Contacts of the strand formed by residues 436 - 442 (chain B) in PDB entry 4JWE
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 VAL 436 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427B SER 4.7 0.2 - - - +
428B THR* 3.9 10.3 - - + -
433B GLN* 3.5 19.7 - - - +
435B ALA* 1.3 70.1 - - - +
437B THR* 1.3 60.3 + - - +
438B ILE* 4.0 11.6 + - + -
458B ASN* 3.3 5.2 - - - +
459B LEU* 2.9 49.6 + - + +
462B ILE* 3.6 20.9 - - + -
472B ILE* 4.3 11.9 - - + -
10C LEU* 3.7 37.0 - - + -
11C PRO 3.4 6.7 - - - +
13C PRO* 4.2 3.4 - - - -
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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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402B GLU 4.9 1.4 - - - +
436B VAL* 1.3 71.7 - - - +
438B ILE* 1.3 74.7 + - - +
439B HIS* 3.9 10.3 + - + +
456B GLN* 3.5 26.0 - - + +
457B PHE 3.6 2.7 - - - +
458B ASN* 2.7 22.7 + - - +
10C LEU* 4.2 12.6 - - - +
11C PRO* 3.0 27.3 + - + +
12C ARG 4.5 2.2 - - - -
13C PRO* 3.0 25.8 - - - +
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Residues in contact with ILE 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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401B ILE* 3.8 25.6 - - + -
436B VAL* 4.0 15.9 - - + +
437B THR* 1.3 72.1 - - - +
439B HIS* 1.3 58.2 + - - +
440B VAL* 3.8 3.3 + - + +
456B GLN* 3.1 5.4 - - - -
457B PHE* 2.8 77.2 + - + +
459B LEU* 5.3 1.3 - - + -
472B ILE* 4.7 0.2 - - + -
474B VAL* 3.9 20.9 - - + -
486B VAL* 4.2 9.4 - - + -
488B ALA* 3.8 9.0 - - + -
10C LEU* 3.7 32.8 - - + -
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Residues in contact with HIS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ILE* 3.1 10.3 - - - +
402B GLU* 2.8 60.0 + - + +
437B THR* 3.9 12.3 + - + +
438B ILE* 1.3 71.3 - - - +
440B VAL* 1.3 64.1 + - - +
441B LEU* 3.6 17.8 + - + +
448B ALA* 5.8 0.9 - - + -
453B SER* 2.8 34.8 + - - -
455B GLY 3.6 10.8 - - - -
456B GLN* 4.0 16.8 - - + -
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Residues in contact with VAL 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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400B GLY 3.5 3.1 - - - -
401B ILE* 4.4 0.2 - - - -
438B ILE* 4.3 11.2 - - + +
439B HIS* 1.3 74.0 - - - +
441B LEU* 1.3 59.0 + - - +
453B SER* 3.6 5.2 - - - -
454B LEU* 2.8 39.5 + - + -
455B GLY 2.9 16.7 + - - +
476B PHE* 3.8 26.7 - - + -
484B LEU* 4.1 7.6 - - + -
486B VAL* 4.0 26.2 - - + -
499B ILE* 4.1 16.6 - - + -
501B ILE* 3.7 21.5 - - + -
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Residues in contact with LEU 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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399B LEU* 3.4 6.9 - - - +
400B GLY 2.8 33.2 + - - +
402B GLU* 3.7 25.1 - - + +
408B MET* 3.7 27.9 - - + +
439B HIS* 3.6 35.2 - - + +
440B VAL* 1.3 77.9 - - - +
442B GLN* 1.3 61.0 + - - +
448B ALA* 3.7 43.5 - - + +
451B ASN* 4.1 4.3 - - + +
452B LYS 3.3 7.6 - - - +
453B SER* 3.9 12.8 - - - +
454B LEU* 4.4 4.3 - - - +
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Residues in contact with GLN 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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395B THR* 5.3 1.6 + - - -
396B PRO* 4.4 17.0 - - - +
397B LEU* 3.7 30.8 + - + +
398B SER 3.3 2.9 - - - -
399B LEU* 3.7 21.9 - - + +
441B LEU* 1.3 75.3 - - - +
443B GLY* 1.3 61.1 + - - +
451B ASN* 3.5 3.9 - - - +
452B LYS* 2.8 41.7 + - + +
454B LEU* 4.0 11.6 - - + +
505B SER 4.9 4.0 + - - -
506B GLY* 3.4 9.2 - - - -
507B LEU* 2.9 42.1 + - - +
515B MET* 4.3 1.9 - - - +
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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