Contacts of the strand formed by residues 364 - 368 (chain B) in PDB entry 2Z1Z
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 TYR 364 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLY* 3.3 25.5 + - - -
208B ASN 4.5 12.8 - - - -
209B ASN* 4.0 14.9 + - - -
210B PRO 3.9 16.4 - - - +
212B GLY* 4.5 5.8 - - - -
240B TYR* 2.8 45.7 + + - -
358B GLY* 3.9 2.1 - - - -
359B GLY* 2.8 22.6 + - - -
362B ALA* 3.1 7.8 + - + +
363B PRO* 1.3 93.4 - - + +
365B VAL* 1.3 64.1 + - - +
366B TRP 4.2 0.5 + - - -
404B ARG* 3.5 44.2 + - + -
405B VAL 3.6 1.6 - - - -
406B SER* 4.0 13.5 - - - -
408B PHE* 3.9 9.3 - + - -
501B PLP 4.4 0.5 + - - -
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B THR* 4.2 13.5 - - - +
345B ILE* 3.5 38.4 - - + -
346B ILE* 4.0 23.8 - - + +
349B PHE* 4.9 2.0 - - + -
356B VAL* 4.3 13.2 - - + -
357B TYR 3.7 8.7 - - - +
359B GLY* 4.4 1.1 - - - +
363B PRO 5.5 0.2 - - - +
364B TYR* 1.3 77.2 - - - +
366B TRP* 1.3 59.4 - - - +
367B VAL* 3.5 25.9 - - + +
403B VAL 3.6 1.2 - - - +
404B ARG* 3.4 8.2 - - - +
405B VAL* 2.8 41.1 + - + +
407B ALA* 5.7 0.2 - - + -
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Residues in contact with TRP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PRO* 3.4 22.6 - - + +
183B CYS 5.3 1.0 + - - -
189B PHE* 3.4 33.4 - + - -
210B PRO* 3.6 35.7 - - + +
211B THR* 3.5 36.4 - - + +
357B TYR* 2.9 43.3 + - + +
364B TYR 4.2 0.6 + - - -
365B VAL* 1.3 71.8 - - - +
367B VAL* 1.3 61.3 + - - +
392B GLY* 3.5 34.8 - - - -
395B PHE* 4.6 0.2 - + - -
398B GLY 4.5 0.6 + - - -
399B GLY 3.6 7.4 - - - -
402B PHE* 3.2 53.7 - + + -
403B VAL 4.1 1.3 - - - -
404B ARG* 4.0 16.2 - - + -
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PHE* 3.7 41.3 - - + -
354B TYR* 3.8 19.7 - - + -
355B ASP 3.5 4.0 - - - +
356B VAL* 4.5 2.5 - - + -
365B VAL* 3.5 28.7 - - + -
366B TRP* 1.3 71.7 - - - +
368B HIS* 1.3 64.4 + - - +
369B PHE* 3.4 28.8 - - + -
402B PHE* 3.1 5.1 - - - -
403B VAL* 2.8 43.9 + - + +
405B VAL* 4.5 7.2 - - + -
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Residues in contact with HIS 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PRO* 5.3 6.8 - - + +
354B TYR* 3.4 24.3 - - - +
355B ASP* 2.9 45.0 + - + +
357B TYR* 4.3 4.0 - + + -
366B TRP 3.8 0.8 + - - -
367B VAL* 1.3 71.3 - - - +
369B PHE* 1.3 64.3 + - - +
370B PRO* 3.6 38.5 - - + +
400B GLU 5.5 0.2 - - - -
401B GLY 3.5 14.7 + - - -
402B PHE* 3.6 39.5 - + + -
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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
------------------------------------------------------------
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