Contacts of the strand formed by residues 472 - 480 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118J LEU* 4.0 7.9 - - + -
136J PHE* 3.6 35.1 - - + +
137J GLN 3.2 13.2 - - - +
139J MET* 3.6 5.6 - - - -
165J CYS* 3.9 22.9 - - + +
242J ARG* 2.7 27.0 + - - -
468J VAL 2.5 26.0 + - - +
469J ARG* 3.0 16.2 + - - +
470J PHE 3.2 0.2 - - - -
471J TYR* 1.3 84.2 - - - +
473J LYS* 1.3 57.9 + - - +
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Residues in contact with LYS 473 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J ARG* 6.2 0.2 - - - +
135J GLU 3.3 1.0 - - - +
136J PHE* 3.3 4.6 - - - -
137J GLN* 2.8 44.8 + - - +
138J PRO 3.3 21.1 + - - -
139J MET* 3.7 33.8 + - + +
218J LYS* 5.9 1.6 - - - +
242J ARG* 3.9 11.4 - - - +
469J ARG* 5.3 1.3 - - - +
472J THR* 1.3 74.3 - - - +
474J ARG* 1.3 64.5 + - - +
475J LYS 3.5 0.2 + - - -
430K GLN* 3.4 23.0 + - - -
452K TRP* 3.4 53.7 - - + +
453K LYS* 6.1 2.4 - - - +
461K HIS* 5.4 1.6 - - - +
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Residues in contact with ARG 474 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J GLU* 4.7 7.9 + - - -
134J SER* 3.6 25.0 + - - -
135J GLU 3.6 4.0 - - - -
136J PHE* 3.8 28.8 - - + -
469J ARG* 3.8 13.5 - - - +
473J LYS* 1.3 72.1 - - - +
475J LYS* 1.3 68.7 + - - +
476J THR* 4.1 6.9 + - - +
432K GLY* 4.1 3.1 - - - +
447K HIS* 4.8 5.1 + - - -
448K SER* 3.7 37.3 - - - +
450K GLY 4.8 0.3 - - - +
452K TRP* 2.8 21.0 + - - -
461K HIS* 3.6 33.2 + - + +
465K PRO* 3.9 18.3 - - - +
466K ASP* 2.6 41.2 + - - +
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Residues in contact with LYS 475 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J SER* 3.3 7.1 - - - -
135J GLU* 2.7 42.1 + - + +
137J GLN* 3.0 28.3 + - - +
473J LYS 3.5 0.2 + - - -
474J ARG* 1.3 75.1 - - - +
476J THR* 1.3 67.9 + - - +
477J VAL* 4.2 10.1 - - + -
426K SER 2.6 29.5 + - - +
427K ASP 2.9 19.2 + - - -
429K ILE* 2.8 28.1 + - - +
431K VAL 3.5 11.2 - - - -
432K GLY 3.1 13.2 - - - +
434K VAL* 4.0 13.7 - - + -
452K TRP* 3.6 13.2 - - + -
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Residues in contact with THR 476 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J SER* 3.8 19.1 - - - +
133J TRP 3.7 7.6 - - - +
134J SER* 5.0 2.1 - - - -
474J ARG* 4.1 10.9 + - - +
475J LYS* 1.3 76.9 + - - +
477J VAL* 1.3 64.1 + - - +
478J THR* 4.8 3.0 + - - +
432K GLY 2.9 11.1 + - - -
433K MET* 3.5 6.2 - - - +
434K VAL 3.0 24.1 + - - +
441K PRO 5.0 1.6 - - - +
443K PRO* 4.0 31.2 - - + -
447K HIS* 4.3 15.7 - - + +
448K SER 3.4 18.2 + - - -
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Residues in contact with VAL 477 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J SER* 2.8 24.7 + - - -
133J TRP* 3.0 68.8 + - + +
135J GLU* 4.9 5.4 - - + +
475J LYS* 4.4 15.0 - - + -
476J THR* 1.3 75.3 - - - +
478J THR* 1.3 60.7 + - - +
426K SER* 4.0 22.9 - - - +
434K VAL* 3.4 16.2 - - + +
436K ILE* 4.2 19.3 - - + -
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Residues in contact with THR 478 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J VAL* 4.8 4.7 - - + -
130J ILE* 3.7 24.9 - - + -
131J ASP 3.7 5.6 - - - +
132J SER* 3.5 11.4 + - - -
476J THR* 4.8 4.3 + - - +
477J VAL* 1.3 77.9 + - - +
479J GLN* 1.3 60.5 + - - +
434K VAL 2.9 11.9 + - - -
435K GLY* 3.4 2.8 - - - -
436K ILE 2.9 27.2 + - - +
438K ILE* 3.8 18.7 - - + +
441K PRO* 4.3 22.9 + - + +
442K VAL 4.9 6.5 + - - +
443K PRO* 5.1 1.6 - - - +
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Residues in contact with GLN 479 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I TRP* 6.0 3.0 - - - -
479I GLN* 4.9 15.7 + - - +
130J ILE* 3.4 8.5 - - - +
131J ASP* 3.1 35.8 + - + +
133J TRP* 3.6 38.5 - - + -
478J THR* 1.3 73.4 - - - +
480J ARG* 1.3 65.4 + - - +
481J TRP* 3.4 39.2 + - + +
422K ALA* 5.3 3.6 - - - +
436K ILE* 3.9 22.0 - - + +
438K ILE* 4.6 0.2 - - - -
423L ARG* 4.9 12.2 - - - +
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Residues in contact with ARG 480 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J PRO 5.6 1.0 + - - -
129J GLY 4.3 8.3 - - - +
130J ILE* 4.0 21.7 - - + +
479J GLN* 1.3 77.7 - - - +
481J TRP* 1.3 72.6 + - - +
482J PRO* 3.5 36.0 - - + +
263K ASN* 3.7 8.1 - - - +
267K GLN* 3.3 34.5 + - - +
436K ILE* 3.1 9.4 + - - +
437K ASN* 3.0 27.2 + - - +
438K ILE* 3.5 33.2 - - + -
423L ARG* 6.4 0.7 - - - +
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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