Contacts of the strand formed by residues 409 - 419 (chain E) in PDB entry 5IXM
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 LEU 409 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400E ALA* 4.2 7.0 - - + -
401E GLN 3.3 17.5 - - - +
402E TYR* 3.3 39.5 - - + +
406E LEU 5.0 0.2 - - - +
407E GLY 3.5 8.0 - - - +
408E SER* 1.3 86.3 + - - +
410E THR* 1.3 59.3 + - - +
411E LEU 3.4 15.3 - - - +
432E TYR* 3.7 26.7 + - + +
434E SER* 3.6 14.7 - - - -
603E C8E 3.7 42.8 - - + -
180G PRO* 5.6 1.6 - - + -
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Residues in contact with THR 410 (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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401E GLN* 2.9 28.6 + - - +
402E TYR* 4.2 0.7 + - - -
403E ASP* 3.9 14.0 - - + +
406E LEU* 3.9 34.8 - - + +
408E SER 3.5 13.9 - - - +
409E LEU* 1.3 75.5 - - - +
411E LEU* 1.3 72.1 + - - +
432E TYR* 4.5 2.7 - - - -
433E ALA* 3.4 3.1 - - - -
434E SER* 2.8 34.7 + - - -
437E TYR* 3.9 24.6 - - + +
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Residues in contact with LEU 411 (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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309E GLN* 3.4 29.6 - - - +
400E ALA* 4.4 0.7 - - - -
401E GLN* 2.9 57.7 + - - +
409E LEU* 3.4 11.6 - - - +
410E THR* 1.3 82.4 + - - +
412E GLY* 1.3 58.9 + - - +
413E ASN* 6.0 0.4 - - - +
431E ARG* 5.8 1.3 - - - +
432E TYR* 3.5 17.7 - - - +
433E ALA* 3.6 19.7 - - + -
437E TYR* 3.5 26.7 - - + -
77F GLU* 3.7 15.7 - - - +
107F PHE* 3.7 7.4 - - + -
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Residues in contact with GLY 412 (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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399E GLY 3.4 11.4 - - - -
400E ALA* 4.2 1.6 - - - -
411E LEU* 1.3 77.9 - - - +
413E ASN* 1.3 67.1 + - - +
431E ARG* 5.5 1.0 + - - -
432E TYR* 2.8 35.9 + - - +
603E C8E 3.9 22.9 - - - -
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Residues in contact with ASN 413 (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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397E LYS* 5.7 4.8 - - - +
398E GLY* 3.2 4.7 - - - -
399E GLY* 2.9 48.1 + - - +
411E LEU* 6.0 0.5 - - - +
412E GLY* 1.3 78.0 + - - +
414E ALA* 1.3 66.1 + - - +
415E ILE* 5.6 5.1 - - - +
430E TYR 3.1 14.4 - - - +
431E ARG* 4.0 33.9 + - + +
603E C8E 3.3 11.8 + - - +
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Residues in contact with ALA 414 (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 LEU* 5.4 4.3 - - + -
397E LYS 3.5 7.0 - - - +
398E GLY* 4.0 0.4 - - - -
413E ASN* 1.3 78.8 - - - +
415E ILE* 1.3 63.5 + - - +
429E ASN* 3.2 3.9 - - - +
430E TYR* 2.9 38.4 + - + +
603E C8E 3.7 30.7 - - - +
213G LEU* 4.3 10.1 - - + -
215G LEU* 6.5 0.4 - - + -
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Residues in contact with ILE 415 (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 LEU* 3.6 5.4 - - - +
397E LYS* 2.9 70.4 + - + +
413E ASN* 5.6 4.3 - - - +
414E ALA* 1.3 78.2 - - - +
416E MET* 1.3 66.5 + - - +
427E GLN* 3.6 32.1 - - + +
428E LEU 3.3 13.9 - - - +
429E ASN* 3.9 8.7 - - + -
553E GLN 5.3 1.1 - - - +
555E ALA* 3.6 27.1 - - + -
556E PHE* 3.9 2.4 - - + -
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Residues in contact with MET 416 (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 LEU* 4.0 15.3 - - + -
395E GLY 3.3 12.1 - - - +
396E LEU* 3.9 15.3 - - + -
415E ILE* 1.3 75.5 - - - +
417E GLU* 1.3 67.3 + - - +
418E TYR 5.2 0.7 - - - +
426E ILE* 5.0 6.3 - - + +
427E GLN* 3.3 3.8 - - - +
428E LEU* 2.9 72.9 + - + +
261G PHE* 3.7 33.2 - - + -
263G VAL* 4.3 13.7 - - + -
603G C8E 4.5 19.7 - - - +
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Residues in contact with GLU 417 (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 GLN 3.6 2.1 - - - +
394E LEU* 3.6 6.4 - - - +
395E GLY* 2.8 37.8 + - - -
416E MET* 1.3 76.7 - - - +
418E TYR* 1.3 68.1 + - - +
419E ARG* 4.2 10.0 - - + +
425E MET* 3.9 8.6 - - + +
426E ILE 3.3 11.0 - - - +
427E GLN* 2.9 28.2 - - + +
552E TYR* 3.1 23.1 + - - -
554E SER* 4.1 5.0 + - - -
555E ALA* 3.0 31.6 + - + +
556E PHE* 3.8 16.7 - - + -
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Residues in contact with TYR 418 (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 ASN* 5.1 1.6 - - - -
393E GLN* 3.2 39.3 - - + +
394E LEU* 3.7 18.3 - - + +
416E MET* 5.2 1.6 - - + +
417E GLU* 1.3 75.0 - - - +
419E ARG* 1.3 68.0 + - - +
420E LYS* 3.6 31.9 - - + +
424E ARG* 4.6 4.1 - - + +
425E MET* 3.3 3.5 - - - +
426E ILE* 2.9 38.1 + - + +
463E TRP* 3.7 34.5 - + - -
603G C8E 3.2 65.6 - - - -
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Residues in contact with ARG 419 (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 ASP 4.9 0.3 - - - +
393E GLN* 3.0 29.6 + - - +
417E GLU* 4.2 10.5 - - + +
418E TYR* 1.3 80.1 - - - +
420E LYS* 1.3 60.7 + - - +
421E ASP 3.0 27.1 + - - +
422E ALA* 4.2 17.8 - - - +
424E ARG 3.4 15.5 - - - +
425E MET* 4.1 15.8 - - + +
552E TYR* 3.0 27.6 + - - -
554E SER* 4.1 13.9 + - - -
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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