - - - +
556B VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B THR* 3.1 46.1 + - + +
503B TYR* 4.5 2.9 - - - +
504B LEU* 3.7 32.3 - - + -
522B MET* 3.7 29.4 - - + -
523B HIS 3.3 13.2 - - - +
524B ILE* 4.3 10.1 - - + -
525B ALA* 4.0 3.0 - - - +
554B TYR 4.3 1.1 - - - +
555B LYS* 1.3 87.5 + - - +
557B LYS* 1.3 63.7 + - - +
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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