Contacts of the strand formed by residues 486 - 494 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B TYR* 3.6 22.0 - - + +
156B HIS* 3.4 34.9 + - + +
157B GLU 3.3 8.9 + - - +
159B VAL* 3.7 10.7 - - - +
185B THR* 4.0 10.9 - - - +
482B LEU 3.5 10.8 + - - -
483B GLN* 3.5 13.5 + - - +
484B ALA 3.4 2.1 - - - +
485B TYR* 1.3 83.1 + - - +
487B LYS* 1.3 75.0 + - - +
488B VAL* 4.5 4.6 - - + +
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Residues in contact with LYS 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLN* 5.0 11.7 - - - +
70B PHE* 6.3 1.0 - - - -
155B ARG 3.6 0.7 - - - +
156B HIS* 3.4 0.9 - - - -
157B GLU* 2.7 51.6 + - + +
158B PRO 4.0 6.8 + - - +
159B VAL* 3.6 42.6 + - + +
239B ASP* 5.8 1.3 + - - -
486B THR* 1.3 78.8 - - - +
488B VAL* 1.3 64.5 + - - +
489B LYS 3.9 0.2 + - - -
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLY* 4.1 12.3 - - - +
480A TYR* 3.5 49.6 - - + +
154B THR* 4.0 19.1 - - + -
155B ARG 3.6 3.6 - - - +
156B HIS* 3.5 16.4 - - + +
486B THR* 4.6 4.5 - - + +
487B LYS* 1.3 76.9 - - - +
489B LYS* 1.3 64.0 + - - +
490B THR* 4.2 4.6 + - - +
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Residues in contact with LYS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A SER 2.8 27.4 + - - +
444A GLN 2.9 21.8 + - - -
446A LEU 3.0 21.2 + - - -
447A GLN* 5.1 1.5 - - - +
448A ALA 3.8 20.4 - - - +
449A GLY* 3.7 3.8 - - - -
451A VAL* 4.3 4.3 - - + -
153B TYR 3.8 0.3 - - - +
154B THR* 3.2 4.6 - - - -
155B ARG* 2.9 58.2 + - + +
157B GLU* 3.3 29.6 + - + +
487B LYS* 3.9 0.8 + - + -
488B VAL* 1.3 75.2 - - - +
490B THR* 1.3 71.6 + - - +
491B VAL* 4.0 12.1 + - + +
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Residues in contact with THR 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A GLY 2.8 17.4 + - - +
450A THR* 3.2 14.9 + - + +
451A VAL 2.9 25.3 + - - -
144B ILE* 5.4 3.6 - - + -
152B SER* 3.8 19.5 - - - +
153B TYR 3.4 10.1 - - - +
154B THR* 3.9 15.0 - - + +
488B VAL* 4.7 5.2 + - - +
489B LYS* 1.3 76.9 - - - +
491B VAL* 1.3 64.5 + - - +
492B THR* 3.9 9.2 - - - +
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Residues in contact with VAL 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A SER* 3.9 27.1 - - - +
451A VAL* 3.4 13.0 - - + +
453A VAL* 4.5 1.8 - - + -
152B SER* 3.3 2.4 - - - -
153B TYR* 2.9 78.3 + - + +
155B ARG* 5.2 3.4 - - + +
489B LYS* 4.1 22.9 - - + +
490B THR* 1.3 77.7 - - - +
492B THR* 1.3 63.1 + - - +
493B VAL* 3.9 14.6 - - + -
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Residues in contact with THR 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A THR* 4.7 2.5 - - - +
451A VAL 2.9 8.3 + - - +
452A TRP* 3.3 31.2 + - + -
453A VAL 2.9 24.3 + - - -
455A CYS* 3.7 3.6 - - - -
458A VAL* 4.0 27.4 + - + +
146B ILE* 4.4 7.2 - - + +
150B PHE* 4.2 18.2 - - + -
151B PHE 3.6 2.5 - - - -
152B SER* 3.1 20.6 + - - +
490B THR* 3.9 9.4 - - - +
491B VAL* 1.3 71.2 - - - +
493B VAL* 1.3 61.3 + - - +
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Residues in contact with VAL 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A VAL* 3.8 35.4 - - + -
150B PHE* 3.1 6.9 - - - -
151B PHE* 2.7 53.2 + - + +
153B TYR* 4.4 9.9 - - + +
491B VAL* 3.9 14.6 - - + -
492B THR* 1.3 76.3 - - - +
494B LYS* 1.3 77.1 - - - +
495B VAL* 3.4 1.3 + - + +
436D LEU* 4.2 9.6 - - + -
440D ASN* 3.9 19.1 - - - +
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Residues in contact with LYS 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A TRP* 3.6 33.5 - - + +
453A VAL 2.9 21.3 + - - +
454A ASN* 3.5 30.7 + - + +
455A CYS* 5.1 0.2 - - + -
149B ASP* 3.7 12.1 - - + +
150B PHE* 3.8 18.8 - - + -
492B THR 4.2 0.2 + - - -
493B VAL* 1.3 85.2 - - - +
495B VAL* 1.3 67.0 + - - +
436D LEU* 4.6 3.1 - - - +
437D ASP* 4.1 20.5 - - - +
440D ASN* 4.4 0.9 + - - -
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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