Contacts of the strand formed by residues 472 - 480 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E LEU* 4.1 10.3 - - + -
136E PHE* 3.4 37.0 - - + +
137E GLN 3.3 11.4 - - - +
139E MET* 3.8 6.7 - - - -
165E CYS* 3.9 20.9 - - + +
242E ARG* 2.8 14.0 + - - -
468E VAL 2.4 28.7 + - - +
469E ARG* 2.6 31.6 + - - +
470E PHE 3.2 0.6 - - - -
471E TYR* 1.3 83.7 - - - +
473E LYS* 1.3 58.8 + - - +
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Residues in contact with LYS 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLU 3.4 0.8 - - - +
136E PHE* 4.4 3.1 - - - -
137E GLN* 3.0 29.4 + - - +
138E PRO 3.3 22.0 - - - -
139E MET* 3.7 27.4 + - + +
218E LYS* 5.8 4.2 - - - +
242E ARG* 3.7 18.8 - - - +
469E ARG* 5.2 0.9 - - - +
472E THR* 1.3 73.6 - - - +
474E ARG* 1.3 64.7 + - - +
475E LYS 3.4 1.7 + - - -
430F GLN* 3.6 12.4 + - - -
452F TRP* 3.5 61.0 - - + +
453F LYS* 5.9 2.8 - - - +
461F HIS* 5.4 1.8 - - - +
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Residues in contact with ARG 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E GLU* 4.8 7.3 + - - -
134E SER* 3.4 26.6 + - - -
135E GLU 3.5 4.9 - - - +
136E PHE* 3.8 29.1 - - + -
242E ARG* 5.3 0.2 - - - +
469E ARG* 3.6 13.7 - - - +
473E LYS* 1.3 71.7 - - - +
475E LYS* 1.3 61.8 + - - +
476E THR* 4.0 11.5 + - - +
432F GLY 4.0 3.8 - - - +
447F HIS* 4.8 6.9 + - - -
448F SER* 3.8 33.6 - - - +
452F TRP* 3.1 17.4 + - - -
461F HIS* 3.4 31.4 + - + +
465F PRO* 3.9 18.5 - - - +
466F ASP* 2.7 42.4 + - - +
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Residues in contact with LYS 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E TRP 3.9 1.0 - - - +
134E SER* 3.3 2.1 - - - -
135E GLU* 2.7 49.1 + - + +
137E GLN* 3.0 24.7 + - + +
473E LYS 3.4 0.8 + - - -
474E ARG* 1.3 74.2 - - - +
476E THR* 1.3 63.1 + - - +
477E VAL* 4.1 12.7 - - + +
426F SER 2.7 21.5 + - - +
427F ASP 2.7 29.5 + - - -
429F ILE* 2.9 23.9 + - - +
431F VAL 3.6 8.1 - - - -
432F GLY 3.4 11.2 - - - +
434F VAL* 4.0 15.3 - - + -
452F TRP* 3.5 22.0 - - + -
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Residues in contact with THR 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E SER* 3.9 17.9 - - - +
133E TRP 3.6 7.9 - - - +
134E SER* 4.4 1.1 - - - +
474E ARG* 4.0 13.3 + - - +
475E LYS* 1.3 75.0 - - - +
477E VAL* 1.3 62.8 + - - +
478E THR* 4.6 3.4 + - - +
432F GLY 3.0 9.8 + - - -
433F MET* 3.4 7.0 - - - +
434F VAL* 3.0 22.2 + - - +
441F PRO 5.0 0.3 - - - +
443F PRO* 4.0 29.6 - - + +
447F HIS* 4.3 19.3 - - + +
448F SER 3.3 19.4 + - - -
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Residues in contact with VAL 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E SER* 2.9 17.7 + - - -
133E TRP* 3.0 66.1 + - + +
135E GLU* 5.3 4.5 - - + -
475E LYS* 4.1 16.8 - - + +
476E THR* 1.3 73.4 - - - +
478E THR* 1.3 66.5 + - - +
479E GLN 4.3 0.2 - - - -
426F SER* 3.9 26.0 - - - +
434F VAL* 3.3 17.3 - - + +
436F ILE* 4.0 20.4 - - + -
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Residues in contact with THR 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL* 4.5 5.2 - - + -
130E ILE* 3.8 17.7 - - + -
131E ASP 3.6 11.9 - - - +
132E SER* 3.5 14.4 + - - +
476E THR* 4.6 5.0 + - - +
477E VAL* 1.3 77.2 - - - +
479E GLN* 1.3 62.8 + - - +
434F VAL 2.8 12.7 + - - +
435F GLY* 3.6 1.0 - - - -
436F ILE* 2.9 26.5 + - - +
438F ILE* 4.2 14.4 - - + +
441F PRO* 3.9 29.7 + - + +
442F VAL 5.1 5.9 + - - +
443F PRO* 5.2 1.4 - - - +
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Residues in contact with GLN 479 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ILE* 3.3 10.0 - - - +
131E ASP* 2.8 42.7 + - + +
133E TRP* 3.9 37.7 - - + -
477E VAL 4.4 0.2 + - - -
478E THR* 1.3 74.2 - - - +
480E ARG* 1.3 62.9 + - - +
481E TRP* 3.5 42.8 + - + +
422F ALA* 4.8 5.7 - - - +
423F ARG 5.9 0.6 - - - +
436F ILE* 3.9 23.9 - - + +
438F ILE* 4.6 0.4 - - - -
423G ARG* 5.2 6.1 - - - +
133H TRP* 5.9 2.8 - - - -
479H GLN* 5.2 14.7 + - - +
481H TRP* 6.3 0.2 - - - -
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Residues in contact with ARG 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E PRO 5.5 1.6 + - - -
129E GLY 4.3 9.2 - - - +
130E ILE* 3.8 22.6 - - + +
479E GLN* 1.3 77.6 - - - +
481E TRP* 1.3 79.7 + - - +
482E PRO* 3.7 30.8 - - + +
263F ASN* 3.7 10.3 + - - +
267F GLN* 3.3 34.9 + - - +
436F ILE* 3.0 16.3 + - - +
437F ASN* 2.9 26.8 + - - +
438F ILE* 3.4 26.9 - - + -
423G ARG* 6.1 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