Contacts of the helix formed by residues 71 - 84 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA* 3.6 7.7 - - - +
31B ARG* 3.9 1.8 - - - -
32B PHE* 3.9 18.4 - - - -
67B ASP 2.9 12.6 + - - -
68B CYS* 2.6 21.7 + - - -
70B ASN* 1.3 79.6 - - - +
72B PRO* 1.4 78.1 - - - +
73B GLU* 3.6 9.6 - - - -
74B TYR* 3.1 16.5 + - - +
75B GLN* 2.9 22.2 + - - +
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Residues in contact with PRO 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ARG* 4.5 5.8 - - - +
70B ASN 3.6 2.4 - - - +
71B SER* 1.4 84.6 - - - +
73B GLU* 1.3 79.7 + - - +
75B GLN* 3.4 5.3 + - + +
76B ALA* 3.0 25.5 + - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 4.4 10.9 - - - +
27B PRO* 5.3 8.5 - - + -
28B ALA* 4.2 19.8 - - + +
31B ARG* 3.1 31.7 + - - -
71B SER* 3.6 3.5 - - - -
72B PRO* 1.3 85.0 - - - +
74B TYR* 1.3 67.6 + - - +
76B ALA* 3.2 7.8 + - - +
77B ALA* 3.1 21.1 + - - +
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TRP* 3.5 12.3 - + - -
21B TYR* 2.6 41.1 + + - -
25B ALA* 3.8 16.4 - - + +
28B ALA* 3.8 11.7 - - + +
29B PHE* 3.6 21.5 - + - -
68B CYS 3.1 24.7 - - - +
69B TYR* 3.5 40.6 - + - +
71B SER* 3.1 6.9 + - - +
73B GLU* 1.3 78.1 - - - +
75B GLN* 1.3 58.8 + - - +
77B ALA* 3.1 5.0 + - - +
78B ALA* 2.8 35.1 + - + -
81B ARG* 2.8 27.3 + - - -
89B MSE 3.4 9.5 - - - +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 2.8 48.4 + - - +
70B ASN* 3.8 14.8 - - - +
71B SER 2.9 20.5 + - - +
72B PRO* 3.8 6.5 - - + +
74B TYR* 1.3 77.1 - - - +
76B ALA* 1.3 62.1 + - - +
78B ALA* 3.4 8.6 + - - +
79B LYS* 3.3 25.9 + - - +
82B GLN* 6.1 0.6 - - - +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO 3.0 17.8 + - - +
73B GLU* 3.6 5.6 - - - +
75B GLN* 1.3 74.6 - - - +
77B ALA* 1.3 64.8 + - - +
79B LYS* 3.3 40.7 - - + +
80B ILE* 3.8 9.4 + - - +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 3.2 16.5 - - + -
24B THR* 3.4 27.5 - - - +
25B ALA* 3.7 26.0 - - + +
73B GLU 3.1 12.5 + - - +
74B TYR* 3.5 7.4 - - + +
76B ALA* 1.3 75.8 - - - +
78B ALA* 1.3 57.5 + - - +
80B ILE* 3.0 29.7 + - - +
81B ARG 3.2 4.3 + - - -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 4.5 1.1 - - - +
21B TYR* 4.2 4.6 - - - -
69B TYR* 5.3 0.4 - - + -
74B TYR* 2.8 27.3 + - + +
75B GLN* 3.6 13.9 - - - +
76B ALA 3.2 0.4 - - - -
77B ALA* 1.3 74.7 - - - +
79B LYS* 1.3 55.2 + - - +
81B ARG* 3.0 28.3 + - - +
82B GLN* 2.8 51.9 + - - +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLN* 3.3 9.7 + - - +
76B ALA* 3.3 32.9 - - + +
77B ALA 3.3 0.4 - - - -
78B ALA* 1.3 77.4 - - - +
80B ILE* 1.3 65.3 + - + +
82B GLN* 3.6 12.6 + - - +
83B GLU* 3.5 25.5 + - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 3.4 45.3 + - + +
20B ASP* 4.1 17.9 - - + +
21B TYR* 4.1 7.0 - - + +
24B THR* 4.0 25.4 - - + +
76B ALA 3.8 10.8 - - - +
77B ALA* 3.0 10.9 + - - +
79B LYS* 1.3 75.8 - - + +
81B ARG* 1.3 67.0 + - - +
83B GLU* 3.2 15.1 + - - +
84B VAL* 3.2 16.9 + - + +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 2.7 41.6 + - - -
10B VAL* 4.8 3.6 - - - -
18B TYR* 3.9 21.5 - - + -
21B TYR* 3.2 49.0 + - + +
74B TYR* 2.8 21.2 + - - -
77B ALA 3.2 2.2 + - - -
78B ALA* 3.0 19.2 + - - +
80B ILE* 1.3 80.3 - - - +
82B GLN* 1.3 65.2 + - - +
84B VAL* 2.9 11.3 + - - -
85B ALA* 2.8 39.1 + - + +
87B ALA* 4.2 19.2 - - + +
89B MSE 3.3 16.7 - - - -
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.1 40.4 + - - +
69B TYR* 4.4 3.6 + - - -
75B GLN* 6.1 1.2 - - - +
78B ALA* 2.8 34.6 + - - +
79B LYS* 4.0 12.7 - - - +
80B ILE 3.2 0.2 - - - -
81B ARG* 1.3 76.2 - - - +
83B GLU* 1.3 60.5 + - + +
85B ALA 3.6 13.5 - - - +
86B ASP* 5.7 0.2 - - - +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 5.4 2.3 - - - +
17B ARG* 3.3 27.7 + - - +
79B LYS 3.5 11.4 + - - +
80B ILE* 3.2 8.8 + - - +
81B ARG 3.2 0.6 - - - -
82B GLN* 1.3 80.9 - - + +
84B VAL* 1.3 65.5 + - + +
85B ALA 3.6 0.6 + - - -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.7 2.1 - - - +
13B ARG* 2.7 35.5 + - - -
14B ASP* 3.2 23.6 + - + +
17B ARG* 3.6 49.1 - - + +
18B TYR* 3.9 33.0 - - + +
80B ILE* 3.2 16.5 + - + +
81B ARG* 2.9 12.1 + - - +
83B GLU* 1.3 80.9 - - - +
85B ALA* 1.3 53.8 + - - +
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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