Contacts of the helix formed by residues 71 - 83 (chain F) in PDB entry 1F9N
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 ASN 71 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68F GLN 3.6 6.5 + - - +
69F ARG 3.3 1.0 + - - -
70F PHE* 1.3 122.2 - - + +
72F PRO* 1.3 68.0 - - - +
74F SER* 4.5 18.3 - - - -
75F LYS* 3.4 24.8 - - + +
109F LEU* 5.8 0.3 - - - +
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Residues in contact with PRO 72 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68F GLN 5.1 2.0 - - - +
69F ARG 3.7 11.7 - - - +
70F PHE 3.4 8.3 - - - +
71F ASN* 1.3 90.6 - - - +
73F LEU* 1.3 58.7 + - + +
74F SER 2.8 14.9 + - - +
75F LYS* 2.9 10.7 + - - +
76F LEU* 3.7 6.9 + - - +
109F LEU* 5.8 3.0 - - - +
112F ASN* 5.1 18.2 - - + +
113F LEU* 4.3 14.6 - - + -
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Residues in contact with LEU 73 (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 PRO* 1.3 77.7 - - + +
74F SER* 1.3 60.5 + - - +
75F LYS 3.4 0.4 - - - -
76F LEU* 4.1 4.0 - - + +
77F LYS* 3.5 19.9 + - - +
113F LEU* 3.9 22.4 - - + +
115F TRP* 4.3 17.7 - - + -
148F LEU* 3.3 43.5 - - + -
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Residues in contact with SER 74 (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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71F ASN* 4.5 19.5 - - - -
72F PRO 2.8 4.2 + - - -
73F LEU* 1.3 75.4 - - - +
75F LYS* 1.3 61.0 + - - +
77F LYS* 4.1 5.9 + - - +
78F ARG* 3.9 18.0 + - - +
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Residues in contact with LYS 75 (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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68F GLN* 3.5 25.6 + - + +
70F PHE* 3.3 33.1 - - - -
71F ASN* 3.4 21.3 + - + +
72F PRO 2.9 4.2 + - - +
74F SER* 1.3 78.1 - - - +
76F LEU* 1.3 64.8 + - - +
77F LYS 3.4 0.4 - - - -
78F ARG* 4.2 4.0 - - - +
79F ALA* 3.3 23.3 + - + +
109F LEU* 3.5 32.4 - - + +
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Residues in contact with LEU 76 (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 PRO 3.7 6.8 + - - +
73F LEU* 3.9 8.0 + - - +
75F LYS* 1.3 78.5 - - - +
77F LYS* 1.3 56.9 + - - +
79F ALA* 3.8 0.2 - - - +
80F LEU* 2.7 60.6 + - + +
106F ILE* 4.2 13.0 - - + -
109F LEU* 3.9 20.3 - - + +
110F MET* 3.5 25.6 - - + +
113F LEU* 3.2 38.6 - - + -
145F LEU* 4.6 9.2 - - + -
148F LEU* 4.4 11.9 - - + -
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Residues in contact with LYS 77 (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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73F LEU 3.5 15.0 + - - +
74F SER* 4.2 6.1 - - - +
75F LYS 3.4 0.4 - - - -
76F LEU* 1.3 78.0 - - - +
78F ARG* 1.3 58.2 + - - +
80F LEU* 4.0 1.4 - - - +
81F MET* 2.8 53.0 + - + +
147F GLU 4.2 4.9 + - - -
148F LEU* 2.6 76.1 + - + +
149F LEU* 4.6 2.2 + - - +
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Residues in contact with ARG 78 (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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74F SER 3.9 13.4 + - - +
75F LYS* 4.3 4.0 - - - +
76F LEU 3.4 0.4 - - - -
77F LYS* 1.3 79.7 - - - +
79F ALA* 1.3 63.1 + - - +
81F MET* 3.3 8.1 + - - +
82F ASP* 3.0 35.0 + - - +
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Residues in contact with ALA 79 (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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75F LYS* 3.3 18.1 + - + +
76F LEU* 3.8 2.9 - - - +
78F ARG* 1.3 79.1 - - - +
80F LEU* 1.3 57.2 + - - +
82F ASP* 3.0 9.0 + - - +
83F ALA* 3.0 30.0 + - - +
105F ALA* 6.4 0.7 - - + -
106F ILE* 4.1 14.8 - - + -
109F LEU* 3.9 16.8 - - + -
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ARG* 4.3 0.3 + - - -
76F LEU* 2.7 38.4 + - + +
77F LYS* 4.0 2.9 - - - +
79F ALA* 1.3 73.2 - - - +
81F MET* 1.3 56.7 + - - +
82F ASP 3.1 0.4 - - - -
84F PHE* 2.9 58.3 + - + +
96F LEU* 3.8 28.7 - - + -
106F ILE* 4.0 27.3 - - + +
110F MET* 6.5 0.2 - - - -
145F LEU* 3.8 36.8 - - + +
148F LEU* 4.8 7.4 - - + +
149F LEU* 5.2 6.5 - - + +
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Residues in contact with MET 81 (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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11A ARG* 2.7 27.0 + - - +
47A GLU 5.7 5.2 - - - +
48A LEU* 4.8 8.6 - - - +
49A HIS* 5.5 12.8 - - - +
65A PRO* 5.1 1.6 - - - +
77F LYS* 2.8 46.8 + - + +
78F ARG* 3.5 9.0 - - - +
79F ALA 3.2 0.4 - - - -
80F LEU* 1.3 76.0 - - - +
82F ASP* 1.3 62.4 + - - +
148F LEU 3.1 27.1 - - - +
149F LEU* 3.9 21.7 - - + +
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Residues in contact with ASP 82 (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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49A HIS* 5.2 7.4 + - - +
64A LEU* 3.4 18.5 - - - +
65A PRO* 3.8 29.5 - - + +
66A ALA* 3.1 27.8 + - + +
78F ARG* 3.0 22.2 - - - +
79F ALA* 3.0 7.8 + - - +
81F MET* 1.3 89.5 - - - +
83F ALA* 1.3 58.9 + - - +
84F PHE 3.9 0.4 - - - -
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Residues in contact with ALA 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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64A LEU* 4.2 1.1 - - - -
66A ALA* 3.5 18.8 - - + -
79F ALA 3.0 12.7 + - - +
82F ASP* 1.3 80.2 - - - +
84F PHE* 1.3 67.7 + - - +
85F VAL* 3.2 3.1 + - - +
98F THR* 3.2 9.3 - - - -
99F MET* 3.0 29.8 + - - +
102F ASN* 3.6 26.2 - - + +
106F ILE* 4.2 6.3 - - + -
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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