Contacts of the helix formed by residues 38 - 47 (chain B) in PDB entry 3GZN
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 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLY 4.6 7.6 - - - -
33B ASP* 3.4 31.8 + - + -
36B GLY 2.9 1.8 + - - -
37B ARG* 1.3 115.9 - - + +
39B ASN* 1.3 57.2 + - - +
40B HIS 3.0 6.5 - - - -
41B VAL* 2.8 37.3 + - + -
42B LYS* 2.9 21.4 + - + +
63B LEU* 3.7 37.5 - - + -
67B LEU* 3.6 28.0 - - + +
89B ALA 3.5 19.1 - - - -
90B LEU* 3.7 23.8 - - + -
92B GLY* 3.8 15.7 - - - -
93B PHE 5.5 0.4 - - - -
94B ARG* 4.2 4.3 - - - -
136B VAL* 5.4 0.9 - - + -
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Residues in contact with ASN 39 (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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75A GLU* 3.3 29.4 + - + +
35B GLU* 5.1 4.9 + - - -
36B GLY* 2.9 34.9 + - - +
37B ARG 3.3 0.4 - - - -
38B TRP* 1.3 76.6 - - - +
40B HIS* 1.3 61.2 + - - +
41B VAL 3.3 0.4 + - - -
42B LYS* 4.0 25.8 + - - +
43B LYS* 3.5 38.2 + - - +
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Residues in contact with HIS 40 (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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75A GLU* 3.3 50.4 + - + +
76A ASP* 4.7 5.2 - - - -
78A GLY 6.0 0.2 - - - -
79A ASN* 3.4 36.1 + - + +
494A ALA 4.8 2.0 + - - -
495A ALA* 3.7 15.0 - - - +
496A GLU* 3.0 44.0 + - + +
497A PRO* 4.5 9.7 - - + +
498A HIS 5.5 0.2 - - - +
37B ARG 4.7 2.6 + - - +
38B TRP 2.9 1.2 + - - -
39B ASN* 1.3 79.0 - - - +
41B VAL* 1.3 63.6 + - + +
43B LYS* 4.9 2.0 - - - -
44B PHE* 3.4 24.4 - - - -
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Residues in contact with VAL 41 (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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497A PRO* 6.6 0.2 - - + -
38B TRP* 2.8 20.0 + - + +
40B HIS* 1.3 83.4 - - + +
42B LYS* 1.3 64.9 + - - +
43B LYS 3.3 2.0 - - - -
44B PHE* 3.0 24.2 + - - +
45B LEU* 3.7 19.2 + - + +
63B LEU* 4.1 15.3 - - + -
66B LEU* 5.4 0.4 - - + -
90B LEU 4.1 11.9 - - - +
91B SER* 3.9 27.1 - - - +
329B PHE* 3.8 28.0 - - + -
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Residues in contact with LYS 42 (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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36B GLY 6.3 0.2 - - - -
38B TRP* 2.9 20.6 + - - +
39B ASN* 4.1 26.0 + - - +
40B HIS 3.7 0.4 - - - -
41B VAL* 1.3 77.8 - - - +
43B LYS* 1.3 59.5 + - + +
45B LEU* 2.9 6.6 + - + +
46B GLU* 2.8 66.0 + - + +
60B THR 5.9 1.3 - - - -
63B LEU* 3.8 31.5 - - + +
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Residues in contact with LYS 43 (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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75A GLU* 5.7 1.6 + - - -
452A VAL* 3.7 22.4 + - - +
454A ASN* 5.4 0.7 - - - +
491A ARG* 3.9 18.8 + - - +
492A TYR 3.9 12.1 + - - +
493A GLY* 3.3 23.2 + - - -
495A ALA* 4.4 11.3 - - + +
39B ASN* 3.5 28.8 + - - +
40B HIS* 5.1 2.1 - - - +
41B VAL 3.3 0.6 + - - -
42B LYS* 1.3 78.3 - - + +
44B PHE* 1.3 68.9 + - + +
46B GLU* 4.3 0.7 - - - -
47B ARG* 3.2 61.1 + - - +
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Residues in contact with PHE 44 (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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164A GLY* 4.3 0.7 - - - -
165A LEU* 4.1 10.5 - - + -
491A ARG* 3.2 26.7 + - + +
492A TYR* 3.7 29.2 - + - -
495A ALA* 4.1 14.6 - - + -
497A PRO* 3.7 29.6 - - + -
40B HIS 3.4 26.2 - - - -
41B VAL* 3.0 12.0 + - - +
43B LYS* 1.3 81.2 - - + +
45B LEU* 1.3 59.2 + - - +
56B PHE* 3.3 13.9 - - - -
329B PHE* 4.4 22.9 - + + -
335B ALA* 3.7 9.7 - - + +
336B TYR* 3.5 34.5 - + - -
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Residues in contact with LEU 45 (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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41B VAL* 4.0 26.0 - - + +
42B LYS* 2.9 6.8 + - - +
44B PHE* 1.3 87.5 - - - +
46B GLU* 1.3 62.8 + - + +
47B ARG 3.4 1.3 - - - -
56B PHE* 3.4 11.4 - - + -
57B GLU 4.3 0.9 - - - +
58B PRO* 3.4 8.3 - - - +
59B SER 3.3 22.1 + - - +
62B SER* 4.1 22.2 + - - +
63B LEU* 3.7 39.3 - - + +
66B LEU* 4.9 3.1 - - + -
329B PHE* 4.3 5.2 - - + -
333B THR* 3.6 43.5 - - + +
335B ALA* 4.7 0.7 - - + -
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Residues in contact with GLU 46 (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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454A ASN* 4.1 20.3 + - - +
42B LYS* 2.8 57.9 + - + +
43B LYS* 5.1 0.2 - - - -
45B LEU* 1.3 74.6 - - + +
47B ARG* 1.3 64.3 + - + +
58B PRO* 3.4 16.0 - - - +
59B SER 3.5 20.9 + - - +
60B THR* 3.7 32.2 - - + +
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Residues in contact with ARG 47 (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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451A GLY 2.7 30.4 + - - -
452A VAL 3.2 18.6 + - - -
453A SER 3.8 2.2 - - - -
454A ASN* 3.3 28.6 + - - +
457A VAL* 3.6 24.3 - - - +
490A CYS 3.2 6.5 + - - -
491A ARG* 2.6 55.3 + - + +
493A GLY* 3.9 0.8 - - - -
43B LYS* 3.2 40.7 + - - +
46B GLU* 1.3 84.6 - - + +
48B SER* 1.3 67.0 + - - +
56B PHE* 3.2 22.2 - - - -
58B PRO* 4.1 0.7 - - - -
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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