Contacts of the strand formed by residues 435 - 442 (chain B) in PDB entry 2J0M
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 ASP 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427B CYS* 3.9 13.9 - - - -
429B GLY 3.6 7.2 - - - +
430B GLU* 3.5 31.1 - - - +
434B GLY* 1.3 75.3 - - - +
436B VAL* 1.3 60.9 + - - +
437B HIS* 3.7 24.6 + - + -
454B LYS* 4.1 0.5 - - - -
455B THR* 3.0 33.2 + - - +
457B LYS* 4.8 14.3 - - - +
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Residues in contact with VAL 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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427B CYS* 3.4 6.2 - - - -
428B ILE* 2.6 39.4 + - + -
429B GLY 3.0 17.4 + - - +
431B GLY* 4.5 4.0 - - - +
434B GLY 4.7 1.3 - - - +
435B ASP* 1.3 74.9 - - - +
437B HIS* 1.3 65.2 + - - +
452B ALA* 4.6 1.8 - - + -
453B ILE 3.5 16.2 - - - +
454B LYS* 4.6 10.1 - - + +
499B MET* 6.4 0.7 - - - -
1687B 4ST 3.4 70.4 - - + +
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Residues in contact with HIS 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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424B LEU* 3.6 33.7 - - + +
425B GLY 3.2 20.6 - - - -
426B ARG 3.3 11.9 - - - +
427B CYS* 3.4 19.8 - - + +
428B ILE* 3.8 6.1 - - - +
435B ASP* 3.7 27.7 + - + -
436B VAL* 1.3 75.3 - - - +
438B GLN* 1.3 60.4 + - - +
452B ALA* 3.3 6.9 - - - +
453B ILE* 2.6 44.0 + - + +
455B THR* 3.8 24.2 - - + +
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Residues in contact with GLN 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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425B GLY* 2.8 29.0 + - - -
426B ARG* 2.8 56.8 + - - +
428B ILE* 3.8 25.4 - - + +
437B HIS* 1.3 75.1 - - - +
439B GLY* 1.3 64.0 + - - +
440B ILE* 6.2 1.6 - - + -
451B VAL 3.5 4.7 - - - +
453B ILE* 3.9 2.8 - - - +
501B LEU* 3.7 30.0 - - + +
1687B 4ST 6.2 0.4 - - - -
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Residues in contact with GLY 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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423B GLU 3.3 12.8 - - - -
425B GLY* 4.0 2.5 - - - -
438B GLN* 1.3 80.2 - - - +
440B ILE* 1.3 75.7 + - - +
450B ALA* 3.7 4.2 - - - +
451B VAL* 2.8 34.0 + - - +
453B ILE* 3.5 12.9 - - - +
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Residues in contact with ILE 440 (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 ARG 3.7 0.5 - - - +
422B ILE* 3.4 7.4 - - - +
423B GLU* 2.9 54.6 + - + +
438B GLN* 6.2 1.8 - - + -
439B GLY* 1.3 85.6 - - - +
441B TYR* 1.3 62.2 + - - +
442B MET* 3.7 15.3 + - + +
448B ALA* 3.5 32.5 - - + +
449B LEU 3.5 8.1 - - - +
450B ALA* 5.1 6.7 - - + -
451B VAL* 4.1 2.5 - - - -
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Residues in contact with TYR 441 (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 ILE* 3.9 29.2 - - + +
421B ARG* 3.2 34.1 - - + -
422B ILE* 3.3 20.2 - - + -
440B ILE* 1.3 73.1 - - - +
442B MET* 1.3 59.9 + - - +
443B SER* 3.0 41.7 + - - -
444B PRO* 4.9 3.3 - - - +
447B PRO 4.0 0.3 - - - +
448B ALA* 3.7 1.2 - - - -
449B LEU* 2.8 55.2 + - + +
451B VAL* 3.7 17.0 - - + +
487B ILE* 4.0 22.2 - - + -
498B ILE* 5.2 0.2 - - + -
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Residues in contact with MET 442 (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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420B GLU 5.6 1.6 - - - +
421B ARG* 2.9 50.7 + - + +
423B GLU* 3.3 40.6 - - - +
440B ILE* 3.7 21.5 - - + +
441B TYR* 1.3 72.5 - - - +
443B SER* 1.3 65.7 + - - +
447B PRO 5.4 0.4 - - - -
448B ALA* 4.2 16.4 - - + +
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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