Contacts of the helix formed by residues 76 - 82 (chain A) in PDB entry 4NZP
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 TYR 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLU* 3.5 18.6 - - - -
72A PHE* 3.1 20.5 + - + +
75A ASP* 1.3 94.6 - - + +
77A VAL* 1.3 66.1 + - - +
79A PRO* 3.5 3.3 - - - +
80A MET* 3.3 23.9 + - - +
97A ILE* 3.5 33.0 - - + +
100A PRO* 4.1 1.1 - - + -
101A LEU* 3.4 48.2 - - + +
104A LYS* 3.4 22.0 + - - +
322A TRP* 3.5 41.3 - + - -
323A PHE* 3.4 19.4 - + - -
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Residues in contact with VAL 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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72A PHE* 2.9 57.6 + - + +
73A VAL* 3.7 15.7 - - + -
76A TYR* 1.3 70.1 - - - +
78A PHE* 1.3 74.4 + - + +
80A MET* 3.1 4.9 + - - +
81A PHE* 3.1 47.9 + - + -
97A ILE* 4.5 9.4 - - + -
187A LEU* 4.2 10.1 - - + -
247A LEU* 4.2 19.3 - - + -
286A LEU* 5.1 2.2 - - + -
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Residues in contact with PHE 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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73A VAL* 2.8 49.2 + - + +
74A LYS* 4.3 7.4 - - - +
77A VAL* 1.3 76.4 - - + +
79A PRO* 1.4 67.1 - - + +
81A PHE* 3.2 14.0 + - + +
82A ARG* 3.2 16.3 + - - +
231A GLY 5.3 0.3 - - - +
232A ASP* 3.4 35.4 - - + +
233A LEU* 3.3 40.6 - - + -
243A PRO* 4.3 14.8 - - + -
246A LEU* 4.3 13.0 - - + -
247A LEU* 5.1 6.5 - - + -
286A LEU* 3.9 26.5 - - + -
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Residues in contact with PRO 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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74A LYS 3.2 21.3 - - - +
75A ASP* 3.5 20.6 - - - +
76A TYR 3.5 15.0 - - - +
78A PHE* 1.4 89.6 - - + +
80A MET* 1.3 60.9 + - - +
82A ARG* 3.4 37.5 - - - +
83A ALA 4.2 1.0 + - - -
313A TYR* 3.6 1.5 + - - -
322A TRP* 4.2 10.5 - - + -
327A ARG* 5.6 0.2 - - - +
331A GLN* 3.2 31.7 + - + +
334A ILE* 4.5 0.3 - - - +
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Residues in contact with MET 80 (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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76A TYR 3.3 13.9 + - - +
77A VAL* 3.1 4.5 + - - +
79A PRO* 1.3 78.4 - - - +
81A PHE* 1.3 89.4 + - + +
83A ALA* 3.1 20.4 + - - +
85A ALA* 3.6 22.1 + - + +
92A LEU 3.8 19.3 - - - +
93A LEU* 3.6 31.6 - - - -
97A ILE* 3.9 33.2 - - + -
187A LEU* 3.9 2.5 - - + -
313A TYR* 3.5 13.2 + - - +
317A ILE* 3.6 16.6 - - + -
322A TRP* 4.4 0.9 - - + -
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Residues in contact with PHE 81 (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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77A VAL* 3.1 39.9 + - + +
78A PHE* 3.2 6.7 + - + +
80A MET* 1.3 95.4 - - + +
82A ARG* 1.3 62.0 + - - +
83A ALA 2.9 5.6 - - - -
84A ASN* 2.9 15.9 + - - +
85A ALA 4.9 4.3 - - - +
92A LEU* 4.5 19.5 - - + -
187A LEU* 4.1 11.2 - - + -
231A GLY 5.6 0.2 - - - -
283A GLY* 3.2 40.4 - - - -
286A LEU* 3.7 30.1 - - + -
287A LEU* 3.8 24.9 - - + -
290A HIS* 3.2 19.4 + - + -
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Residues in contact with ARG 82 (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 LYS 4.7 3.2 + - - -
78A PHE 3.2 12.0 + - - +
79A PRO* 3.4 41.6 - - - +
80A MET 3.2 0.4 - - - -
81A PHE* 1.3 75.8 - - - +
83A ALA* 1.3 57.5 + - - +
230A LYS 4.3 6.6 + - - -
231A GLY 4.4 3.8 + - - +
232A ASP* 2.7 39.9 + - - +
290A HIS* 3.1 18.2 - - - -
294A GLU* 3.5 0.2 - - - +
306A LYS* 2.8 26.5 + - - +
331A GLN* 4.1 0.6 - - - +
334A ILE* 3.6 12.3 - - + -
335A ASP* 3.0 37.6 + - - -
338A GLN* 3.8 25.3 + - + +
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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