Contacts of the strand formed by residues 472 - 480 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118F LEU* 4.2 10.8 - - + -
136F PHE* 3.4 37.2 - - + +
137F GLN 3.1 14.1 - - - +
139F MET* 4.0 3.8 - - - -
165F CYS* 4.1 19.1 - - + +
242F ARG* 2.9 11.5 + - - -
468F VAL* 2.7 24.7 + - - +
469F ARG* 2.6 35.0 + - - +
470F PHE 3.2 1.0 + - - -
471F TYR* 1.3 83.2 - - - +
473F LYS* 1.3 60.7 + - - +
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Residues in contact with LYS 473 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E GLN* 3.4 14.5 + - - -
452E TRP* 3.3 61.7 - - + +
453E LYS* 5.9 3.2 - - - +
461E HIS* 5.3 2.9 - - - +
57F ARG* 6.3 0.2 - - - +
135F GLU 3.6 0.2 - - - +
136F PHE* 3.6 3.4 - - - -
137F GLN 3.0 30.4 + - - +
138F PRO 3.4 21.1 - - - -
139F MET* 3.9 27.2 + - + +
218F LYS* 6.1 3.0 - - - +
242F ARG* 3.7 20.4 - - - +
469F ARG* 5.2 0.2 - - - +
472F THR* 1.3 75.6 - - - +
474F ARG* 1.3 62.6 + - - +
475F LYS 3.6 0.5 + - - -
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Residues in contact with ARG 474 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E GLY 4.0 3.6 - - - +
447E HIS* 4.7 4.6 + - - -
448E SER* 3.8 39.2 - - - +
450E GLY 4.4 0.2 - - - +
452E TRP* 3.0 17.8 + - - -
461E HIS* 3.4 33.9 + - + +
465E PRO* 4.2 16.5 - - - +
466E ASP* 2.8 34.8 + - - -
121F GLU* 4.7 8.5 + - - -
134F SER* 3.6 25.2 + - - -
135F GLU 3.6 4.5 - - - -
136F PHE* 3.7 34.4 - - + -
469F ARG* 3.8 11.6 - - - +
473F LYS* 1.3 72.1 - - - +
475F LYS* 1.3 63.0 + - - +
476F THR* 3.9 11.9 + - - +
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Residues in contact with LYS 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E SER 2.6 29.5 + - - +
427E ASP 3.1 16.4 + - - -
429E ILE* 2.8 30.1 + - - +
431E VAL 3.5 12.8 - - - -
432E GLY 3.4 10.1 - - - +
434E VAL* 3.8 16.8 - - + -
452E TRP* 3.8 14.4 - - + -
134F SER* 3.4 4.0 - - - -
135F GLU* 2.7 52.0 + - + +
137F GLN* 3.1 22.7 + - + +
473F LYS 3.6 0.4 + - - -
474F ARG* 1.3 73.4 - - - +
476F THR* 1.3 66.4 + - - +
477F VAL* 4.2 14.3 + - + -
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Residues in contact with THR 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E GLY 3.0 12.5 + - - -
433E MET* 3.5 6.2 - - - +
434E VAL 3.1 21.9 + - - +
441E PRO 5.1 1.2 - - - +
443E PRO* 4.1 26.9 - - + -
447E HIS* 4.3 17.7 - - + +
448E SER 3.5 16.6 + - - -
132F SER* 3.9 17.0 - - - +
133F TRP 3.5 11.0 - - - +
134F SER* 4.8 1.1 - - - -
474F ARG* 3.9 14.6 + - - +
475F LYS* 1.3 75.9 + - - +
477F VAL* 1.3 63.6 + - - +
478F THR* 3.9 3.8 + - - +
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Residues in contact with VAL 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426E SER* 4.2 24.0 - - - +
434E VAL* 3.4 11.4 - - + +
436E ILE* 4.1 20.0 - - + -
132F SER* 2.9 17.2 + - - -
133F TRP* 3.0 67.6 + - + +
135F GLU* 5.0 6.3 - - + -
475F LYS* 4.2 20.0 - - + -
476F THR* 1.3 75.0 - - - +
478F THR* 1.3 64.7 + - - +
479F GLN 4.2 0.2 - - - -
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Residues in contact with THR 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E VAL 2.9 10.7 + - - -
435E GLY* 3.5 2.9 - - - -
436E ILE* 2.9 25.5 + - - +
438E ILE* 3.9 19.0 - - + +
441E PRO* 4.3 21.2 + - + +
442E VAL 5.1 2.6 + - - +
443E PRO* 5.0 7.1 - - - +
126F VAL* 4.6 4.7 - - + -
130F ILE* 3.6 24.7 - - + -
131F ASP 3.5 5.6 - - - +
132F SER* 3.1 19.0 + - - +
476F THR* 4.7 5.0 + - - +
477F VAL* 1.3 73.0 - - - +
479F GLN* 1.3 61.0 + - - +
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Residues in contact with GLN 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422E ALA* 4.8 5.5 - - - +
436E ILE* 3.8 24.6 - - + +
438E ILE* 4.6 0.2 - - - -
129F GLY 4.2 0.3 - - - +
130F ILE* 3.3 9.6 - - - +
131F ASP* 2.8 43.4 + - + +
133F TRP* 3.6 39.3 - - + -
478F THR* 1.3 74.2 - - - +
480F ARG* 1.3 65.2 + - - +
481F TRP* 3.3 41.7 + - + +
479G GLN* 5.5 8.4 + - - +
423H ARG* 5.2 6.1 - - - +
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Residues in contact with ARG 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E ASN* 3.7 18.8 + - - +
267E GLN* 3.6 23.9 + - - +
436E ILE* 3.1 15.4 + - - +
437E ASN* 3.2 35.5 + - - +
438E ILE* 3.4 26.0 - - + -
128F PRO 5.7 1.4 + - - -
129F GLY 4.2 8.3 - - - +
130F ILE* 4.0 23.2 - - + +
479F GLN* 1.3 79.0 - - - +
481F TRP* 1.3 78.8 + - - +
482F PRO* 3.9 22.0 - - + +
423H ARG* 6.3 0.4 - - - +
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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