Contacts of the strand formed by residues 486 - 494 (chain G) in PDB entry 1ZUM
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 486 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G TYR* 3.4 32.4 + - + -
156G HIS* 4.3 18.6 - - + +
157G GLU 3.1 13.0 - - - +
159G VAL* 3.6 5.8 - - - +
185G THR* 3.8 20.2 - - + +
264G ARG* 3.4 13.9 + - - -
482G LEU 3.3 15.0 + - - +
483G GLN* 3.3 14.4 + - - +
484G ALA 3.5 0.6 - - - -
485G TYR* 1.3 86.2 - - - +
487G LYS* 1.3 60.1 + - - +
488G VAL* 4.4 4.4 + - - +
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Residues in contact with LYS 487 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ARG 3.6 0.7 - - - +
156G HIS* 3.5 3.1 - - - -
157G GLU* 2.6 39.4 + - + +
158G PRO 3.9 10.1 - - - +
159G VAL* 2.7 48.9 + - + +
239G ASP* 4.6 8.7 + - - +
264G ARG* 4.6 9.0 - - - +
486G THR* 1.3 74.8 - - - +
488G VAL* 1.3 61.6 + - - +
489G LYS 3.9 0.2 + - - -
468H TYR* 3.7 58.8 - - + +
475H ARG* 4.0 8.3 - - - +
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Residues in contact with VAL 488 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G THR* 3.9 25.6 - - + -
155G ARG 3.6 2.5 - - - -
156G HIS* 3.6 13.9 - - + -
486G THR* 5.3 4.7 - - - +
487G LYS* 1.3 75.0 - - - +
489G LYS* 1.3 63.3 + - - +
490G THR* 4.6 0.8 + - - +
449H GLY 3.9 3.8 - - - +
464H PRO* 4.5 10.5 - - + -
468H TYR* 4.1 1.8 - - - -
475H ARG* 2.8 48.9 + - + +
480H TYR* 3.3 43.7 - - + +
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Residues in contact with LYS 489 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G TYR 3.8 0.2 - - - +
154G THR* 3.1 5.1 - - - -
155G ARG* 2.9 46.2 + - + +
157G GLU* 3.0 31.7 + - + +
487G LYS 3.9 0.2 + - - -
488G VAL* 1.3 73.9 - - - +
490G THR* 1.3 72.1 + - - +
491G VAL* 4.0 13.2 + - + +
443H SER 3.1 18.5 + - - +
444H GLN 3.1 18.0 + - - -
446H LEU 2.7 28.9 + - - -
447H GLN* 4.9 0.4 - - - +
448H ALA 3.4 20.6 - - - +
449H GLY 3.5 3.6 - - - -
451H VAL* 4.5 5.4 - - + -
468H TYR* 3.5 14.4 - - - +
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Residues in contact with THR 490 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G SER* 3.7 22.0 - - - +
153G TYR 3.4 7.9 - - - +
154G THR* 3.7 5.3 - - + +
488G VAL* 4.6 1.2 + - - +
489G LYS* 1.3 74.9 - - - +
491G VAL* 1.3 65.0 + - - +
492G THR* 3.8 8.3 - - - +
449H GLY 2.8 12.7 + - - -
450H THR* 3.2 11.6 - - + +
451H VAL 2.8 25.5 + - - +
463H SER* 3.8 13.0 - - - +
464H PRO* 3.0 44.3 + - + +
475H ARG* 6.1 0.2 - - - -
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Residues in contact with VAL 491 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G PHE 3.7 1.7 - - - +
152G SER* 3.3 3.1 + - - -
153G TYR* 2.9 75.0 + - + +
155G ARG* 5.0 2.2 - - - +
489G LYS* 4.1 23.1 - - + +
490G THR* 1.3 77.7 - - - +
492G THR* 1.3 61.7 + - - +
493G VAL* 4.1 13.2 - - + -
3123G EDO 3.8 11.0 - - - +
443H SER* 3.8 20.9 - - - +
451H VAL* 3.3 12.1 - - + +
453H VAL* 4.2 4.0 - - + -
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Residues in contact with THR 492 (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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146G ILE* 4.6 3.2 - - + +
150G PHE* 4.2 18.2 - - + -
151G PHE 3.6 2.9 - - - -
152G SER* 2.8 25.4 + - - -
490G THR* 3.8 9.4 - - - +
491G VAL* 1.3 70.7 - - - +
493G VAL* 1.3 61.5 + - - +
450H THR* 5.0 1.8 - - - +
451H VAL 2.9 9.5 + - - -
452H TRP* 3.4 22.8 + - + -
453H VAL 2.9 22.7 + - - -
455H CYS* 3.5 4.6 - - - -
458H VAL* 3.8 33.6 + - + +
463H SER* 4.2 2.9 + - - -
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Residues in contact with VAL 493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E LEU* 4.2 11.4 - - + -
440E ASN* 4.0 18.2 - - - +
150G PHE* 3.1 7.2 - - - -
151G PHE* 2.8 55.3 + - + +
153G TYR* 4.5 11.4 - - + +
491G VAL* 4.1 13.7 - - + -
492G THR* 1.3 76.8 - - - +
494G LYS* 1.3 76.0 + - - +
495G VAL* 3.5 0.9 + - + +
453H VAL* 3.7 35.0 - - + +
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Residues in contact with LYS 494 (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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436E LEU* 4.9 2.1 - - - +
437E ASP* 4.0 13.4 - - - +
440E ASN* 4.8 0.9 + - - -
149G ASP* 3.7 13.7 - - - +
150G PHE* 3.8 19.5 - - + -
492G THR 4.2 0.2 + - - -
493G VAL* 1.3 85.5 - - - +
495G VAL* 1.3 69.0 + - - +
285H TRP* 3.9 34.7 - - + +
453H VAL 3.1 12.1 + - - +
454H ASN* 3.4 36.4 + - + +
455H CYS* 4.3 0.6 - - + -
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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