Contacts of the helix formed by residues 348 - 354 (chain B) in PDB entry 3NZG
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 GLY 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B GLN* 3.5 20.9 - - - -
346B CYS 3.9 0.6 + - - +
347B ASP* 1.3 76.3 - - - +
349B GLU* 1.3 69.8 + - - -
350B LEU 3.4 2.9 - - - -
351B ARG* 3.5 9.8 + - - +
352B LYS* 3.0 33.3 + - - +
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Residues in contact with GLU 349 (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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22B TYR* 3.0 49.3 + - + +
29B GLN* 2.9 19.6 - - - +
348B GLY* 1.3 74.0 + - - -
350B LEU* 1.3 57.9 + - - +
352B LYS* 2.9 4.2 + - - +
353B TYR* 2.6 66.4 + - + +
382B PHE* 4.0 4.0 - - + -
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Residues in contact with LEU 350 (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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20B VAL* 3.9 18.4 - - + +
22B TYR* 3.1 33.2 - - + -
29B GLN* 2.9 35.7 - - + +
30B ASN* 3.4 40.6 - - - +
31B THR* 4.2 10.3 - - + +
317B LYS 5.5 0.4 - - - +
318B THR* 4.0 16.2 - - + -
319B GLY 4.8 0.3 + - - -
348B GLY 3.4 0.4 - - - -
349B GLU* 1.3 73.9 - - - +
351B ARG* 1.3 64.4 + - - +
354B LEU* 2.9 33.7 + - + +
355B VAL 4.7 0.2 + - - -
382B PHE* 4.3 10.3 - - + -
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Residues in contact with ARG 351 (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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29B GLN* 4.9 0.4 - - - +
316B TRP* 6.2 1.1 - - - +
317B LYS 3.8 17.0 + - - +
318B THR* 3.8 15.4 - - - +
319B GLY* 3.8 14.6 + - - -
322B SER* 3.2 20.4 + - - -
340B TYR* 3.5 10.3 + - - -
341B VAL* 2.6 61.0 + - + +
343B PRO* 3.7 16.0 - - + +
346B CYS* 4.9 8.1 - - - +
348B GLY* 3.5 12.9 + - - +
350B LEU* 1.3 80.4 - - - +
352B LYS* 1.3 63.5 + - + +
354B LEU 4.9 0.3 + - - -
355B VAL* 5.6 2.3 + - - +
358B GLU* 3.1 36.0 + - - +
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Residues in contact with LYS 352 (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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343B PRO* 3.2 47.0 + - + +
346B CYS 3.3 13.2 + - - +
347B ASP* 3.9 18.2 + - - +
348B GLY 3.0 29.5 + - - +
349B GLU* 2.9 8.3 + - - +
351B ARG* 1.3 80.8 - - + +
353B TYR* 1.3 95.0 + - + +
355B VAL 4.5 6.9 - - - +
358B GLU* 4.8 6.4 - - - +
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Residues in contact with TYR 353 (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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349B GLU* 2.6 46.5 + - + +
352B LYS* 1.3 109.9 + - + +
354B LEU* 1.3 64.8 + - - +
355B VAL* 3.2 6.3 + - - +
379B ASN* 2.9 31.0 + - - +
382B PHE* 3.5 36.8 - + + +
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Residues in contact with LEU 354 (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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20B VAL* 4.2 24.9 - - + -
31B THR* 4.0 16.4 - - + -
33B VAL* 4.0 15.0 - - + -
318B THR* 3.8 32.5 - - + +
320B ILE* 4.3 4.5 - - + -
350B LEU* 2.9 26.6 + - + +
352B LYS 3.9 0.2 - - - -
353B TYR* 1.3 75.4 - - - +
355B VAL* 1.3 66.6 + - + +
378B LEU* 3.5 10.9 - - + -
379B ASN* 2.8 23.2 + - - +
382B PHE* 3.9 19.8 - - + -
383B LEU* 5.0 13.9 - - + -
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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