Contacts of the helix formed by residues 61 - 71 (chain A) in PDB entry 2FIU
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MSE 3.8 29.1 - - - -
2A ALA 3.4 9.2 - - - -
4A GLY* 3.5 8.1 + - - +
59A PHE* 3.0 8.3 + - - +
60A PRO* 1.3 80.7 - - - +
62A VAL* 1.3 63.8 + - - +
63A GLN* 3.3 10.5 + - - +
64A HIS* 2.8 41.2 + - - +
65A ALA 3.3 8.1 + - - -
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Residues in contact with VAL 62 (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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2A ALA 4.1 1.6 + - - -
3A LYS 4.1 0.2 - - - +
4A GLY* 3.7 14.4 - - - +
61A SER* 1.3 73.3 - - - +
63A GLN* 1.3 58.5 + - - +
65A ALA* 3.1 5.2 + - - +
66A ILE* 2.9 46.6 + - + +
91A ILE* 4.1 17.0 - - + -
93A GLU* 3.6 52.6 + - + +
42B SER* 5.3 3.4 - - - +
44B THR* 4.1 9.6 - - - +
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Residues in contact with GLN 63 (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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61A SER* 3.2 9.7 + - - +
62A VAL* 1.3 74.0 - - - +
64A HIS* 1.3 61.6 + - - +
66A ILE* 4.0 24.5 - - - +
67A ASP* 2.9 68.2 + - - +
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Residues in contact with HIS 64 (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 PHE* 3.6 41.5 - + - +
59A PHE* 4.0 3.1 - - + -
60A PRO* 3.7 28.5 - - + +
61A SER* 2.8 41.1 + - - +
63A GLN* 1.3 78.2 - - - +
65A ALA* 1.3 56.6 + - - +
67A ASP* 3.4 6.7 + - - +
68A CYS* 3.0 29.1 + - - +
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Residues in contact with ALA 65 (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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4A GLY* 4.9 1.8 - - - -
6A TRP* 3.5 9.5 - - + -
59A PHE* 3.6 35.8 - - + -
61A SER 3.3 5.7 + - - +
62A VAL 3.1 10.4 + - - +
64A HIS* 1.3 78.7 - - - +
66A ILE* 1.3 57.6 + - - +
68A CYS* 3.3 4.5 + - - +
69A TYR* 3.0 23.2 + - - +
91A ILE* 3.6 31.4 - - + -
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Residues in contact with ILE 66 (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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62A VAL* 2.9 37.2 + - + +
63A GLN* 3.7 28.3 - - - +
65A ALA* 1.3 72.3 - - - +
67A ASP* 1.3 61.8 + - - +
69A TYR* 3.2 4.9 + - - +
70A ASN* 2.9 47.6 + - - +
91A ILE* 3.7 17.7 - - + -
44B THR* 4.2 20.0 - - + +
46B LEU* 5.4 3.8 - - + -
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Residues in contact with ASP 67 (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 PHE* 3.5 28.3 - - + -
63A GLN* 2.9 51.7 + - - +
64A HIS* 3.7 3.0 - - - +
66A ILE* 1.3 77.5 - - - +
68A CYS* 1.3 62.3 + - - +
70A ASN* 3.4 5.6 + - - +
71A SER* 3.1 24.8 + - - -
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Residues in contact with CYS 68 (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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6A TRP* 4.1 3.8 - - + -
28A ALA* 3.8 28.3 - - - -
29A PHE* 3.7 35.0 - - - -
32A PHE* 3.5 15.8 - - + -
59A PHE* 3.8 15.3 - - + -
64A HIS 3.0 14.0 + - - +
65A ALA 3.4 9.0 - - - +
67A ASP* 1.3 75.2 - - - +
69A TYR* 1.3 62.1 + - - +
71A SER* 2.8 22.9 + - - -
74A TYR* 3.2 10.5 - - - +
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Residues in contact with TYR 69 (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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6A TRP* 3.7 20.6 - + + -
65A ALA 3.0 9.9 + - - +
66A ILE 3.2 7.6 + - - +
68A CYS* 1.3 77.5 - - - +
70A ASN* 1.3 69.8 + - - +
71A SER 3.5 0.5 + - - +
74A TYR* 3.5 33.0 - + - -
75A GLN* 2.8 47.1 + - - +
78A ALA* 5.4 0.7 - - + -
82A GLN* 4.2 4.3 + - - -
89A MSE 3.9 9.6 - - + -
46B LEU* 3.7 49.5 + - + -
47B GLU* 2.6 43.2 + - + +
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Residues in contact with ASN 70 (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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66A ILE* 2.9 39.9 + - - +
67A ASP* 3.4 5.9 + - - +
68A CYS 3.3 0.2 - - - -
69A TYR* 1.3 90.4 - - - +
71A SER* 1.3 65.2 + - - +
72A PRO* 3.6 3.6 - - - +
75A GLN* 3.9 12.4 - - - +
46B LEU* 6.3 0.2 - - - +
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Residues in contact with SER 71 (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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28A ALA* 4.0 6.9 - - - +
31A ARG* 3.8 15.5 - - - -
32A PHE* 4.1 3.4 - - - -
67A ASP 3.1 12.7 + - - -
68A CYS 2.8 19.8 + - - -
70A ASN* 1.3 78.7 - - - +
72A PRO* 1.4 72.6 - - - +
73A GLU* 3.5 14.6 + - - -
74A TYR* 3.1 14.7 + - - +
75A GLN* 2.9 22.7 + - - +
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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