Contacts of the strand formed by residues 498 - 502 (chain E) in PDB entry 3E20
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 ASN 498 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493E ILE* 5.2 0.2 - - - +
497E SER* 1.3 84.5 - - - +
499E VAL* 1.3 66.3 - - - +
507E THR* 4.4 17.6 - - + +
508E LEU 3.4 11.0 - - - +
509E GLU* 3.7 16.5 - - - +
548E THR 4.8 0.7 - - - +
549E SER* 5.1 2.6 - - - -
550E THR* 5.0 16.1 + - + +
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Residues in contact with VAL 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469E PHE* 4.1 19.7 - - + -
493E ILE* 3.8 16.8 - - + -
498E ASN* 1.3 80.6 - - - +
500E LEU* 1.3 62.2 + - - +
501E VAL 4.0 0.2 + - - -
507E THR* 3.5 4.7 - - - +
508E LEU* 3.0 48.8 + - + +
510E VAL* 3.6 28.3 - - + -
534E VAL* 5.2 1.8 - - + -
547E LEU* 4.3 24.2 - - + -
548E THR 3.5 10.5 - - - +
549E SER* 5.9 0.2 - - - -
550E THR* 4.4 5.2 - - - -
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Residues in contact with LEU 500 (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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499E VAL* 1.3 74.1 - - - +
501E VAL* 1.3 62.5 + - - +
502E MET* 3.7 21.5 - - + -
505E ASN* 3.4 44.4 - - - +
506E GLN 3.4 13.2 - - - +
507E THR* 3.8 12.8 - - - +
546E VAL 3.4 4.2 - - - +
547E LEU* 3.5 3.0 - - - -
548E THR* 2.7 41.6 + - + +
550E THR* 3.6 24.3 - - + +
553E PRO* 3.8 22.4 - - + -
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Residues in contact with VAL 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473E ILE* 4.4 4.0 - - + -
499E VAL 4.9 0.4 - - - +
500E LEU* 1.3 72.0 - - - +
502E MET* 1.3 54.3 + - - +
504E ILE* 3.1 17.4 - - + +
505E ASN 2.8 29.9 + - - -
506E GLN* 2.5 27.6 + - + +
508E LEU* 3.6 30.1 - - + -
541E VAL* 3.7 25.8 - - + -
545E TYR* 4.0 20.9 - - + -
546E VAL 3.9 2.2 - - - +
547E LEU* 3.6 20.4 - - + -
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Residues in contact with MET 502 (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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500E LEU* 3.7 22.9 - - + -
501E VAL* 1.3 74.1 - - - +
503E PRO* 1.3 82.6 - - + +
504E ILE 3.3 1.6 - - - -
505E ASN* 4.3 9.9 - - - +
545E TYR* 3.0 9.6 - - - +
546E VAL 2.9 35.2 + - - +
548E THR* 3.6 24.0 - - + -
553E PRO* 4.3 7.4 - - + -
554E VAL* 3.4 25.1 - - + +
555E HIS* 5.0 0.7 - - - -
556E ALA* 4.2 15.9 - - + +
630E CYS* 3.4 15.8 - - - -
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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