Contacts of the helix formed by residues 418 - 422 (chain A) in PDB entry 3N9Z
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 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PHE* 3.3 78.3 - + + -
73A LYS* 5.1 1.8 - - - -
75A GLU* 3.4 19.9 - - + +
355A LEU* 4.7 0.8 - - - +
357A ARG* 3.4 20.7 + - - +
411A PHE* 3.6 14.4 - + - -
414A LEU* 5.0 1.8 - - + -
417A GLY* 1.3 74.8 - - - +
419A GLY* 1.3 88.4 + - - +
420A VAL 4.0 0.2 + - - -
421A ARG 4.1 0.2 + - - -
422A GLN* 3.5 10.4 + - - +
426A ARG* 5.7 0.7 - - - +
601A HEM 3.5 5.1 + - - -
53C SER* 4.0 18.7 + - - -
54C THR* 6.1 4.7 - - + -
77C MET* 5.7 5.8 - - + -
80C LEU* 3.3 54.5 - - + +
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Residues in contact with GLY 419 (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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75A GLU* 4.5 0.7 - - - -
418A TRP* 1.3 102.0 - - - +
420A VAL* 1.3 64.4 + - - -
422A GLN* 3.0 31.0 + - - +
51C ALA 3.0 7.7 - - - +
52C CYS* 4.3 11.6 - - - +
53C SER* 5.5 1.3 - - - -
77C MET* 5.4 3.4 - - - +
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Residues in contact with VAL 420 (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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75A GLU* 4.6 4.9 + - - +
76A GLY 5.1 1.8 - - - +
77A PRO* 3.9 9.6 - - + +
79A PRO* 3.7 31.0 - - + -
108A TRP* 3.6 18.4 - - + -
109A LYS* 4.9 3.1 - - - +
112A ARG* 3.4 24.2 + - - +
116A ASN* 5.0 2.8 + - - -
418A TRP 4.0 0.2 + - - -
419A GLY* 1.3 72.1 - - - -
421A ARG* 1.3 59.3 + - - +
422A GLN 3.5 0.7 - - - -
45C ALA* 3.5 33.0 - - + +
46C CYS* 4.0 10.3 - - + +
51C ALA 3.9 6.8 - - - +
52C CYS* 3.7 16.6 - - + -
54C THR* 5.3 2.9 - - + -
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Residues in contact with ARG 421 (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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79A PRO* 3.0 41.3 + - + +
80A GLU* 4.0 12.8 - - - +
81A ARG* 2.8 50.6 + - - +
83A LEU* 5.4 2.8 - - - +
100A VAL 2.9 20.8 + - - -
101A LEU 3.3 15.2 + - - -
103A LYS 2.8 29.4 + - - -
104A LYS* 4.5 5.7 - - - +
105A SER 5.6 0.2 - - - +
108A TRP* 3.2 31.3 - - + +
112A ARG* 3.7 3.1 + - - +
357A ARG* 4.1 12.8 - - - +
418A TRP 4.1 1.4 + - - -
419A GLY 3.2 1.0 - - - -
420A VAL* 1.3 79.4 - - - +
422A GLN* 1.3 63.5 + - - +
601A HEM 2.7 26.4 + - - +
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Residues in contact with GLN 422 (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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112A ARG* 2.9 23.5 + - - +
120A MET* 3.9 12.2 - - + +
416A PHE 3.4 11.7 - - - +
417A GLY 4.0 0.7 - - - -
418A TRP 3.5 16.7 + - - +
419A GLY 3.0 15.8 + - - +
420A VAL 3.5 0.2 - - - -
421A ARG* 1.3 84.5 - - - +
423A CYS* 1.3 72.0 + - - +
424A LEU 3.1 0.5 + - - -
426A ARG* 3.0 49.2 - - - +
427A ARG* 5.0 1.6 - - - +
601A HEM 3.6 12.4 - - - +
51C ALA 3.0 26.2 - - - +
77C MET* 3.7 16.7 - - - +
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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
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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