Contacts of the strand formed by residues 472 - 479 (chain K) in PDB entry 4ZZ7
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 THR 472 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118K LEU* 4.1 11.4 - - + -
136K PHE* 3.4 36.0 - - - +
137K GLN 3.2 14.1 - - - +
139K MET* 3.8 4.5 - - - -
165K CYS* 3.9 20.9 - - + +
242K ARG* 2.7 26.4 + - - -
468K VAL 2.7 24.9 + - - +
469K ARG* 2.9 16.2 + - - +
470K PHE 3.3 0.6 - - - -
471K TYR* 1.3 83.9 - - - +
473K LYS* 1.3 59.7 + - - +
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Residues in contact with LYS 473 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430J GLN* 3.3 23.2 + - - -
452J TRP* 3.5 50.6 - - + +
453J LYS* 6.3 0.8 - - - +
461J HIS* 5.5 1.8 - - - +
57K ARG* 6.1 0.9 - - - +
135K GLU 3.4 1.2 - - - +
136K PHE* 4.3 3.6 - - - -
137K GLN* 2.9 35.6 + - - +
138K PRO 3.2 22.1 + - - -
139K MET* 3.8 28.7 + - + +
218K LYS* 5.8 4.2 - - - +
242K ARG* 3.6 17.5 - - - +
469K ARG* 5.2 1.1 - - - +
472K THR* 1.3 75.7 - - - +
474K ARG* 1.3 63.2 + - - +
475K LYS 3.4 0.7 + - - -
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Residues in contact with ARG 474 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432J GLY* 4.0 4.3 - - - +
447J HIS* 4.5 9.3 + - - -
448J SER* 3.8 31.7 - - - +
450J GLY 4.6 0.5 - - - +
452J TRP* 3.1 18.0 + - - -
461J HIS* 3.5 30.7 + - + +
465J PRO* 4.0 18.1 - - - +
466J ASP* 2.9 42.1 + - - +
121K GLU* 4.8 7.9 + - - -
134K SER* 3.5 26.8 + - - -
135K GLU 3.7 4.0 - - - -
136K PHE* 3.8 33.4 - - + -
469K ARG* 3.9 8.3 - - - +
473K LYS* 1.3 70.6 - - - +
475K LYS* 1.3 63.7 + - - +
476K THR* 4.0 11.4 + - - +
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Residues in contact with LYS 475 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426J SER 2.8 30.3 + - - +
427J ASP 3.4 6.7 + - - -
428J ASN 4.3 0.2 - - - -
429J ILE* 2.6 29.3 + - - +
431J VAL 3.5 9.4 - - - +
432J GLY 3.3 10.8 - - - +
434J VAL* 4.2 7.9 - - + -
452J TRP* 3.5 21.1 - - + -
133K TRP 3.8 0.5 - - - +
134K SER* 3.2 5.0 - - - -
135K GLU* 2.7 47.5 + - + +
137K GLN* 3.3 32.4 + - - +
473K LYS 3.4 0.6 + - - -
474K ARG* 1.3 74.1 - - - +
476K THR* 1.3 64.3 + - - +
477K VAL* 4.1 15.4 + - + -
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Residues in contact with THR 476 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432J GLY 3.0 9.7 + - - -
433J MET* 3.5 4.9 - - - +
434J VAL 2.9 24.6 + - - +
441J PRO 5.1 1.8 - - - +
443J PRO* 4.1 28.5 - - + -
447J HIS* 4.4 14.8 - - + +
448J SER 3.5 17.0 + - - -
132K SER* 3.7 20.9 - - - +
133K TRP 3.5 8.3 - - - +
134K SER* 4.9 2.4 - - - -
474K ARG* 4.0 12.6 + - - +
475K LYS* 1.3 74.7 + - - +
477K VAL* 1.3 64.0 + - - +
478K THR* 4.8 3.0 + - - +
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Residues in contact with VAL 477 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426J SER* 4.0 26.9 - - - -
434J VAL* 3.0 13.5 - - + +
436J ILE* 4.2 15.5 - - + -
132K SER* 2.9 18.0 + - - -
133K TRP* 2.9 69.5 + - + +
135K GLU* 5.1 4.5 - - - +
475K LYS* 4.3 19.5 - - + +
476K THR* 1.3 75.5 - - - +
478K THR* 1.3 65.0 + - - +
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Residues in contact with THR 478 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434J VAL 2.8 8.1 + - - -
435J GLY* 3.3 3.6 - - - -
436J ILE 3.0 22.8 + - - -
438J ILE* 3.8 18.3 - - + +
441J PRO* 4.2 27.0 + - + -
442J VAL 4.8 6.8 + - - +
443J PRO* 5.1 1.4 - - - +
126K VAL* 4.6 4.5 - - + -
130K ILE* 3.6 25.4 - - + -
131K ASP 3.5 5.4 - - - +
132K SER* 3.4 19.1 + - - -
476K THR* 4.2 4.4 + - - +
477K VAL* 1.3 71.4 - - - +
479K GLN* 1.3 61.5 + - - +
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Residues in contact with GLN 479 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423I ARG* 5.1 8.0 - - - +
422J ALA* 5.2 2.6 - - - +
436J ILE* 3.9 19.5 - - + +
129K GLY 4.2 0.5 - - - +
130K ILE* 3.5 9.1 - - - +
131K ASP* 2.8 42.5 + - + +
133K TRP* 3.8 37.1 - - + -
478K THR* 1.3 74.3 - - - +
480K ARG* 1.3 63.5 + - - +
481K TRP* 3.3 44.3 + - + +
479L GLN* 5.2 10.7 + - - +
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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