Contacts of the helix formed by residues 71 - 84 (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 71 (chain A).
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Specific contacts
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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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Residues in contact with PRO 72 (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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31A ARG* 4.8 3.8 - - - +
70A ASN 3.6 4.0 - - - +
71A SER* 1.4 85.8 - - - +
73A GLU* 1.3 70.1 - - - +
75A GLN* 3.8 6.6 - - + +
76A ALA* 2.9 31.9 + - - +
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Residues in contact with GLU 73 (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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24A THR* 4.3 9.2 - - - +
27A PRO* 5.9 4.7 - - + -
28A ALA* 4.2 12.6 - - + +
31A ARG* 2.6 42.0 + - - +
71A SER* 3.5 7.6 - - - +
72A PRO* 1.3 90.6 - - - +
74A TYR* 1.3 62.6 + - - +
76A ALA* 3.4 5.7 + - - +
77A ALA* 3.2 20.4 + - - +
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Residues in contact with TYR 74 (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* 3.5 18.7 - + - -
21A TYR* 2.6 40.4 + + - -
25A ALA* 3.9 18.2 - - + +
28A ALA* 3.9 11.5 - - + +
29A PHE* 3.9 13.0 - + - -
68A CYS* 3.2 24.0 - - - +
69A TYR* 3.5 45.8 - + - -
71A SER* 3.1 5.5 + - - +
73A GLU* 1.3 78.4 - - - +
75A GLN* 1.3 58.9 + - - +
77A ALA* 3.2 5.4 + - - +
78A ALA* 2.8 38.8 + - + -
81A ARG* 2.8 19.2 + - - -
89A MSE 3.3 9.7 - - - +
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Residues in contact with GLN 75 (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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69A TYR* 2.8 49.9 + - - +
70A ASN* 3.9 13.7 - - - +
71A SER 2.9 20.0 + - - +
72A PRO* 3.8 6.7 - - + +
74A TYR* 1.3 77.0 - - - +
76A ALA* 1.3 62.0 + - - +
78A ALA* 3.5 4.2 + - - +
79A LYS* 3.1 54.0 + - - +
82A GLN* 5.7 1.0 - - - +
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Residues in contact with ALA 76 (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 PRO 2.9 18.3 + - - +
73A GLU* 3.6 6.3 - - - +
74A TYR 3.2 0.2 - - - -
75A GLN* 1.3 74.7 - - - +
77A ALA* 1.3 65.0 + - - +
79A LYS* 3.3 19.7 + - - +
80A ILE* 3.9 7.5 + - - +
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Residues in contact with ALA 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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21A TYR* 3.2 23.3 - - + -
24A THR* 3.3 31.5 - - - +
25A ALA* 3.6 26.0 - - + +
73A GLU 3.2 7.3 + - - +
74A TYR 3.2 8.4 + - - +
76A ALA* 1.3 78.0 - - - +
78A ALA* 1.3 58.9 + - - +
80A ILE* 3.0 26.0 + - - +
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Residues in contact with ALA 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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21A TYR* 4.1 11.2 - - - -
74A TYR* 2.8 29.9 + - + +
75A GLN* 3.6 13.0 - - - +
76A ALA 3.2 0.4 - - - -
77A ALA* 1.3 70.5 - - - +
79A LYS* 1.3 58.4 + - - +
81A ARG* 3.1 23.1 + - - +
82A GLN* 2.8 50.3 + - - +
47B GLU* 4.7 0.7 - - - +
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Residues in contact with LYS 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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75A GLN* 3.1 52.7 + - - +
76A ALA* 3.3 11.6 + - - +
77A ALA 3.2 1.0 - - - -
78A ALA* 1.3 79.6 - - - +
80A ILE* 1.3 65.9 + - + +
82A GLN* 3.2 27.4 + - + +
83A GLU* 3.3 25.4 + - - +
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Residues in contact with ILE 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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17A ARG* 3.4 49.1 - - + +
20A ASP* 4.2 12.1 - - + +
21A TYR* 4.2 13.7 - - + +
24A THR* 3.9 26.5 - - + +
76A ALA 4.3 6.1 - - - +
77A ALA* 3.0 10.7 + - - +
79A LYS* 1.3 77.0 - - + +
81A ARG* 1.3 63.0 + - - +
83A GLU* 3.1 17.9 + - - +
84A VAL* 3.2 12.9 + - + +
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Residues in contact with ARG 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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10A VAL* 4.9 2.7 - - - -
18A TYR* 4.0 20.0 - - + -
21A TYR* 3.3 51.9 + - + +
74A TYR* 2.8 21.4 + - - -
77A ALA 3.4 1.8 + - - -
78A ALA* 3.1 21.2 + - - +
80A ILE* 1.3 79.9 - - - +
82A GLN* 1.3 69.7 + - - +
84A VAL* 3.0 9.1 + - - -
85A ALA* 2.9 35.9 + - + +
87A ALA* 4.2 17.7 - - + +
89A MSE 3.2 17.8 - - - +
47B GLU* 2.7 42.0 + - - -
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Residues in contact with GLN 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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13A ARG* 4.5 2.9 + - - -
69A TYR* 4.2 3.8 + - - -
75A GLN* 5.7 1.0 + - - +
78A ALA* 2.8 31.2 + - - +
79A LYS* 3.2 35.5 - - + +
80A ILE 3.3 0.2 - - - -
81A ARG* 1.3 86.1 - - - +
83A GLU* 1.3 59.9 + - - +
85A ALA 3.9 11.9 - - - +
47B GLU* 2.9 32.7 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 2.7 22.3 + - - -
17A ARG* 2.9 38.4 + - - +
79A LYS 3.3 14.6 + - - +
80A ILE* 3.1 12.0 + - - +
82A GLN* 1.3 77.9 - - - +
84A VAL* 1.3 56.3 + - + +
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Residues in contact with VAL 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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12A VAL* 3.9 0.5 - - - -
13A ARG* 2.8 38.1 + - - +
14A ASP* 3.4 22.0 + - + +
17A ARG* 3.6 48.2 - - + +
18A TYR* 4.1 31.2 - - + +
80A ILE 3.4 14.8 - - - +
81A ARG* 3.0 12.4 + - - +
83A GLU* 1.3 79.7 - - - +
85A ALA* 1.3 59.8 + - - +
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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