Contacts of the strand formed by residues 486 - 494 (chain F) in PDB entry 1O04
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139F TYR* 3.3 19.4 - - + -
156F HIS* 3.6 43.9 - - + +
157F GLU 3.3 7.5 + - - +
159F VAL* 4.4 4.9 - - - +
185F THR* 4.2 6.9 - - - +
482F LEU 3.1 12.7 + - - -
483F GLN* 3.3 17.6 + - - +
484F ALA 3.4 1.9 - - - -
485F TYR* 1.3 79.5 + - - +
487F GLU* 1.3 68.5 + - - +
488F VAL* 4.1 10.2 + - + +
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Residues in contact with GLU 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E GLY 3.2 1.6 - - - +
468E TYR* 3.4 39.7 + - + +
474E GLY 5.4 1.2 + - - -
475E ARG* 2.9 22.2 + - - -
155F ARG 3.6 0.3 - - - +
156F HIS 3.9 0.2 - - - -
157F GLU* 2.8 34.7 + - - +
158F PRO 4.0 16.6 - - - +
159F VAL* 3.5 19.4 - - - +
264F ARG* 2.8 45.2 + - - +
486F THR* 1.3 75.5 - - - +
488F VAL* 1.3 62.4 + - - +
489F LYS 3.8 0.2 + - - -
6806F GAI 4.6 2.9 - - - +
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Residues in contact with VAL 488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E GLY 3.8 2.6 - - - +
464E PRO* 4.0 22.9 - - + -
468E TYR* 3.7 2.6 - - - -
475E ARG* 2.8 51.7 + - + +
480E TYR* 3.6 39.5 - - + -
483E GLN* 6.0 0.2 - - - +
154F THR* 4.0 13.9 - - + -
155F ARG 3.6 4.0 - - - +
156F HIS* 4.2 10.1 - - + +
486F THR* 4.2 11.0 + - + +
487F GLU* 1.3 76.5 - - - +
489F LYS* 1.3 62.3 + - - +
490F THR* 4.9 0.2 - - - +
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Residues in contact with LYS 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443E SER 2.9 26.2 + - - +
444E GLN* 2.9 10.9 + - - +
446E LEU 2.7 29.8 + - - -
448E ALA 3.4 20.6 - - - +
449E GLY 3.4 3.6 - - - -
451E VAL* 4.1 7.0 - - + -
468E TYR* 3.4 16.2 - - - +
153F TYR 3.7 0.2 - - - +
154F THR* 3.1 6.4 - - - -
155F ARG* 2.8 46.2 + - + +
157F GLU* 2.8 30.0 + - - +
487F GLU 3.8 0.6 + - - -
488F VAL* 1.3 71.3 - - - +
490F THR* 1.3 73.0 + - - +
491F VAL* 3.9 13.1 + - + +
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Residues in contact with THR 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E GLY 2.9 10.9 + - - -
450E THR* 3.2 13.2 - - + +
451E VAL 2.7 31.5 + - - -
463E SER* 4.0 13.9 - - - -
464E PRO* 2.7 44.6 + - + +
475E ARG* 6.0 0.2 - - - -
144F ILE* 5.7 0.2 - - + -
152F SER* 3.8 11.4 - - - +
153F TYR 3.4 6.5 - - - +
154F THR* 3.8 2.1 - - + +
488F VAL* 4.2 0.7 - - - +
489F LYS* 1.3 73.9 - - - +
491F VAL* 1.3 58.1 + - - +
492F THR* 3.5 21.8 - - - +
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Residues in contact with VAL 491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443E SER* 4.0 19.5 - - - -
451E VAL* 3.3 11.2 - - + +
453E VAL* 4.2 5.2 - - + -
151F PHE 3.7 1.6 - - - +
152F SER* 3.2 2.8 - - - -
153F TYR* 2.8 80.7 + - + +
155F ARG* 4.5 2.9 - - - -
489F LYS* 4.1 22.9 - - + +
490F THR* 1.3 77.6 - - - +
492F THR* 1.3 65.2 + - - +
493F VAL* 3.9 13.0 - - + -
6906F EDO 4.1 7.4 - - - +
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Residues in contact with THR 492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E THR* 5.0 0.6 - - - +
451E VAL 3.0 7.1 + - - -
452E TRP* 3.3 23.6 + - + +
453E VAL 2.9 23.0 + - - -
455E CYS* 3.5 5.3 - - - -
458E VAL* 3.8 32.1 + - + +
463E SER* 4.9 0.2 - - - -
146F ILE* 4.3 10.1 - - + +
150F PHE* 4.1 17.5 - - + -
151F PHE 3.5 2.9 - - - -
152F SER* 2.9 22.2 + - - -
490F THR* 3.5 12.3 + - - +
491F VAL* 1.3 71.8 - - - +
493F VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E VAL* 3.7 29.8 - - + +
150F PHE* 3.1 6.4 - - - -
151F PHE* 2.8 52.8 + - + +
153F TYR* 4.4 11.7 - - + +
491F VAL* 3.9 21.5 - - + -
492F THR* 1.3 77.8 - - - +
494F LYS* 1.3 75.2 + - - +
495F VAL* 3.7 0.9 - - + +
436H LEU* 4.2 10.1 - - + -
440H ASN* 4.0 20.0 - - - +
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Residues in contact with LYS 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E TRP* 3.8 35.0 - - + +
453E VAL 3.0 11.9 + - - +
454E ASN* 3.3 37.1 + - + +
455E CYS* 4.2 1.7 - - + -
149F ASP* 3.7 13.2 + - - +
150F PHE* 3.7 18.4 - - + -
493F VAL* 1.3 83.2 - - - +
495F VAL* 1.3 71.7 + - - +
436H LEU* 5.1 1.7 - - - +
437H ASP* 4.0 13.0 - - - +
440H ASN* 4.9 1.0 + - - -
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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