Contacts of the strand formed by residues 435 - 439 (chain B) in PDB entry 5MJ6
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 435 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B LEU* 3.9 19.1 - - + +
329B SER* 3.7 37.7 - - - +
330B ASN* 4.3 3.4 - - - +
360B ALA* 3.9 17.5 - - + +
361B PHE* 3.9 9.9 - - - +
362B ILE* 3.7 21.3 - - + -
418B ASP* 3.4 13.9 - - + +
420B VAL* 3.7 29.2 - - + -
432B ASN* 3.0 31.3 + - + +
433B TRP 3.1 1.8 - - - +
434B GLY* 1.3 78.9 - - - +
436B LEU* 1.3 61.5 + - - +
437B THR* 3.6 1.8 + - + +
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B LEU* 3.9 14.6 - - + -
418B ASP 2.7 12.5 + - - +
419B LEU* 3.3 13.0 - - + -
420B VAL* 2.7 28.1 + - - +
430B MET 3.6 12.8 - - - +
431B GLU* 4.4 0.9 - - - -
432B ASN 3.3 16.6 - - - +
435B LEU* 1.3 74.1 - - - +
437B THR* 1.3 61.5 + - - +
438B PHE* 3.6 15.9 - - + -
465B GLU* 3.5 29.8 - - + +
466B LEU* 3.9 26.5 - - + -
469B GLN* 3.6 25.4 - - - +
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Residues in contact with THR 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ALA* 5.8 1.3 - - + -
292B THR 4.8 6.0 + - - +
360B ALA* 5.9 1.1 - - + -
362B ILE* 3.8 30.3 - - + -
420B VAL* 3.5 3.6 - - + -
422B ILE* 4.2 10.8 - - + -
425B PHE* 3.2 29.1 - - + -
429B ALA* 3.3 7.4 - - - +
430B MET* 3.0 42.2 + - - +
432B ASN* 3.7 9.2 + - - +
435B LEU* 3.6 9.8 + - + +
436B LEU* 1.3 76.5 - - - +
438B PHE* 1.3 65.6 + - - +
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LEU* 3.7 30.5 - - + -
420B VAL 2.9 16.4 + - - +
421B ALA* 4.7 0.2 - - - -
422B ILE* 2.9 31.7 + - - +
425B PHE* 4.0 6.5 - - - -
428B GLY 3.8 4.7 - - - -
429B ALA* 3.6 11.9 - - + +
436B LEU* 3.6 24.7 - - + -
437B THR* 1.3 76.6 - - - +
439B ARG* 1.3 69.2 + - - +
442B THR* 3.7 5.2 - - - +
443B LEU* 3.7 28.3 - - + -
461B ILE* 3.6 33.4 - - + -
462B ILE* 4.4 3.4 - - + -
465B GLU* 3.6 33.2 - - + -
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Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B ALA* 4.6 0.2 - - - +
422B ILE 3.9 4.9 - - - -
425B PHE* 3.1 28.2 + - + +
426B GLU* 3.0 24.5 + - - -
427B ALA 3.2 19.4 + - - +
428B GLY* 3.1 17.5 + - - +
438B PHE* 1.3 81.5 - - - +
440B GLU* 1.3 66.5 + - - +
441B GLU* 3.3 42.3 + - + -
442B THR* 3.2 22.0 + - - +
443B LEU* 3.5 4.0 + - - +
922B GLN* 3.0 52.8 + - - +
923B LYS* 3.8 10.9 - - - +
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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