Contacts of the strand formed by residues 439 - 444 (chain B) in PDB entry 4ZTZ
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 PHE 439 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B LYS 3.4 2.8 + - - -
383B VAL* 3.3 12.9 - - + +
384B ALA 2.9 24.4 + - - -
437B ILE* 3.3 7.7 - - - +
438B LEU* 1.3 91.6 - - + +
440B THR* 1.3 63.8 + - - +
455B LEU* 3.6 34.3 - - + -
456B ARG 3.5 2.7 - - - -
457B SER* 3.6 33.2 - - - -
459B ASP* 5.7 1.3 - - - -
474B PHE* 3.8 20.9 - + - -
475B LEU* 3.9 16.8 - - + -
478B TYR* 3.4 56.3 - + - -
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Residues in contact with THR 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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384B ALA* 3.6 7.4 - - - +
386B ASP* 4.1 5.6 - - + +
428B LEU* 5.6 0.9 - - + -
429B TYR* 4.0 19.0 - - + +
432B TYR* 3.6 44.1 - - + +
437B ILE* 5.0 2.1 + - - +
439B PHE* 1.3 74.4 + - - +
441B VAL* 1.3 63.6 + - - +
442B LEU* 3.7 6.3 + - + +
454B HIS* 4.2 0.3 - - - +
455B LEU* 3.3 6.2 + - - -
456B ARG* 2.9 54.6 + - - +
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B VAL* 3.7 23.3 - - + +
384B ALA 3.0 19.4 + - - +
385B LEU* 3.6 29.6 - - + +
386B ASP* 3.3 17.3 + - - +
402B LEU* 4.1 12.1 - - + -
406B LEU* 5.3 1.1 - - + -
439B PHE 4.0 1.2 - - - -
440B THR* 1.3 72.2 - - - +
442B LEU* 1.3 62.7 + - - +
443B VAL* 4.6 0.4 - - + -
453B ILE* 3.6 26.0 - - + -
454B HIS 3.3 5.2 - - - -
455B LEU* 4.4 2.0 - - + -
471B LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 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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386B ASP* 4.0 11.0 - - + -
387B VAL 3.7 13.9 - - - +
388B GLY* 3.4 39.7 - - - +
389B ARG* 6.0 0.7 - - + -
425B LEU* 6.2 4.9 - - + -
429B TYR* 5.6 8.5 - - - +
440B THR* 3.7 7.8 + - + +
441B VAL* 1.3 73.3 - - - +
443B VAL* 1.3 68.2 - - - +
444B THR* 3.8 6.5 + - - +
453B ILE* 3.3 4.5 - - - +
454B HIS* 2.9 67.7 + - + +
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 3.7 26.0 - - + -
386B ASP 3.7 10.1 + - - +
387B VAL* 3.8 4.5 - - - +
388B GLY 2.9 26.8 + - - +
396B ARG* 4.2 20.2 + - - +
398B VAL* 4.4 11.2 - - + -
399B CYS* 4.1 22.2 - - - -
402B LEU* 4.5 9.2 - - + -
441B VAL* 4.6 0.9 - - + -
442B LEU* 1.3 76.1 - - - +
444B THR* 1.3 61.0 + - - +
447B THR* 3.6 15.0 - - - +
448B LEU* 5.9 0.4 - - + -
453B ILE* 4.2 15.0 - - + -
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Residues in contact with THR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLY* 2.6 21.1 + - - -
389B ARG* 3.1 23.7 - - + +
396B ARG* 4.8 3.4 - - - +
442B LEU* 3.8 12.1 + - - +
443B VAL* 1.3 77.9 - - - +
445B GLU* 1.3 57.5 + - - +
446B THR* 3.1 35.2 - - + +
447B THR* 2.6 44.7 + - + +
448B LEU* 3.0 4.5 + - - +
454B HIS* 4.1 12.6 - - - +
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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