Contacts of the strand formed by residues 405 - 409 (chain A) in PDB entry 5E2Q
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 LYS 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TRP* 3.0 53.1 + - + +
301A ILE* 3.8 17.3 - - - +
303A ASP* 2.8 28.0 + - - +
306A PRO* 4.4 0.2 - - - +
309A GLU* 2.7 39.2 + - - +
372A ASP* 3.6 25.4 - - + +
390A ILE 4.0 0.3 - - - +
391A ASN* 3.6 5.4 - - - -
392A ILE* 2.7 41.7 + - - +
404A PHE* 1.3 78.8 - - - +
406A ASN* 1.3 68.0 + - - +
407A VAL* 5.4 4.5 - - + -
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Residues in contact with ASN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO* 3.6 13.3 - - - +
372A ASP 2.7 18.5 + - - +
373A PHE* 3.2 30.2 - - + +
374A THR* 3.2 22.3 + - - -
390A ILE 3.5 5.6 - - - +
391A ASN* 2.5 29.6 + - - -
404A PHE* 3.4 20.8 - - - -
405A LYS* 1.3 75.6 - - - +
407A VAL* 1.3 67.5 + - - +
451A ALA* 3.0 16.4 - - + +
452A LEU* 3.5 14.3 + - - +
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TRP* 5.9 1.8 - - + -
309A GLU* 4.6 13.2 - - + +
331A PHE* 4.8 7.9 - - + -
373A PHE* 4.0 4.1 - - - -
374A THR* 3.4 14.6 - - - +
376A LEU* 3.6 33.4 - - + -
389A GLY* 3.2 4.7 - - - -
390A ILE* 3.0 65.2 + - + +
392A ILE* 4.9 5.2 - - + -
405A LYS* 5.4 5.4 - - + -
406A ASN* 1.3 81.7 - - - +
408A SER* 1.3 60.6 + - - +
409A LEU* 4.0 5.6 - - + -
447A VAL* 5.0 1.2 - - - +
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE* 3.7 35.9 - - - -
373A PHE* 3.9 6.7 - - - -
374A THR 3.0 8.6 + - - -
375A SER* 3.3 3.8 + - - -
376A LEU 2.8 24.7 + - - -
388A ALA 4.1 2.9 - - - -
389A GLY* 4.5 1.1 - - - -
407A VAL* 1.3 71.4 - - - +
409A LEU* 1.3 59.4 + - - +
410A GLY* 2.8 6.2 + - - -
413A LEU* 3.6 24.8 - - - +
447A VAL* 3.8 14.1 - - - +
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A PHE* 5.6 2.2 - - + -
376A LEU* 3.4 29.4 - - + -
378A VAL* 3.8 23.8 - - + -
381A PHE* 3.7 31.2 - - + -
386A ILE* 4.0 5.6 - - + -
387A PRO* 3.2 26.0 - - + +
388A ALA 3.1 17.3 + - - +
389A GLY* 4.7 2.7 - - - +
390A ILE* 5.0 1.8 - - + -
407A VAL* 4.5 11.7 - - + -
408A SER* 1.3 67.6 - - - +
410A GLY* 1.3 64.9 + - - +
411A ASN 3.4 2.5 - - - -
412A VAL* 3.1 22.6 + - + +
413A LEU* 3.1 17.6 + - - +
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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
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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