Contacts of the helix formed by residues 393 - 400 (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 SER 393 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374B SER* 2.8 23.4 + - - -
375B TRP* 3.1 31.2 + - - -
391B PRO* 3.9 1.9 - - - +
392B GLY* 1.3 72.0 - - - +
394B GLY* 1.3 60.7 + - - +
395B PHE 3.0 6.1 + - - -
396B GLY* 3.1 23.1 + - - +
397B PRO* 6.0 0.7 - - - -
399B GLY 3.5 3.8 + - - -
400B GLU* 3.7 22.1 + - - -
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Residues in contact with GLY 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.8 36.4 - - - +
153B PRO* 3.9 11.6 - - - +
375B TRP* 4.6 5.1 - - - +
391B PRO* 3.1 16.2 + - - +
393B SER* 1.3 78.1 + - - +
395B PHE* 1.3 62.2 + - - +
396B GLY 3.4 0.8 + - - -
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Residues in contact with PHE 395 (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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38B LEU* 4.4 2.5 - - + -
39B PHE* 4.3 11.9 - + - -
150B PRO* 3.2 21.8 - - + +
151B SER 3.0 42.9 + - - +
152B TYR* 4.3 2.0 - + - -
153B PRO* 4.0 19.3 - - + -
209B ASN* 4.0 11.7 - - - -
210B PRO* 3.6 27.6 - - + -
390B THR* 3.4 33.2 - - + -
391B PRO 3.8 7.2 - - - -
392B GLY* 2.9 17.0 + - - +
394B GLY* 1.3 80.9 - - - +
396B GLY* 1.3 57.9 + - - +
404B ARG* 3.3 35.2 - - + -
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Residues in contact with GLY 396 (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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149B ASP* 3.6 4.9 - - - -
180B TYR* 5.2 5.4 - - - -
393B SER* 3.1 19.1 + - - +
394B GLY 3.4 1.8 + - - -
395B PHE* 1.3 78.3 - - - +
397B PRO* 1.4 71.8 - - - +
398B GLY 3.3 3.1 - - - -
399B GLY* 2.9 21.2 - - - -
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Residues in contact with PRO 397 (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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149B ASP* 3.6 10.5 - - - +
172B VAL 3.6 16.8 - - - +
173B GLN* 3.6 24.4 - - + +
174B LYS* 3.6 35.7 - - + -
180B TYR* 4.2 10.3 - - + -
182B ARG* 4.6 5.0 + - - -
393B SER* 5.7 1.3 - - - -
396B GLY* 1.4 82.5 - - - +
398B GLY* 1.3 56.0 + - - +
400B GLU* 2.9 30.6 + - + +
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Residues in contact with GLY 398 (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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149B ASP* 2.7 32.4 + - - +
150B PRO* 3.6 14.0 - - - +
182B ARG* 4.0 22.3 + - - +
183B CYS 4.5 5.4 - - - +
184B THR* 5.5 2.4 - - - +
366B TRP* 4.5 1.0 + - - -
397B PRO* 1.3 72.1 - - - +
399B GLY* 1.3 51.5 + - - +
400B GLU 3.5 8.0 - - - +
402B PHE* 4.1 12.0 - - - -
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Residues in contact with GLY 399 (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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150B PRO* 3.5 19.7 - - - +
366B TRP* 3.6 6.6 - - - -
392B GLY* 3.1 33.1 - - - -
396B GLY 2.9 23.8 - - - -
398B GLY* 1.3 61.8 + - - -
400B GLU* 1.3 59.9 + - - -
402B PHE* 3.1 20.5 + - - -
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Residues in contact with GLU 400 (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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182B ARG* 5.3 3.5 + - - -
368B HIS* 5.5 0.3 - - - -
372B GLN 3.7 1.9 - - - +
373B SER* 3.3 23.1 - - - -
374B SER* 3.1 18.5 + - - -
375B TRP* 5.3 1.2 + - - -
393B SER* 3.7 18.7 + - - +
396B GLY 4.0 1.0 + - - -
397B PRO* 2.9 21.2 + - + +
398B GLY* 3.8 5.4 - - - +
399B GLY* 1.3 71.7 - - - -
401B GLY* 1.3 79.3 + - - +
402B PHE* 3.6 14.1 - - - -
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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