Contacts of the strand formed by residues 477 - 483 (chain E) in PDB entry 1XMI
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 PRO 477 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397E VAL* 3.8 18.2 - - + -
398E THR 3.5 5.6 - - - +
399E ALA* 3.9 4.6 - - + -
470E MET* 4.4 1.8 - - + +
475E LEU 4.1 4.7 - - - +
476E GLU* 1.3 91.8 - - + +
478E SER* 1.3 60.5 + - - +
479E GLU 3.7 18.6 - - - +
480E GLY 5.2 5.6 - - - +
482E ILE* 3.6 23.1 - - + +
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Residues in contact with SER 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398E THR 2.8 11.8 + - - -
399E ALA* 4.2 0.2 - - - +
400E PHE* 3.9 16.8 + - - -
406E GLY* 3.1 39.7 + - - -
409E PHE* 4.3 18.8 - - - -
410E GLU* 4.7 13.0 - - - +
476E GLU 3.8 2.2 + - - -
477E PRO* 1.3 73.2 - - - +
479E GLU* 1.3 60.7 + - - +
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Residues in contact with GLU 479 (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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396E ASN* 3.7 15.0 - - + +
397E VAL* 3.3 5.0 - - - -
398E THR* 3.3 36.8 + - - -
409E PHE* 3.3 30.8 - - + +
477E PRO* 3.4 11.4 - - - +
478E SER* 1.3 81.8 - - - +
480E GLY* 1.3 65.6 + - - +
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Residues in contact with GLY 480 (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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395E GLU 3.1 15.9 - - - -
396E ASN* 3.5 8.1 - - - -
397E VAL* 4.3 1.6 - - - -
477E PRO* 5.2 6.3 - - - +
479E GLU* 1.3 83.0 - - - +
481E LYS* 1.3 60.1 + - - +
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Residues in contact with LYS 481 (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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393E VAL* 3.7 1.4 - - - +
394E MET* 3.4 4.2 - - - -
395E GLU* 2.9 59.9 + - + +
397E VAL* 3.5 2.2 - - - +
480E GLY* 1.3 74.6 - - - +
482E ILE* 1.3 63.3 - - - +
483E LYS* 4.2 10.1 - - + +
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Residues in contact with ILE 482 (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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392E VAL* 5.6 1.6 - - + -
393E VAL 3.3 6.1 - - - +
394E MET* 4.0 19.7 - - + -
397E VAL* 3.7 17.3 - - + -
470E MET* 3.8 34.5 - - + +
471E ILE* 5.4 2.5 - - + -
477E PRO* 3.6 32.6 - - + +
481E LYS* 1.3 77.5 - - - +
483E LYS* 1.3 66.0 + - - +
484E HIS* 3.4 31.7 + - + +
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Residues in contact with LYS 483 (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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391E GLU 3.4 2.5 - - - +
392E VAL* 3.2 4.3 - - - +
393E VAL* 2.8 66.2 + - + +
395E GLU* 3.7 22.0 + - - +
481E LYS* 5.3 8.2 - - + +
482E ILE* 1.3 79.4 - - - +
484E HIS* 1.3 65.7 + - - +
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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