Contacts of the helix formed by residues 72 - 79 (chain A) in PDB entry 2NZ2
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 PHE 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU 3.7 10.5 - - - -
68A PHE* 3.2 19.3 + - + +
70A GLU 3.6 0.4 - - - -
71A GLU* 1.3 86.4 - - + +
73A ILE* 1.3 66.8 + - - +
74A TRP 3.3 0.9 - - - -
75A PRO* 3.3 4.9 - - - +
76A ALA* 3.2 21.1 + - - +
93A LEU* 3.6 29.4 - - + +
96A PRO* 3.7 20.4 - - + -
97A CYS* 3.8 30.5 - - + -
100A ARG* 3.5 41.5 - - - -
326A TRP* 3.4 48.7 - + + -
327A HIS* 5.0 0.4 - + - -
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Residues in contact with ILE 73 (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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68A PHE* 3.0 48.8 + - + +
69A VAL* 3.5 20.2 - - + +
72A PHE* 1.3 73.8 - - - +
74A TRP* 1.3 65.8 + - + +
76A ALA* 3.2 8.2 + - - +
77A ILE* 2.9 35.2 + - + +
93A LEU* 4.6 2.5 - - + -
185A LEU* 5.2 0.7 - - + -
186A MET* 3.9 27.4 - - + +
251A PHE* 3.8 44.4 - - + -
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Residues in contact with TRP 74 (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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69A VAL* 3.0 43.2 + - + -
70A GLU* 3.4 24.5 - - + +
73A ILE* 1.3 78.2 - - + +
75A PRO* 1.4 64.5 - - + +
77A ILE* 3.3 29.1 + - + +
78A GLN* 2.9 29.7 + - - +
231A VAL* 3.5 38.6 - - + +
232A PRO* 3.4 37.9 + - + -
247A SER* 3.9 24.7 - - - -
250A LEU* 4.1 8.3 - - + -
251A PHE* 3.9 21.1 - + - -
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Residues in contact with PRO 75 (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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70A GLU 4.1 2.2 - - - +
71A GLU* 3.4 24.0 - - - +
72A PHE 3.3 15.3 - - - +
74A TRP* 1.4 94.3 - - + +
76A ALA* 1.3 56.2 + - - +
78A GLN* 3.3 19.4 + - - +
79A SER* 3.0 28.1 + - - -
317A PHE* 4.2 7.3 - - + -
326A TRP* 4.3 12.6 - - + -
335A ARG* 4.5 15.3 - - + +
338A ILE* 4.5 4.0 - - + +
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Residues in contact with ALA 76 (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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72A PHE 3.2 14.2 + - - +
73A ILE* 3.2 10.6 + - + +
75A PRO* 1.3 75.3 - - - +
77A ILE* 1.3 60.9 + - + +
79A SER* 2.7 21.3 + - - -
80A SER* 3.8 2.3 + - - -
81A ALA 4.5 4.7 + - - +
88A LEU 5.7 0.4 - - - +
89A LEU* 5.3 3.8 - - + -
93A LEU* 3.7 33.4 - - + -
186A MET* 5.6 2.7 - - + -
317A PHE* 3.6 16.0 - - + -
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Residues in contact with ILE 77 (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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73A ILE* 2.9 20.7 + - + +
74A TRP* 3.5 43.5 - - + +
76A ALA* 1.3 73.5 - - + +
78A GLN* 1.3 68.6 + - - +
80A SER* 3.1 8.4 + - - +
186A MET* 6.1 2.9 - - + -
227A PHE* 4.6 5.6 - - + -
230A GLY 3.6 11.2 - - - +
232A PRO* 4.2 5.4 - - + -
251A PHE* 5.1 0.2 - - + -
287A GLY* 6.0 2.0 - - - +
290A LEU* 4.1 32.5 - - + +
291A TYR* 5.5 3.1 - - - +
294A HIS* 2.9 48.8 + - + -
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Residues in contact with GLN 78 (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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74A TRP 2.9 17.9 + - - +
75A PRO* 3.3 22.0 + - - +
77A ILE* 1.3 77.9 - - - +
79A SER* 1.3 49.9 + - - +
80A SER 3.1 0.5 + - - -
229A LYS* 2.8 24.4 + - - +
230A GLY 3.9 4.9 - - - +
231A VAL* 3.8 15.8 - - + +
294A HIS* 3.3 14.6 + - - -
310A LYS* 2.6 30.8 + - - -
335A ARG 5.0 1.2 - - - +
338A ILE* 3.8 9.5 - - + +
339A ALA* 3.9 24.1 + - - +
342A GLN* 3.7 28.4 + - + +
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Residues in contact with SER 79 (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 PRO 3.0 10.5 + - - -
76A ALA 2.7 18.3 + - - -
77A ILE 3.1 0.6 - - - -
78A GLN* 1.3 76.1 - - - +
80A SER* 1.3 61.2 + - - +
81A ALA* 3.2 16.1 + - - +
310A LYS* 3.0 13.5 + - - +
311A GLN* 3.3 6.4 + - - -
314A GLY* 3.6 23.1 - - - -
317A PHE* 3.6 32.7 - - - -
338A ILE* 3.8 11.0 - - - +
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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