Contacts of the strand formed by residues 486 - 494 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I TYR* 3.4 33.8 + - + -
156I HIS* 4.2 17.8 - - + +
157I GLU 3.1 14.8 - - - +
159I VAL* 3.8 6.3 - - - +
185I THR* 3.8 27.1 - - + +
264I ARG* 3.4 20.8 + - - -
482I LEU 3.4 5.4 + - - +
483I GLN* 3.4 10.3 + - - +
484I ALA 3.5 0.6 - - - -
485I TYR* 1.3 85.4 - - - +
487I LYS* 1.3 60.5 + - - +
488I VAL* 4.4 4.8 + - - +
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Residues in contact with LYS 487 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I ARG 3.4 2.4 - - - +
156I HIS* 3.5 2.1 - - - -
157I GLU* 2.6 40.9 + - + +
158I PRO 3.8 12.1 - - - +
159I VAL* 2.9 46.6 + - + +
239I ASP* 4.6 7.5 + - - +
264I ARG* 5.1 4.7 - - - +
486I THR* 1.3 73.2 - - - +
488I VAL* 1.3 62.1 + - - +
489I LYS 3.7 0.7 + - - -
467J GLY 5.5 1.3 - - - +
468J TYR* 3.9 63.3 - - + +
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Residues in contact with VAL 488 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I THR* 4.0 30.5 - - + -
155I ARG 3.6 3.6 - - - +
156I HIS* 4.0 9.4 - - + -
486I THR* 5.4 5.2 - - - +
487I LYS* 1.3 74.6 - - - +
489I LYS* 1.3 63.6 + - - +
490I THR* 4.5 0.4 + - - +
449J GLY* 3.8 8.7 - - - +
464J PRO* 4.2 13.0 - - + -
466J GLY* 5.9 2.4 + - - -
468J TYR* 4.2 10.0 - - - -
480J TYR* 3.6 39.5 - - + -
483J GLN* 5.8 2.2 - - - +
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Residues in contact with LYS 489 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I TYR 3.8 0.5 - - - +
154I THR* 3.1 5.7 - - - -
155I ARG* 2.8 50.1 + - + +
157I GLU* 3.3 25.2 + - - +
487I LYS 3.7 1.0 + - - -
488I VAL* 1.3 73.7 - - - +
490I THR* 1.3 70.4 + - - +
491I VAL* 4.1 12.5 + - + +
443J SER 3.1 23.8 + - - +
444J GLN 3.1 14.6 + - - -
446J LEU 2.7 26.1 + - - -
447J GLN* 4.7 0.8 - - - +
448J ALA 3.2 26.5 - - - +
449J GLY 3.4 3.6 - - - +
451J VAL* 4.3 5.6 - - + -
468J TYR* 3.2 22.7 - - - +
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Residues in contact with THR 490 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I SER* 3.7 12.6 - - - +
153I TYR 3.4 7.0 - - - +
154I THR* 3.5 4.7 - - + +
488I VAL* 4.5 1.0 + - - +
489I LYS* 1.3 75.2 - - - +
491I VAL* 1.3 64.2 + - - +
492I THR* 3.7 19.3 - - - +
449J GLY 2.8 11.5 + - - -
450J THR* 3.1 10.9 - - + +
451J VAL 2.9 24.9 + - - +
463J SER* 4.0 9.4 - - - +
464J PRO* 3.1 49.8 + - + +
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Residues in contact with VAL 491 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I PHE 3.6 2.1 - - - +
152I SER* 3.3 2.4 - - - -
153I TYR* 2.8 79.3 + - + +
155I ARG* 4.7 5.4 - - - +
489I LYS* 4.2 21.8 - - + +
490I THR* 1.3 76.4 - - - +
492I THR* 1.3 62.1 + - - +
493I VAL* 4.0 13.9 - - + -
443J SER* 4.1 25.8 - - - +
451J VAL* 3.3 14.1 - - + +
453J VAL* 4.5 3.8 - - + -
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Residues in contact with THR 492 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I ILE* 4.4 3.4 - - + -
150I PHE* 4.1 16.6 - - + -
151I PHE 3.5 2.2 - - - -
152I SER* 3.0 23.7 + - - +
490I THR* 3.7 10.4 - - - +
491I VAL* 1.3 72.3 - - - +
493I VAL* 1.3 61.5 + - - +
450J THR* 4.8 2.3 - - - +
451J VAL 3.0 7.5 + - - -
452J TRP* 3.4 19.5 + - - -
453J VAL 3.1 21.5 + - - -
455J CYS* 3.5 5.2 - - - -
458J VAL* 3.7 39.5 + - + +
463J SER* 4.3 2.9 + - - -
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Residues in contact with VAL 493 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I PHE* 3.1 7.6 - - - -
151I PHE* 2.8 53.0 + - + +
153I TYR* 4.5 10.5 - - + +
491I VAL* 4.0 20.9 - - + -
492I THR* 1.3 76.9 - - - +
494I LYS* 1.3 75.5 + - - +
495I VAL* 3.7 1.8 - - + +
453J VAL* 3.8 29.6 - - + -
436K LEU* 4.3 9.0 - - + -
440K ASN* 4.0 20.2 - - - +
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Residues in contact with LYS 494 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149I ASP* 4.5 3.4 - - + +
150I PHE* 3.5 24.7 - - + -
493I VAL* 1.3 82.3 - - - +
495I VAL* 1.3 70.7 + - - +
496I PRO* 5.9 1.2 - - - +
285J TRP* 3.7 34.4 - - + +
453J VAL 3.1 11.5 + - - +
454J ASN* 3.2 38.2 + - + +
455J CYS* 4.1 2.4 - - + -
436K LEU* 5.2 1.6 - - - +
437K ASP* 4.1 21.0 + - - +
440K ASN* 4.9 0.5 + - - -
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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