Contacts of the strand formed by residues 408 - 415 (chain A) in PDB entry 3MX0
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 TYR 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A VAL* 5.8 1.3 - - + -
366A CYS* 5.0 2.7 - - - -
367A GLU 3.8 12.1 - - - -
368A GLN* 4.2 15.3 + - + -
379A CYS* 4.2 20.4 - - - -
383A VAL* 3.8 18.6 - - + +
402A LEU* 3.8 29.2 - - + -
403A GLU* 3.2 47.0 + - + +
406A MET* 2.4 38.7 + - + -
407A ASN 1.3 59.8 - - - -
409A THR* 1.3 63.4 + - - +
410A PHE* 3.5 13.9 + + + -
430A ALA 3.9 0.2 - - - +
431A SER* 3.1 4.2 - - - -
432A VAL* 2.6 51.7 + - + +
433A SER* 5.2 2.9 - - - -
434A ILE* 5.7 3.1 - - + -
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Residues in contact with THR 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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366A CYS 3.7 0.9 - - - -
367A GLU* 3.1 66.4 + - - +
368A GLN 5.4 0.2 - - - -
369A CYS* 4.4 10.3 - - - -
407A ASN* 2.6 22.3 + - - -
408A TYR* 1.3 71.2 - - - +
410A PHE* 1.3 77.5 + - - +
411A THR* 5.4 1.3 - - + -
429A THR* 5.5 4.0 - - - -
431A SER* 3.4 15.9 + - - +
501A NAG 4.8 6.3 + - + +
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Residues in contact with PHE 410 (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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335A LEU* 6.0 0.7 - - - -
337A ALA* 5.6 0.7 - - + -
344A VAL* 4.6 12.3 - - + -
346A LEU* 4.5 29.8 - - + -
364A VAL* 5.9 2.2 - - + -
365A THR 3.4 14.6 - - - -
366A CYS* 3.2 33.4 - - + -
379A CYS* 5.3 0.4 - - - -
383A VAL* 6.2 1.1 - - + -
385A TYR* 4.7 8.3 - + - -
399A VAL* 4.1 35.2 - - + -
402A LEU* 5.6 2.2 - - + -
408A TYR* 4.6 13.9 - + + -
409A THR* 1.3 85.4 - - - +
411A THR* 1.3 60.2 + - - +
429A THR* 3.1 7.3 - - - -
430A ALA* 2.6 45.4 + - + +
432A VAL* 4.6 17.7 - - + -
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Residues in contact with THR 411 (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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335A LEU* 5.4 0.2 - - - -
364A VAL* 3.5 4.2 - - - +
365A THR* 2.8 68.9 + - + +
367A GLU* 4.6 11.9 - - - +
409A THR* 5.4 1.1 - - + -
410A PHE* 1.3 75.1 - - - +
412A VAL* 1.3 60.7 + - - +
427A PHE* 2.7 37.2 - - + -
428A ARG 3.7 1.8 - - - -
429A THR* 3.0 22.4 - - - +
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Residues in contact with VAL 412 (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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332A PRO* 3.4 20.5 - - + +
335A LEU* 3.4 19.8 - - + +
346A LEU* 6.0 1.6 - - + -
348A TRP* 4.1 32.5 - - + +
362A TYR* 4.3 7.6 - - + -
363A SER 3.6 6.1 - - - +
364A VAL* 3.7 24.9 - - + -
411A THR* 1.3 74.4 - - - +
413A GLU* 1.3 73.9 + - - +
427A PHE* 2.9 19.9 - - - +
428A ARG 3.0 26.7 + - - +
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Residues in contact with GLU 413 (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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332A PRO* 4.6 0.9 - - - -
362A TYR* 3.1 13.9 - - - -
363A SER* 2.8 46.3 + - - +
365A THR* 6.0 3.4 - - + -
411A THR* 5.8 0.2 - - - +
412A VAL* 1.3 77.7 - - - +
414A ALA* 1.3 59.2 + - - +
415A ARG* 3.0 37.3 + - + +
425A ARG* 2.8 49.1 + - - +
426A SER 3.2 25.3 + - - +
427A PHE* 3.7 10.1 - - + -
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Residues in contact with ALA 414 (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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329A PRO* 2.9 26.9 - - + +
330A SER 3.3 24.9 - - - +
331A ALA* 4.2 1.1 - - - -
332A PRO* 3.9 10.1 - - + +
351A PRO* 3.5 20.0 - - + -
360A ILE* 4.3 1.6 - - + -
362A TYR* 3.8 15.7 - - + -
413A GLU* 1.3 72.8 - - - +
415A ARG* 1.3 63.2 + - - +
426A SER* 3.6 11.3 + - - +
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Residues in contact with ARG 415 (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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329A PRO* 3.5 3.4 - - - -
360A ILE* 3.2 2.0 - - - +
361A VAL* 2.5 56.6 + - + +
363A SER* 3.6 11.9 - - - +
413A GLU* 3.0 45.7 + - + +
414A ALA* 1.3 72.7 - - - +
416A ASN* 1.3 57.9 + - - +
419A SER* 2.6 50.2 + - - +
420A GLY* 4.1 3.4 - - - +
422A VAL* 4.7 6.5 + - - +
425A ARG* 4.4 14.6 - - - +
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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