Contacts of the strand formed by residues 360 - 364 (chain B) in PDB entry 5ZR1
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 CYS 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ALA* 4.1 15.5 - - - +
331B ILE* 3.9 20.0 - - + -
335B SER* 5.1 2.0 - - - +
358B ILE 4.3 6.3 - - - +
359B PRO* 1.3 72.0 - - - +
361B LEU* 1.3 60.5 + - - +
362B ILE* 3.1 21.7 + - - +
421B ILE* 3.4 12.6 - - + -
423B VAL* 3.7 28.0 - - - -
24C THR* 4.5 0.6 - - - +
25C VAL* 3.0 37.3 + - + +
27C PRO* 4.7 5.4 - - + -
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PRO 3.8 3.6 + - - -
360B CYS* 1.3 69.2 - - - +
362B ILE* 1.3 67.1 + - - +
363B LEU* 4.8 5.1 - - + +
375B VAL* 4.6 9.6 - - + +
378B GLU* 3.6 23.6 - - + -
379B ILE* 3.7 32.1 - - + -
382B LEU* 4.3 13.5 - - + -
420B LEU* 4.8 5.6 - - + +
421B ILE 3.2 7.0 + - - +
422B LEU* 3.2 17.0 - - + +
423B VAL 3.0 20.6 + - - -
22C HIS* 3.9 12.1 - - + -
23C TYR 3.3 21.5 - - - +
24C THR* 3.4 22.8 - - - +
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Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ARG* 5.2 0.2 - - - +
327B GLU* 3.6 14.8 - - + +
330B ALA* 5.8 0.2 - - + -
331B ILE* 4.7 12.1 - - + -
360B CYS* 3.1 32.3 + - - +
361B LEU* 1.3 76.6 - - - +
363B LEU* 1.3 61.9 + - - +
364B ASN* 4.3 4.5 - - - +
423B VAL* 3.3 20.9 - - + +
425B HIS* 3.5 23.1 - - + -
22C HIS* 3.3 3.8 + - - -
23C TYR* 2.9 79.0 + - + +
25C VAL* 4.9 1.6 - - + -
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 4.8 7.9 - - + +
362B ILE* 1.3 78.6 - - - +
364B ASN* 1.3 60.9 + - - +
365B GLY 3.2 5.4 + - - +
370B CYS* 3.6 19.7 - - - -
375B VAL* 3.7 36.1 - - + -
422B LEU* 5.0 7.4 - - + -
423B VAL 2.8 14.6 + - - +
424B VAL* 4.2 18.4 - - + -
425B HIS* 2.9 28.9 + - - +
432B ILE* 3.6 29.8 - - + -
437B PHE* 4.3 7.0 - - + -
441B LEU* 4.9 5.6 - - + -
22C HIS* 4.1 10.1 - - + +
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Residues in contact with ASN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ARG* 3.9 10.9 - - - +
362B ILE* 4.8 0.4 - - - +
363B LEU* 1.3 71.5 - - - +
365B GLY* 1.3 59.7 + - - +
366B TYR* 2.6 47.2 + - + -
367B ASN* 3.3 22.6 - - + +
370B CYS* 4.1 7.6 - - - +
425B HIS* 3.8 15.3 + - - -
17C ASP 3.6 11.8 - - - +
18C ALA 4.1 2.2 + - - -
20C ARG 2.9 29.5 - - - +
21C SER* 4.3 3.6 - - - -
22C HIS 4.1 7.1 + - - +
23C TYR* 3.7 16.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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