Contacts of the strand formed by residues 392 - 399 (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 VAL 392 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390E THR* 4.4 2.7 - - + -
391E GLU* 1.3 79.0 - - - +
393E VAL* 1.3 66.3 + - - +
394E MET* 5.0 2.9 - - + -
446E PHE* 3.8 23.7 - - + +
447E LYS* 3.3 4.0 - - - -
448E ILE* 3.0 51.9 + - + +
471E ILE* 4.7 17.0 - - + -
482E ILE* 5.6 0.7 - - + -
483E LYS 3.2 7.0 - - - +
484E HIS* 4.3 9.0 - - + +
568E LEU* 3.6 38.8 - - + -
599E THR* 4.5 1.8 - - + -
601E ILE* 4.6 2.9 - - + -
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Residues in contact with VAL 393 (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* 3.8 24.0 - - + +
392E VAL* 1.3 79.1 - - - +
394E MET* 1.3 68.1 + - - +
395E GLU* 3.9 25.1 - - + -
446E PHE 3.5 6.3 - - - +
447E LYS* 3.9 22.4 - - + +
481E LYS 4.2 0.9 - - - +
482E ILE* 3.3 6.2 - - - +
483E LYS* 2.8 66.0 + - + +
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Residues in contact with MET 394 (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* 5.0 2.0 - - + -
393E VAL* 1.3 80.4 - - - +
395E GLU* 1.3 65.3 + - - +
397E VAL* 4.0 6.7 - - + -
444E ILE* 3.8 16.2 - - - +
445E ASN* 3.3 6.8 - - - +
446E PHE* 2.9 61.1 + - + +
467E LEU* 3.8 13.7 - - + -
470E MET* 3.7 33.4 - - + -
471E ILE* 3.6 31.4 - - + -
481E LYS 3.4 3.1 - - - -
482E ILE* 4.0 23.6 - - + -
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Residues in contact with GLU 395 (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* 3.9 19.0 - - + +
394E MET* 1.3 76.8 - - - +
396E ASN* 1.3 76.8 + - - +
397E VAL* 3.1 2.4 + - - +
445E ASN* 3.4 5.2 - - - +
480E GLY* 3.1 3.8 - - - -
481E LYS* 2.9 49.6 + - + +
483E LYS* 3.7 20.2 + - - -
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Residues in contact with ASN 396 (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* 1.3 79.3 - - - +
397E VAL* 1.3 61.3 + - - +
398E THR* 3.6 4.0 + - - -
443E ASP* 3.4 28.4 + - - +
444E ILE 3.3 3.4 + - - -
445E ASN* 2.8 26.8 + - - +
479E GLU* 3.7 13.9 - - + +
480E GLY* 3.5 14.2 + - - -
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Residues in contact with VAL 397 (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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394E MET* 4.0 11.9 - - + -
395E GLU 3.5 19.3 - - - +
396E ASN* 1.3 75.9 - - - +
398E THR* 1.3 63.3 + - - +
441E LEU* 4.2 1.1 - - + +
442E LYS* 3.6 1.9 - - - -
443E ASP 2.9 20.1 + - - -
444E ILE* 2.9 24.1 + - + +
470E MET* 3.6 36.3 - - + -
477E PRO* 3.8 16.8 - - + -
479E GLU 3.3 4.5 - - - +
481E LYS 3.5 23.3 - - - +
482E ILE* 3.7 14.1 - - + -
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Residues in contact with THR 398 (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 3.6 2.4 + - - -
397E VAL* 1.3 73.4 - - - +
399E ALA* 1.3 59.3 + - - +
400E PHE* 4.8 5.8 - - + -
409E PHE* 4.4 22.8 - - + -
439E PRO* 4.0 17.7 - - + -
441E LEU 3.3 12.3 - - - +
442E LYS* 3.9 10.8 - - + +
443E ASP* 3.2 19.9 + - - +
477E PRO* 3.5 2.4 - - - +
478E SER* 2.8 31.3 + - - -
479E GLU* 3.3 30.1 + - - -
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Residues in contact with ALA 399 (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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398E THR* 1.3 75.8 - - - +
400E PHE* 1.3 65.5 + - - +
439E PRO* 3.4 5.7 - - - +
440E VAL* 2.9 27.0 + - + +
441E LEU* 2.9 14.4 + - + +
470E MET* 3.7 27.4 - - - -
475E LEU* 4.1 13.9 - - + -
476E GLU 3.6 17.9 - - - +
477E PRO* 3.9 0.7 - - + -
478E SER 4.2 2.0 - - - +
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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