Contacts of the helix formed by residues 77 - 90 (chain A) in PDB entry 1F89
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 SER 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLU 4.6 1.0 + - - -
70A VAL* 2.9 31.9 - - - +
71A ILE 3.3 27.8 - - - -
76A PRO* 1.3 73.3 - - - +
78A THR* 1.3 63.5 + - - +
80A VAL* 3.4 16.1 - - - +
81A GLN* 2.6 32.6 + - - +
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Residues in contact with THR 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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25A LYS* 4.8 10.1 - - + -
26A MET* 3.7 29.8 - - + -
29A LEU* 4.2 8.2 - - + +
70A VAL* 4.8 4.5 - - - -
77A SER* 1.3 78.5 + - - +
79A SER* 1.3 58.5 + - - +
81A GLN* 4.1 3.5 - - - +
82A PHE* 3.3 22.1 + - + +
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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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25A LYS* 3.2 27.2 - - - -
29A LEU* 3.9 15.8 - - - +
55A PHE* 6.1 0.2 - - - -
56A ASN* 3.2 10.3 + - - -
70A VAL* 3.2 17.0 - - - +
77A SER 3.2 0.2 - - - -
78A THR* 1.3 76.2 - - - +
80A VAL* 1.3 65.7 - - - +
81A GLN 3.2 0.2 - - - -
82A PHE* 3.4 4.1 + - - +
83A LEU* 3.1 31.5 + - - +
99A ILE* 3.9 19.5 - - - -
114A ILE* 4.9 2.0 - - - -
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Residues in contact with VAL 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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70A VAL* 4.9 4.5 - - + -
71A ILE 3.9 3.1 - - - +
72A ASN* 3.1 34.5 - - + +
73A PRO* 5.4 3.4 - - + +
76A PRO* 4.4 10.1 - - + -
77A SER* 3.1 31.8 + - - +
79A SER* 1.3 76.3 - - - +
81A GLN* 1.3 57.6 + - - +
84A SER* 3.0 29.5 + - - -
99A ILE* 5.1 0.4 - - + -
114A ILE* 4.5 3.4 - - + -
116A PHE* 3.5 24.1 - - + -
122A LEU* 4.1 18.6 - - + -
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Residues in contact with GLN 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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76A PRO* 3.1 33.5 - - + +
77A SER 2.6 24.2 + - - +
78A THR* 4.1 3.4 - - - +
80A VAL* 1.3 72.2 - - - +
82A PHE* 1.3 63.5 + - - +
84A SER* 3.1 9.4 + - - -
85A ASN* 2.6 66.1 + - - +
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Residues in contact with PHE 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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26A MET* 5.6 7.2 - - + -
29A LEU* 3.1 58.8 - - + -
30A GLN* 3.4 28.0 - - - -
32A ALA 5.3 0.2 - - - -
33A ALA* 3.7 17.0 - - + -
78A THR 3.3 17.4 + - - +
79A SER* 3.4 7.1 + - - +
81A GLN* 1.3 80.0 - - - +
83A LEU* 1.3 65.1 + - + +
85A ASN* 3.3 11.7 + - - +
86A LEU* 3.2 34.8 + - + +
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Residues in contact with LEU 83 (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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29A LEU* 5.2 1.1 - - + -
32A ALA* 5.4 2.0 - - + -
36A ILE* 5.4 0.2 - - + -
51A LEU* 4.1 9.0 - - + -
55A PHE* 3.9 27.1 - - + -
79A SER* 3.1 15.7 + - - +
82A PHE* 1.3 82.5 - - + +
84A SER* 1.3 60.0 + - - +
86A LEU* 3.2 14.6 + - + +
87A ALA* 2.8 29.9 + - - +
94A LEU* 3.9 23.8 - - + +
96A GLY* 3.6 26.2 - - - +
99A ILE* 5.1 2.0 - - + -
114A ILE* 3.5 28.5 - - + -
116A PHE* 3.7 15.7 - - + -
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Residues in contact with SER 84 (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 PRO* 6.3 1.3 - - - -
80A VAL* 3.0 23.6 + - - -
81A GLN* 3.1 13.5 + - - -
83A LEU* 1.3 78.3 - - - +
85A ASN* 1.3 64.6 + - - +
87A ALA* 3.2 14.0 - - - +
88A ASN* 2.9 16.0 - - - +
116A PHE* 3.8 14.7 - - - -
120A GLY* 2.6 27.5 + - - -
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Residues in contact with ASN 85 (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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81A GLN* 2.6 54.5 + - - +
82A PHE* 3.7 9.9 - - - +
83A LEU 3.2 0.2 - - - -
84A SER* 1.3 74.6 + - - +
86A LEU* 1.3 63.7 + - + +
88A ASN* 3.4 7.7 - - - +
89A LYS* 3.2 25.9 + - - +
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Residues in contact with LEU 86 (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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32A ALA* 4.8 0.9 - - + -
33A ALA* 4.0 31.4 - - + +
36A ILE* 4.1 21.5 - - + -
37A GLU* 4.8 3.8 - - - +
82A PHE* 3.2 39.8 + - + +
83A LEU* 3.2 18.7 + - + +
85A ASN* 1.3 75.1 - - + +
87A ALA* 1.3 69.6 + - - +
89A LYS* 4.4 7.4 - - + +
90A PHE* 3.3 47.8 + - + -
92A ILE* 3.9 4.8 - - - +
94A LEU* 4.1 7.2 - - + -
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Residues in contact with ALA 87 (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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83A LEU 2.8 13.0 + - - +
84A SER 3.2 12.6 - - - +
86A LEU* 1.3 78.0 - - - +
88A ASN* 1.3 51.3 + - - +
90A PHE 2.4 27.9 - - - +
91A LYS 3.7 0.3 - - - +
92A ILE* 3.2 23.5 - - - +
94A LEU* 4.5 8.0 - - + +
116A PHE* 3.7 17.3 - - + -
117A ASN 3.4 19.3 - - - +
120A GLY* 3.7 7.4 - - - -
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Residues in contact with ASN 88 (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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84A SER 2.9 15.9 - - - +
85A ASN* 3.4 12.6 - - - +
87A ALA* 1.3 73.2 - - - +
89A LYS* 1.3 68.0 + - - +
90A PHE 3.0 8.3 + - - +
118A GLU 3.2 14.2 - - - +
119A ASP* 3.0 35.2 + - - +
120A GLY* 4.1 0.5 - - - -
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Residues in contact with LYS 89 (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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37A GLU* 4.7 14.3 + - - +
85A ASN 3.2 21.4 + - - +
86A LEU* 4.0 9.6 - - + +
87A ALA 3.5 0.4 - - - -
88A ASN* 1.3 81.0 - - - +
90A PHE* 1.3 90.2 + - + +
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Residues in contact with PHE 90 (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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36A ILE* 4.2 9.2 - - + -
37A GLU* 3.8 31.2 - - + -
40A MET* 3.5 38.1 - - + -
86A LEU* 3.3 44.1 + - + -
87A ALA 2.4 24.3 - - - +
88A ASN* 3.2 9.4 - - - +
89A LYS* 1.3 105.6 - - + +
91A LYS* 1.3 64.0 + - - +
92A ILE* 3.7 22.9 - - + -
118A GLU 3.9 0.5 - - - +
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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