Contacts of the strand formed by residues 486 - 494 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139L TYR* 3.5 18.1 - - + +
156L HIS* 3.3 38.2 + - + +
157L GLU 3.3 9.4 + - - +
159L VAL* 3.5 5.6 - - - +
185L THR* 3.7 12.0 - - - +
264L ARG* 3.4 17.7 + - - -
482L LEU 3.3 16.2 + - - -
483L GLN* 3.5 12.2 + - - +
484L ALA 3.4 1.2 - - - -
485L TYR* 1.3 79.3 + - - +
487L LYS* 1.3 70.7 + - - +
488L VAL* 4.7 5.4 - - + +
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Residues in contact with LYS 487 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L ARG 3.4 1.4 - - - +
157L GLU* 2.6 48.6 + - + +
158L PRO 3.9 11.0 - - - +
159L VAL* 2.9 44.5 + - + +
239L ASP* 4.5 8.7 + - - +
264L ARG* 4.7 8.7 - - - +
486L THR* 1.3 77.7 - - - +
488L VAL* 1.3 63.1 + - - +
489L LYS* 4.0 0.4 - - + -
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Residues in contact with VAL 488 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449K GLY* 3.8 12.6 - - - +
464K PRO* 4.2 15.3 - - + -
480K TYR* 3.5 48.2 - - + -
483K GLN* 6.0 0.7 - - - +
154L THR* 4.1 18.6 - - + -
155L ARG 3.6 2.5 - - - +
156L HIS* 4.0 10.5 - - + +
486L THR* 4.7 7.0 - - + +
487L LYS* 1.3 76.4 - - - +
489L LYS* 1.3 63.3 + - - +
490L THR* 5.2 0.2 + - - -
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Residues in contact with LYS 489 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443K SER 2.9 27.6 + - - +
444K GLN 3.1 13.7 + - - -
446K LEU 3.0 24.3 + - - -
447K GLN* 5.1 1.1 - - - +
448K ALA 3.4 23.1 - - - +
449K GLY* 3.3 4.3 - - - +
451K VAL* 4.1 8.3 - - + -
153L TYR 3.8 0.2 - - - +
154L THR* 3.1 4.4 - - - -
155L ARG* 2.8 50.4 + - + +
157L GLU* 2.9 40.4 + - - +
487L LYS 3.9 0.6 + - - -
488L VAL* 1.3 74.1 - - - +
490L THR* 1.3 72.0 + - - +
491L VAL* 4.0 11.1 + - + +
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Residues in contact with THR 490 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449K GLY 2.8 13.5 + - - +
450K THR* 3.2 11.0 - - + +
451K VAL 2.8 25.8 + - - +
463K SER* 4.1 14.8 - - - +
464K PRO* 3.2 41.3 + - + +
144L ILE* 5.2 0.2 - - + -
152L SER* 3.5 22.7 - - - +
153L TYR 3.3 7.2 - - - +
154L THR* 3.5 7.0 - - + +
488L VAL* 4.2 1.2 + - - +
489L LYS* 1.3 74.6 - - - +
491L VAL* 1.3 64.0 + - - +
492L THR* 3.7 9.6 - - - +
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Residues in contact with VAL 491 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443K SER* 3.9 20.6 - - - -
451K VAL* 3.2 13.9 - - + +
453K VAL* 4.4 3.4 - - + -
151L PHE 3.6 1.6 - - - +
152L SER* 3.2 2.6 - - - -
153L TYR* 2.8 80.1 + - + +
155L ARG* 4.7 2.7 - - - -
489L LYS* 4.1 21.8 - - + +
490L THR* 1.3 77.4 - - - +
492L THR* 1.3 63.3 + - - +
493L VAL* 4.1 13.7 - - + -
3129L EDO 3.9 7.9 - - - +
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Residues in contact with THR 492 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450K THR* 5.2 1.5 - - - +
451K VAL 3.0 7.5 + - - -
452K TRP* 3.3 22.2 + - + -
453K VAL 3.0 21.7 + - - -
455K CYS* 3.4 6.3 - - - -
458K VAL* 3.8 34.7 + - + +
463K SER* 4.3 3.5 + - - -
146L ILE* 3.8 17.2 - - + +
150L PHE* 4.1 10.1 - - + -
151L PHE 3.4 2.9 - - - +
152L SER* 2.9 18.9 + - - -
490L THR* 3.7 9.8 + - - +
491L VAL* 1.3 70.3 - - - +
493L VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 493 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436J LEU* 4.5 10.5 - - + -
440J ASN* 4.0 19.7 - - - +
453K VAL* 3.8 35.2 - - + +
150L PHE* 3.2 7.1 - - - -
151L PHE* 2.7 54.1 + - + +
153L TYR* 4.5 10.3 - - + +
491L VAL* 4.1 13.7 - - + -
492L THR* 1.3 77.6 - - - +
494L LYS* 1.3 76.9 + - - +
495L VAL* 3.4 1.1 + - + +
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Residues in contact with LYS 494 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436J LEU* 5.3 1.0 - - - +
437J ASP* 4.2 22.5 + - - +
440J ASN* 4.7 0.9 + - - -
285K TRP* 3.6 33.7 - - + +
453K VAL 3.1 12.0 + - - +
454K ASN* 3.2 37.2 - - + +
455K CYS* 4.1 7.5 - - + -
149L ASP 4.5 3.4 - - - +
150L PHE* 3.7 16.9 - - + -
493L VAL* 1.3 84.1 - - - +
495L VAL* 1.3 70.2 + - - +
496L PRO* 5.8 1.6 - - - +
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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