Contacts of the strand formed by residues 486 - 494 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E TYR* 3.6 28.7 + - + -
156E HIS* 4.3 17.5 - - + +
157E GLU 3.1 13.7 - - - +
159E VAL* 3.7 10.8 - - - +
185E THR* 3.8 20.0 - - + +
264E ARG* 5.5 3.3 + - - -
482E LEU 3.5 11.3 + - - +
483E GLN* 3.3 19.5 + - - +
484E ALA 3.5 1.1 - - - -
485E TYR* 1.3 84.6 - - - +
487E LYS* 1.3 60.0 + - - +
488E VAL* 4.4 5.7 + - - +
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Residues in contact with LYS 487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E ARG 3.5 0.5 - - - +
156E HIS* 3.6 1.0 - - - -
157E GLU* 2.6 48.1 + - + +
158E PRO 3.7 13.2 - - - +
159E VAL* 2.7 47.5 + - + +
239E ASP* 4.5 8.9 + - - +
264E ARG* 4.3 20.1 - - - +
486E THR* 1.3 74.5 - - - +
488E VAL* 1.3 63.9 + - - +
467F GLY 6.0 2.7 - - - +
475F ARG* 4.5 12.8 - - - +
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Residues in contact with VAL 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E THR* 3.8 32.3 - - + -
155E ARG 3.6 4.3 - - - +
156E HIS* 3.9 12.1 - - + +
486E THR* 4.4 6.0 + - - +
487E LYS* 1.3 74.4 - - - +
489E LYS* 1.3 62.3 + - - +
490E THR* 4.2 0.7 + - - +
449F GLY* 3.9 5.4 - - - +
464F PRO* 4.4 11.0 - - + -
475F ARG* 3.0 44.4 + - + +
480F TYR* 3.6 37.2 - - + -
483F GLN* 5.7 0.9 - - - +
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Residues in contact with LYS 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E TYR 3.8 0.2 - - - +
154E THR* 3.1 4.9 - - - -
155E ARG* 2.8 45.3 + - + +
157E GLU* 3.0 39.4 + - - +
487E LYS 3.8 0.8 + - - -
488E VAL* 1.3 74.1 - - - +
490E THR* 1.3 72.6 + - - +
491E VAL* 4.2 13.0 - - + +
443F SER 2.9 25.0 + - - +
444F GLN 2.9 15.4 + - - -
446F LEU 2.9 29.7 + - - -
447F GLN* 5.1 0.7 - - - +
448F ALA 3.5 23.3 - - - +
449F GLY* 3.5 4.3 - - - -
451F VAL* 4.2 5.4 - - + -
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Residues in contact with THR 490 (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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144E ILE* 5.5 0.2 - - + -
152E SER* 3.7 12.1 - - - +
153E TYR 3.4 6.7 - - - +
154E THR* 3.6 4.9 - - + +
488E VAL* 4.2 1.4 + - - +
489E LYS* 1.3 73.7 - - - +
491E VAL* 1.3 58.8 + - - +
492E THR* 3.6 19.5 - - - +
449F GLY 2.9 12.5 + - - -
450F THR* 3.2 11.2 - - + +
451F VAL 2.8 31.7 + - - -
463F SER* 4.1 11.2 - - - +
464F PRO* 3.1 46.8 + - + +
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Residues in contact with VAL 491 (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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151E PHE 3.8 1.0 - - - +
152E SER* 3.3 3.1 + - - -
153E TYR* 2.9 77.1 + - + +
155E ARG* 5.0 4.3 - - - -
489E LYS* 4.2 22.4 - - + +
490E THR* 1.3 76.6 - - - +
492E THR* 1.3 64.9 + - - +
493E VAL* 4.0 13.7 - - + -
443F SER* 4.0 25.6 - - - +
451F VAL* 3.2 12.8 - - + +
453F VAL* 4.2 4.9 - - + -
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Residues in contact with THR 492 (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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146E ILE* 3.7 27.3 - - + +
150E PHE* 4.0 9.9 - - + -
151E PHE 3.5 2.2 - - - -
152E SER* 2.9 19.2 + - - -
490E THR* 3.6 10.9 - - - +
491E VAL* 1.3 70.7 - - - +
493E VAL* 1.3 62.3 + - - +
450F THR* 4.9 1.6 - - - +
451F VAL 2.9 8.9 + - - -
452F TRP* 3.3 24.2 + - + -
453F VAL 3.0 22.6 + - - -
455F CYS* 3.5 5.8 - - - -
458F VAL* 3.9 22.4 + - + +
463F SER* 4.5 2.6 + - - -
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Residues in contact with VAL 493 (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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150E PHE* 3.1 6.4 - - - -
151E PHE* 2.8 52.4 + - + +
153E TYR* 4.4 11.0 - - + +
491E VAL* 4.0 20.9 - - + -
492E THR* 1.3 77.5 - - - +
494E LYS* 1.3 78.0 + - - +
495E VAL* 3.4 1.7 + - + +
453F VAL* 3.8 28.3 - - + +
436G LEU* 4.3 10.1 - - + -
440G ASN* 4.1 19.5 - - - +
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Residues in contact with LYS 494 (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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149E ASP* 4.2 8.4 - - - +
150E PHE* 3.7 23.3 - - + -
493E VAL* 1.3 82.9 - - - +
495E VAL* 1.3 67.6 + - - +
285F TRP* 3.7 38.4 - - + +
453F VAL 3.2 11.5 + - - +
454F ASN* 3.3 36.3 - - + +
455F CYS* 4.1 1.6 - - + -
436G LEU* 5.1 2.3 - - - +
437G ASP* 4.0 12.7 - - - +
440G ASN* 4.8 1.2 + - - -
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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