Contacts of the strand formed by residues 468 - 474 (chain E) in PDB entry 2IO1
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 ILE 468 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E ASN* 5.9 0.2 - - - +
433E PRO* 3.9 19.3 - - + -
434E ALA 3.1 5.2 + - - +
435E LEU* 3.3 25.2 - - + +
436E HIS 2.8 26.2 + - - -
466E GLN* 3.8 0.7 - - - +
467E GLU* 1.3 89.0 - - + +
469E ILE* 1.3 66.2 + - - +
470E LEU* 4.1 15.9 - - + -
483E VAL* 4.3 11.4 - - + -
484E ILE 3.5 5.6 - - - +
485E ASP* 4.2 7.6 - - - +
487E ARG* 3.3 30.7 - - - +
559E ILE* 3.8 24.7 - - + +
560E SER* 4.4 6.5 - - - +
562E ASP* 4.2 1.6 - - - +
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Residues in contact with ILE 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E HIS* 3.3 19.5 - - + +
438E PHE* 3.7 31.2 - - + -
463E LEU* 3.7 30.7 - - + +
466E GLN* 4.8 1.8 - - + -
468E ILE* 1.3 78.5 - - - +
470E LEU* 1.3 65.7 + - - +
471E VAL* 4.3 8.7 - - + -
482E VAL 3.8 0.3 - - - +
483E VAL* 3.6 4.0 - - - -
484E ILE* 2.8 49.8 + - + +
486E LEU* 4.0 33.7 - - + -
512E LEU* 4.6 9.6 - - + -
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Residues in contact with LEU 470 (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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420E MET* 4.5 3.4 - - + -
423E LEU* 4.4 4.3 - - + -
435E LEU* 3.6 29.6 - - + -
436E HIS 3.0 6.9 + - - -
437E VAL* 3.8 20.4 - - + -
438E PHE 3.1 25.8 + - - -
468E ILE* 4.1 12.6 - - + -
469E ILE* 1.3 79.9 - - - +
471E VAL* 1.3 65.0 + - - +
472E PRO* 3.7 3.8 - - - +
481E LEU* 4.3 13.2 - - + -
482E VAL 3.5 1.6 - - - +
483E VAL* 3.8 26.7 - - + -
556E ALA* 3.5 36.1 - - + +
559E ILE* 4.8 4.9 - - + -
560E SER* 4.8 0.4 - - - +
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Residues in contact with VAL 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E PHE* 4.1 19.3 - - + -
439E SER 5.3 0.2 - - - +
442E PHE* 4.1 24.0 - - + -
443E TYR* 4.7 4.5 - - + +
469E ILE* 4.3 1.6 - - + -
470E LEU* 1.3 78.3 - - - +
472E PRO* 1.3 76.9 - - + +
473E ILE* 3.4 15.7 + - + +
481E LEU* 4.0 3.1 - - - +
482E VAL* 2.9 41.1 + - + +
484E ILE* 4.2 19.1 - - + -
508E LEU* 4.2 24.7 - - + -
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Residues in contact with PRO 472 (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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416E ILE* 4.5 8.3 - - + -
417E ASN* 5.3 0.7 - - - +
420E MET* 4.2 27.8 - - + -
438E PHE 3.4 27.4 - - - +
439E SER 4.3 3.5 - - - +
440E THR* 4.0 38.9 - - + +
443E TYR* 4.5 3.6 - - - +
470E LEU 3.7 3.4 - - - +
471E VAL* 1.3 92.0 - - + +
473E ILE* 1.3 64.6 + - - +
474E HIS 4.2 0.7 + - - -
479E TRP* 4.9 4.7 - - + -
480E SER 3.7 7.6 - - - +
481E LEU* 4.1 6.2 - - + -
552E THR* 4.9 2.7 - - + -
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Residues in contact with ILE 473 (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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443E TYR* 3.7 43.7 - - + -
471E VAL* 3.5 19.7 - - + +
472E PRO* 1.3 80.2 - - - +
474E HIS* 1.3 64.3 + - - +
475E ARG* 4.3 12.3 - - + +
478E HIS 3.9 0.2 - - - +
479E TRP* 3.6 7.6 - - - -
480E SER* 2.7 56.8 + - - +
482E VAL* 3.6 24.7 - - + -
493E TYR* 4.4 3.1 - - + -
504E ILE* 3.9 24.5 - - + -
508E LEU* 4.6 0.2 - - + -
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Residues in contact with HIS 474 (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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440E THR 4.9 3.4 + - - +
443E TYR* 5.6 2.7 - - - -
444E PRO* 4.8 13.7 - - + +
472E PRO 4.2 1.2 + - - -
473E ILE* 1.3 76.2 - - - +
475E ARG* 1.3 85.2 + - - +
476E LYS* 3.7 7.8 + - - -
478E HIS 4.2 3.4 - - - -
479E TRP* 3.4 34.1 - + + -
89F GLN* 3.5 53.9 + - + +
90F THR 3.2 24.6 + - - -
91F GLY* 4.8 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
------------------------------------------------------------
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