Contacts of the strand formed by residues 364 - 368 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLY* 6.2 1.8 - - - -
207A PRO 4.2 0.2 + - - -
208A ASN 2.4 37.4 + - - -
209A ASN* 3.1 16.1 + - - +
210A PRO* 3.5 25.4 - - + -
212A GLY* 3.6 10.1 - - - -
240A TYR* 3.7 40.6 - + - -
342A THR* 4.5 0.4 - - - +
358A GLY* 3.9 2.8 - - - -
359A GLY 3.1 20.8 + - - -
362A ALA* 3.2 16.9 + - + +
363A PRO* 1.3 87.8 - - + +
365A VAL* 1.3 65.8 + - - +
404A ARG* 4.1 17.9 - - + -
405A VAL 3.3 15.5 - - - +
406A SER* 3.7 10.3 - - - +
407A ALA* 4.3 1.1 - - - +
408A PHE* 5.5 2.7 - + - -
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PRO 4.8 0.4 - - - -
342A THR* 4.0 14.8 - - - +
345A ILE* 3.5 30.3 - - + -
346A ILE* 3.8 29.6 - - + +
349A PHE* 4.9 1.3 - - + -
356A VAL* 4.7 6.5 - - + -
357A TYR 3.7 11.4 - - - +
359A GLY* 4.1 5.6 - - - -
364A TYR* 1.3 80.7 - - - +
366A TRP* 1.3 61.1 + - - +
367A VAL* 3.6 21.5 - - + -
403A VAL 3.7 0.7 - - - +
404A ARG* 3.4 7.4 - - - +
405A VAL* 2.8 37.0 + - + +
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Residues in contact with TRP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PRO* 3.7 19.0 - - + +
189A PHE* 3.8 27.4 - + - -
210A PRO* 3.5 40.8 - - + +
211A THR* 3.7 36.1 - - + +
356A VAL* 3.3 2.6 - - - -
357A TYR* 2.8 44.8 + - + +
365A VAL* 1.3 73.2 - - - +
367A VAL* 1.3 60.4 + - - +
392A GLY* 3.6 29.8 - - - -
395A PHE* 4.5 0.4 - + - -
398A GLY 4.4 0.9 + - - -
399A GLY 3.9 7.0 - - - -
402A PHE* 3.2 58.1 - + + -
404A ARG* 3.9 19.7 - - + -
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 3.7 33.9 - - + -
354A TYR* 4.0 17.9 - - + -
355A ASP 3.7 3.1 - - - +
356A VAL* 4.2 6.5 - - + +
365A VAL* 3.6 29.2 - - + -
366A TRP* 1.3 73.7 - - - +
368A HIS* 1.3 64.4 + - - +
369A PHE* 3.5 25.9 + - + -
402A PHE* 3.0 8.7 - - - -
403A VAL 2.9 42.1 + - - +
405A VAL* 4.2 9.2 - - + -
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Residues in contact with HIS 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PRO* 5.7 2.0 - - + +
354A TYR* 3.0 28.8 - - - +
355A ASP* 2.9 40.8 + - + +
357A TYR* 5.0 4.5 - - - -
366A TRP 3.9 0.6 + - - -
367A VAL* 1.3 69.9 - - - +
369A PHE* 1.3 61.1 + - - +
370A PRO* 3.5 38.2 - - + +
400A GLU 5.2 0.4 - - - -
401A GLY 3.0 22.8 + - - -
402A PHE* 3.6 38.7 - + + -
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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