Contacts of the helix formed by residues 82 - 91 (chain F) in PDB entry 4NAW
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 PRO 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F ARG 4.1 8.5 - - - +
42F VAL* 4.6 8.1 - - - +
43F SER 3.4 11.7 - - - +
44F TYR* 4.1 19.3 - - + +
80F HIS 3.9 6.1 - - - +
81F TYR* 1.3 87.4 - - + +
83F ILE* 1.3 67.1 + - - +
85F LEU* 3.0 34.1 + - + +
86F LEU* 3.2 10.2 + - - +
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Residues in contact with ILE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 4.2 9.2 - - + -
39F LEU* 3.9 25.4 - - + -
40F PRO* 3.3 28.7 - - + +
41F ARG 3.5 0.4 + - - -
43F SER* 2.8 18.0 + - - +
44F TYR 3.5 21.5 - - - +
45F LEU* 3.6 25.8 - - + +
48F VAL* 3.8 20.2 - - + -
81F TYR 3.5 2.4 + - - +
82F PRO* 1.3 70.6 - - - +
84F GLY* 1.3 62.6 + - - +
85F LEU 3.3 0.3 + - - -
86F LEU* 3.3 10.6 + - - +
87F PHE* 3.1 21.0 + - - +
98F TRP* 4.0 17.3 - - + -
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Residues in contact with GLY 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 3.9 11.2 - - - -
41F ARG* 2.8 42.3 + - - -
83F ILE* 1.3 75.1 - - - +
85F LEU* 1.3 56.1 + - - +
87F PHE* 3.9 0.2 - - - +
88F ASP* 3.0 36.8 + - - +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F TYR* 3.9 27.8 - - + -
82F PRO* 3.0 31.2 + - + +
84F GLY* 1.3 74.9 - - - +
86F LEU* 1.3 67.6 + - - +
88F ASP* 3.4 5.9 + - + +
89F LEU* 2.9 42.6 + - + +
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Residues in contact with LEU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 4.0 23.6 - - + -
77F LEU* 4.3 9.9 - - + -
78F LYS* 3.5 32.3 - - + +
81F TYR* 3.6 37.5 - - + +
82F PRO 3.2 8.2 + - - +
83F ILE* 3.6 9.9 - - - +
85F LEU* 1.3 80.1 - - - +
87F PHE* 1.3 56.8 + - - +
89F LEU* 3.8 5.8 - - + -
90F LEU* 2.9 51.4 + - + +
98F TRP* 4.1 12.6 - - + -
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Residues in contact with PHE 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 3.4 37.5 - - + -
41F ARG* 3.9 13.9 - - - -
83F ILE 3.1 9.3 + - - +
84F GLY 3.9 0.9 - - - +
86F LEU* 1.3 74.2 - - - +
88F ASP* 1.3 76.7 + - - +
91F ALA* 2.8 43.5 + - + +
92F SER* 3.0 32.2 + - - -
94F SER 5.2 2.2 - - - -
96F LEU* 3.6 26.5 - - + -
98F TRP* 3.6 47.7 - + + -
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Residues in contact with ASP 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ARG* 3.0 33.0 + - - -
84F GLY 3.0 19.5 + - - +
85F LEU* 3.7 9.4 - - + +
87F PHE* 1.3 78.3 - - - +
89F LEU* 1.3 64.0 + - - +
91F ALA 4.4 0.2 + - - -
92F SER* 2.8 30.0 + - - -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F TYR* 5.5 11.2 - - + -
85F LEU* 2.9 34.2 + - + +
86F LEU* 3.9 6.5 - - + +
88F ASP* 1.3 79.9 - - - +
90F LEU* 1.3 72.2 + - + +
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F TYR* 3.3 29.3 + - + -
75F THR* 4.3 27.8 - - + +
76F PRO 5.6 0.2 - - - +
77F LEU* 3.5 31.6 - - + -
86F LEU* 2.9 30.8 + - + +
87F PHE* 5.1 0.2 - - - -
89F LEU* 1.3 95.0 - - + +
91F ALA* 1.3 59.0 + - + +
92F SER 3.9 0.4 - - - -
93F SER* 5.4 2.5 + - - -
98F TRP* 5.4 1.6 - - + -
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Residues in contact with ALA 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F TYR* 3.5 22.2 - - + -
87F PHE* 2.8 22.7 + - + +
90F LEU* 1.3 75.9 - - + +
92F SER* 1.3 61.8 + - - +
93F SER* 3.1 4.0 - - - -
94F SER* 2.9 29.2 + - - +
98F TRP* 3.5 35.0 - - + +
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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