Contacts of the helix formed by residues 457 - 461 (chain A) in PDB entry 3NA0
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 TRP 457 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A PHE* 3.2 77.1 - + + -
112A LYS* 5.2 8.1 - - + -
114A GLU* 3.3 18.6 - - + +
396A ARG* 3.3 15.1 + - - +
450A PHE* 3.4 28.2 - + - -
453A LEU* 5.0 3.4 - - + -
456A GLY* 1.3 74.2 - - - +
458A GLY* 1.3 94.6 + - - +
460A ARG 3.9 0.5 + - - -
461A GLN* 3.3 15.1 + - - +
601A HEM 3.5 6.5 + - - -
53C SER* 4.2 18.9 + - - -
54C THR* 6.0 6.3 - - + -
77C MET* 6.4 1.1 - - - -
80C LEU* 3.1 44.8 + - + +
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Residues in contact with GLY 458 (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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114A GLU* 4.6 0.7 - - - -
457A TRP* 1.3 106.4 - - - +
459A VAL* 1.3 63.2 + - - -
460A ARG 3.1 1.2 + - - -
461A GLN* 3.0 26.4 + - - +
51C ALA 3.1 5.9 - - - +
52C CYS* 4.2 13.8 - - - +
53C SER* 5.3 1.3 - - - -
77C MET* 6.0 2.6 - - - +
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Residues in contact with VAL 459 (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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114A GLU* 4.7 5.2 + - - +
115A GLY 5.0 2.7 - - - +
116A PRO* 3.9 9.4 - - + +
118A PRO* 3.7 30.1 - - + -
147A TRP* 3.5 19.2 - - + -
148A LYS* 4.6 2.9 - - - +
151A ARG* 3.4 24.0 + - - +
155A ASN* 4.9 2.4 + - - -
457A TRP 3.9 0.2 + - - -
458A GLY* 1.3 71.2 - - - -
460A ARG* 1.3 59.6 + - - +
461A GLN 3.6 0.4 - - - -
45C ALA* 3.5 34.3 - - + +
46C CYS* 3.9 16.4 - - + +
51C ALA 3.7 8.1 - - - +
52C CYS* 4.0 10.1 - - + +
54C THR* 5.5 1.8 - - + -
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Residues in contact with ARG 460 (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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118A PRO* 2.8 53.5 + - + +
119A GLU* 3.9 17.2 - - - +
120A ARG* 2.8 51.8 + - - +
122A LEU* 5.6 2.2 - - - +
139A VAL 3.1 20.2 + - - -
140A LEU 3.4 14.3 + - - -
142A LYS 2.8 28.6 + - - -
143A LYS* 4.7 2.2 - - - +
147A TRP* 3.2 26.9 - - + +
151A ARG* 3.9 2.0 - - - +
396A ARG* 4.1 7.4 - - - +
457A TRP 3.9 3.2 + - - -
458A GLY 3.1 0.8 - - - -
459A VAL* 1.3 77.7 - - - +
461A GLN* 1.3 65.5 + - - +
601A HEM 2.7 30.6 + - - +
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Residues in contact with GLN 461 (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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151A ARG* 2.9 24.3 + - - +
159A MET* 3.7 14.5 - - + +
455A PHE 3.4 12.6 - - - +
456A GLY 3.9 0.9 - - - -
457A TRP* 3.3 15.3 + - - +
458A GLY 3.0 25.1 + - - +
460A ARG* 1.3 83.1 - - - +
462A CYS* 1.3 76.2 + - - +
463A LEU 3.2 0.2 + - - -
465A ARG* 2.9 47.2 - - - +
466A ARG* 4.8 1.0 - - - +
601A HEM 3.7 10.5 - - - +
51C ALA* 3.0 19.8 - - - +
52C CYS 3.9 0.7 + - - -
77C MET* 3.9 12.5 - - - +
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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
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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