Contacts of the helix formed by residues 393 - 400 (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 SER 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A GLN* 6.2 1.8 - - - -
374A SER* 2.9 18.9 + - - -
375A TRP* 3.4 25.2 - - - -
391A PRO* 4.6 0.2 - - - +
392A GLY* 1.3 70.8 - - - +
394A GLY* 1.3 59.1 + - - +
395A PHE 2.9 5.2 + - - -
396A GLY* 3.4 22.7 + - - +
397A PRO* 5.5 1.8 - - - -
399A GLY* 3.4 3.7 + - - -
400A GLU* 3.9 24.6 + - - -
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Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.2 44.0 - - - +
153A PRO* 3.9 14.6 - - - +
375A TRP* 4.4 6.9 - - - +
391A PRO* 2.9 11.8 + - - -
393A SER* 1.3 76.7 + - - +
395A PHE* 1.3 61.6 + - - +
396A GLY 3.4 0.6 + - - -
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.2 1.3 - - + -
39A PHE* 4.0 10.3 - + - -
150A PRO* 3.4 5.8 - - + +
151A SER 2.8 45.2 + - - +
152A TYR* 4.1 0.7 - - - -
153A PRO* 3.7 27.8 - - + -
209A ASN* 3.5 19.1 - - - -
210A PRO* 3.6 34.8 - - + -
366A TRP* 4.5 0.2 - + - -
390A THR* 3.4 30.5 - - + -
391A PRO 3.9 7.9 - - - -
392A GLY* 2.7 25.7 + - - +
394A GLY* 1.3 74.7 - - - +
396A GLY* 1.3 55.9 + - - +
404A ARG* 3.1 34.3 - - + -
433A MLT 4.7 0.2 - - - -
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Residues in contact with GLY 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASP* 3.5 4.7 - - - -
150A PRO* 4.9 0.2 - - - -
173A GLN* 5.7 0.2 - - - -
180A TYR* 5.3 4.0 - - - -
393A SER* 3.4 15.8 + - - -
394A GLY 3.4 1.6 + - - -
395A PHE* 1.3 77.4 - - - +
397A PRO* 1.4 70.0 - - - +
398A GLY 3.3 2.9 - - - -
399A GLY* 2.9 23.8 - - - -
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Residues in contact with PRO 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASP* 3.4 19.5 - - - +
172A VAL 3.5 20.6 - - - +
173A GLN* 3.2 35.4 - - + +
174A LYS* 3.8 17.9 - - + -
180A TYR* 4.1 11.7 - - + -
182A ARG* 5.1 3.0 + - - +
393A SER* 5.6 2.9 - - - -
396A GLY* 1.4 80.0 - - - +
398A GLY* 1.3 55.2 + - - +
400A GLU* 3.3 23.4 + - + +
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Residues in contact with GLY 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASP* 2.5 35.4 + - - +
150A PRO* 3.8 18.7 - - - +
182A ARG* 4.2 15.4 - - - +
183A CYS 5.0 2.3 - - - +
184A THR* 5.9 2.4 - - - +
366A TRP* 4.4 1.0 + - - -
396A GLY 3.3 0.6 + - - -
397A PRO* 1.3 65.3 - - - +
399A GLY* 1.3 49.6 + - - -
400A GLU 3.7 2.2 - - - +
402A PHE* 4.1 17.5 - - - -
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Residues in contact with GLY 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PRO* 3.7 13.0 - - - +
366A TRP* 3.9 3.6 - - - -
392A GLY* 3.2 38.9 - - - -
393A SER 3.6 0.2 - - - -
396A GLY 2.9 26.0 - - - -
398A GLY* 1.3 63.2 + - - -
400A GLU* 1.3 64.7 + - - +
402A PHE* 3.4 12.3 + - - +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A HIS* 5.2 0.5 - - - -
372A GLN 3.7 4.8 - - - +
373A SER* 3.4 14.8 - - - -
374A SER* 2.6 45.7 + - - -
375A TRP* 5.5 1.4 + - - -
393A SER* 3.9 16.7 + - - +
397A PRO* 3.3 15.3 + - + +
398A GLY* 4.2 3.6 - - - +
399A GLY* 1.3 74.1 - - - +
401A GLY* 1.3 50.4 + - - +
402A PHE* 3.5 16.1 - - - -
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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