Contacts of the strand formed by residues 472 - 480 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G LEU* 4.0 11.9 - - + -
136G PHE* 3.4 34.6 - - + +
137G GLN 3.2 17.5 - - - +
139G MET* 3.7 6.1 - - - -
165G CYS* 4.0 20.2 - - + +
242G ARG* 2.8 25.3 + - - -
468G VAL* 2.6 25.4 + - - +
469G ARG* 2.9 15.1 + - - +
470G PHE 3.2 0.6 - - - -
471G TYR* 1.3 83.7 - - - +
473G LYS* 1.3 61.1 + - - +
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Residues in contact with LYS 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G ARG* 6.2 0.4 - - - +
135G GLU 3.6 0.2 - - - +
136G PHE* 4.4 2.7 - - - -
137G GLN 2.9 34.7 + - - +
138G PRO 3.1 20.6 - - - -
139G MET* 3.7 29.1 + - + +
218G LYS* 5.7 4.4 - - - +
242G ARG* 3.7 17.7 - - - +
469G ARG* 5.4 0.4 - - - +
472G THR* 1.3 74.5 - - - +
474G ARG* 1.3 64.9 + - - +
475G LYS 3.4 1.4 + - - -
430H GLN* 3.3 22.1 + - - -
452H TRP* 3.5 53.5 - - + +
453H LYS* 6.0 3.2 - - - +
461H HIS* 5.5 2.2 - - - +
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Residues in contact with ARG 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G GLU* 4.6 6.7 + - - -
134G SER* 3.5 27.3 + - - -
135G GLU 3.7 4.3 - - - -
136G PHE* 3.8 31.5 - - + -
469G ARG* 3.6 13.5 - - - +
473G LYS* 1.3 71.4 - - - +
475G LYS* 1.3 63.5 + - - +
476G THR* 4.0 10.2 + - - +
432H GLY* 4.0 4.0 - - - +
447H HIS* 4.6 5.5 + - - -
448H SER* 3.7 37.3 - - - +
450H GLY 4.5 0.5 - - - +
452H TRP* 3.2 16.4 + - - -
461H HIS* 3.5 29.5 + - + +
465H PRO* 4.0 18.8 - - - +
466H ASP* 2.8 44.6 + - - +
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Residues in contact with LYS 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G TRP 3.9 0.7 - - - +
134G SER* 3.3 3.3 - - - -
135G GLU* 2.8 43.7 + - + +
137G GLN* 3.3 24.7 + - + +
473G LYS 3.4 0.4 + - - -
474G ARG* 1.3 74.3 - - - +
476G THR* 1.3 63.3 + - - +
477G VAL* 4.0 11.1 + - + -
426H SER 2.7 30.9 + - - +
427H ASP 3.1 15.4 + - - -
429H ILE* 2.7 27.3 + - - +
431H VAL 3.4 17.0 - - - -
432H GLY 3.2 11.9 - - - +
434H VAL* 3.7 15.9 - - + -
452H TRP* 3.6 13.2 - - + -
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Residues in contact with THR 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G SER* 3.9 17.7 - - - +
133G TRP 3.6 6.7 - - - +
134G SER* 4.5 2.0 - - - +
474G ARG* 4.0 12.3 + - - +
475G LYS* 1.3 74.7 - - - +
477G VAL* 1.3 62.0 + - - +
478G THR* 4.1 2.5 + - - +
432H GLY 2.9 10.4 + - - -
433H MET* 3.6 7.5 - - - +
434H VAL 3.1 22.7 + - - +
441H PRO 4.9 2.3 - - - +
443H PRO* 3.9 30.7 - - + +
447H HIS* 4.2 19.7 - - + +
448H SER 3.3 18.2 + - - -
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Residues in contact with VAL 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G SER* 2.7 25.8 + - - -
133G TRP* 2.9 67.9 + - + +
135G GLU* 5.2 4.3 - - - -
475G LYS* 4.3 20.0 - - + +
476G THR* 1.3 73.7 - - - +
478G THR* 1.3 59.2 + - - +
479G GLN 4.2 0.2 - - - -
426H SER* 4.0 25.1 - - - +
434H VAL* 3.2 11.7 - - + +
436H ILE* 4.2 19.3 - - + -
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Residues in contact with THR 478 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G VAL* 4.7 4.5 - - + -
130G ILE* 3.7 25.1 - - + -
131G ASP 3.7 5.2 - - - +
132G SER* 3.2 18.0 + - - +
476G THR* 4.8 2.6 + - - +
477G VAL* 1.3 72.3 + - - +
479G GLN* 1.3 60.8 + - - +
434H VAL 2.9 9.5 + - - -
435H GLY* 3.3 3.3 - - - -
436H ILE 2.9 23.1 + - - -
438H ILE* 3.7 20.0 - - + +
441H PRO* 4.2 27.6 + - + +
442H VAL 4.8 6.7 + - - +
443H PRO* 5.1 2.6 - - - +
444H VAL* 6.2 0.3 - - - +
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Residues in contact with GLN 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ARG* 5.2 5.8 - - - +
479F GLN* 5.5 8.6 + - - +
481F TRP* 6.4 0.4 - - - -
129G GLY 4.4 0.3 - - - +
130G ILE* 3.5 6.7 - - - +
131G ASP* 2.8 44.9 + - + +
133G TRP* 3.9 32.2 - - + -
477G VAL 4.2 0.2 - - - -
478G THR* 1.3 73.9 - - - +
480G ARG* 1.3 66.5 + - - +
481G TRP* 3.3 41.9 + - + +
422H ALA* 5.0 4.0 - - - +
436H ILE* 3.8 24.8 - - + +
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Residues in contact with ARG 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E ARG* 6.4 0.2 - - - +
128G PRO 5.6 1.2 + - - -
129G GLY 4.3 8.7 - - - +
130G ILE* 4.0 23.9 - - + +
479G GLN* 1.3 78.4 - - - +
481G TRP* 1.3 74.6 + - - +
482G PRO* 3.7 31.7 + - + +
263H ASN* 3.7 9.7 + - - +
267H GLN* 3.4 34.0 + - - +
436H ILE 3.0 12.1 + - - +
437H ASN* 3.0 29.8 + - - +
438H ILE* 3.5 30.7 - - + -
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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