Contacts of the helix formed by residues 94 - 99 (chain D) 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 THR 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D TYR* 4.0 15.7 - - - +
67D TRP 3.3 3.4 - - - -
68D LEU* 5.0 0.7 - - - +
69D THR* 3.4 27.1 - - - +
70D ASN 4.6 0.7 - - - +
71D ILE* 4.0 27.6 - - + +
90D MSE 2.6 25.1 + - - +
91D TYR* 3.1 9.3 + - - -
93D ALA* 1.3 81.6 - - + +
95D GLN* 1.3 58.7 + - - +
96D TRP 3.0 5.2 + - - -
97D GLN* 3.1 4.7 + - - +
98D GLY* 2.8 34.8 + - - -
107D LEU* 5.0 2.3 - - - +
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B TYR* 5.9 0.7 - - - -
242B GLN* 4.0 18.5 + - - +
243B HIS* 4.6 6.6 + - - +
244B ASP* 5.0 1.6 - - - +
265B MSE 4.0 20.4 - - + +
290B ARG* 4.7 0.7 + - - -
67D TRP* 3.3 26.3 + - + +
91D TYR* 3.3 19.7 + - + +
92D ASP* 2.9 43.6 + - - +
93D ALA 3.7 0.4 - - - -
94D THR* 1.3 76.3 - - - +
96D TRP* 1.3 63.8 + - - +
97D GLN 3.2 0.7 + - - -
98D GLY 4.0 1.7 + - - -
99D MSE 3.3 51.0 + - + +
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Residues in contact with TRP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP* 2.8 35.0 + - - -
50B GLY* 5.1 2.5 - - - -
214B TYR* 6.0 1.1 - + - -
264B GLU* 5.0 8.5 - - + -
265B MSE 3.7 36.1 - - + -
287B ASP* 5.6 0.2 - - - -
290B ARG* 2.8 48.6 + - - +
314B HIS* 4.0 32.3 - + - -
601B GOL 5.2 7.4 - - - -
65D HIS* 4.1 21.7 + + + -
67D TRP* 2.9 42.5 + + + +
68D LEU* 4.1 25.5 - - + +
95D GLN* 1.3 73.0 - - - +
97D GLN* 1.3 63.2 + - + +
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Residues in contact with GLN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY* 3.3 7.6 - - - -
51B SER* 2.9 47.5 + - - -
54B ALA* 5.1 0.2 - - - +
101B GLY* 5.4 1.8 - - - -
102B LEU* 4.0 29.5 + - + +
105B PHE* 3.8 20.4 - - + -
58D TYR* 3.6 30.8 + - + +
61D ILE* 3.3 15.0 - - - +
68D LEU* 3.2 26.9 - - + +
69D THR 6.1 0.2 - - - +
94D THR* 3.1 3.9 + - - +
95D GLN 4.2 0.2 - - - -
96D TRP* 1.3 79.1 - - + +
98D GLY* 1.3 59.1 + - - +
99D MSE 3.8 1.3 - - - -
100D ARG 4.4 2.6 - - - +
103D GLY* 4.3 3.8 - - - -
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Residues in contact with GLY 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TYR* 3.8 13.5 - - - -
91D TYR* 4.7 1.6 - - - -
94D THR* 2.8 22.4 + - - -
97D GLN* 1.3 80.3 - - - +
99D MSE 1.3 65.2 + - - +
100D ARG 3.2 4.5 - - - -
103D GLY* 4.1 9.8 - - - -
104D MSE 3.1 27.5 + - - +
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Residues in contact with MSE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B HIS* 3.6 31.2 - - + +
244B ASP* 4.0 15.3 - - - +
265B MSE 3.7 29.6 - - + +
266B SER* 5.6 0.7 - - - -
290B ARG* 5.2 0.9 - - - +
91D TYR* 3.4 30.4 + - + +
94D THR 4.2 0.2 + - - -
95D GLN* 3.3 49.5 + - + +
97D GLN 3.8 0.8 - - - -
98D GLY* 1.3 77.9 - - - +
100D ARG* 1.3 84.0 + - + +
104D MSE 3.4 2.0 - - - +
268D THR* 3.1 18.0 - - - +
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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