Contacts of the helix formed by residues 71 - 88 (chain F) in PDB entry 3UF2
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 THR 71 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ASP* 3.7 43.1 + - + +
25E SER* 5.6 0.7 - - - -
67F PHE* 4.1 3.1 - - - +
68F ARG* 2.9 35.2 + - + +
69F ASP 3.9 3.1 - - - +
70F ASN* 1.3 82.6 - - - +
72F PRO* 1.3 75.5 - - + +
73F ASN* 3.8 3.5 + - - +
74F ALA* 2.8 23.4 + - - +
75F ILE* 2.9 14.9 + - - +
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Residues in contact with PRO 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ARG* 5.9 9.4 - - + -
24E ASP* 6.0 1.3 - - + -
25E SER* 6.5 0.2 - - - -
21F ARG* 3.1 39.7 + - - +
70F ASN 4.6 1.8 - - - +
71F THR* 1.3 88.1 - - + +
73F ASN* 1.3 58.0 + - - +
75F ILE* 3.7 13.5 + - + +
76F ALA* 3.2 24.9 + - - +
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Residues in contact with ASN 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E SER* 2.8 39.4 + - - +
18F SER 4.9 0.5 - - - +
21F ARG* 4.6 8.1 + - - +
22F LEU* 3.5 32.6 + - + +
25F SER* 3.2 18.4 + - - -
26F GLN* 3.9 0.8 - - - +
67F PHE* 3.7 22.1 - - + -
71F THR* 3.1 5.4 + - - +
72F PRO* 1.3 78.8 - - - +
74F ALA* 1.3 66.7 + - - +
76F ALA* 3.1 15.4 + - - +
77F ILE* 3.1 18.0 + - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F PHE* 3.8 21.0 - - + +
68F ARG 3.1 27.8 - - - +
69F ASP* 4.5 1.8 - - - -
70F ASN 4.0 6.7 - - - +
71F THR* 2.8 17.7 + - - +
73F ASN* 1.3 74.6 - - - +
75F ILE* 1.3 62.1 + - - +
77F ILE* 3.3 5.9 + - - +
78F VAL* 3.2 27.0 + - + +
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Residues in contact with ILE 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ASN* 4.5 22.7 - - - +
71F THR 2.9 25.2 + - - +
72F PRO* 3.8 11.4 - - + +
74F ALA* 1.3 76.7 - - + +
76F ALA* 1.3 64.2 + - - +
78F VAL* 3.2 9.1 + - + +
79F GLN* 3.0 48.8 + - + +
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F SER* 4.1 28.6 + - - +
22F LEU* 4.1 12.3 - - + -
72F PRO 3.2 11.9 + - - +
73F ASN* 3.1 15.6 + - - +
75F ILE* 1.3 80.8 - - - +
77F ILE* 1.3 59.8 + - - +
79F GLN* 3.7 11.1 + - - +
80F LEU* 3.1 33.7 + - + +
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Residues in contact with ILE 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LEU* 3.6 17.0 - - + -
61F MET* 4.0 24.0 - - + +
65F MET* 3.5 37.7 - - + +
67F PHE* 3.7 20.2 - - + -
73F ASN 3.1 12.9 + - - +
74F ALA* 3.7 7.0 - - - +
75F ILE 3.2 0.4 - - - -
76F ALA* 1.3 76.1 - - - +
78F VAL* 1.3 60.6 + - + +
80F LEU* 3.1 13.2 + - + +
81F GLN* 2.8 49.2 + - + +
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Residues in contact with VAL 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.2 23.7 - - + +
86B ARG* 4.2 25.6 - - - +
74F ALA 3.2 13.9 + - - +
75F ILE* 3.2 11.1 + - + +
77F ILE* 1.3 78.6 - - + +
79F GLN* 1.3 60.7 + - + +
81F GLN* 3.2 16.1 + - - +
82F GLU* 2.8 37.8 + - + +
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Residues in contact with GLN 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 4.3 17.3 + - + +
18F SER* 5.4 4.5 + - - -
75F ILE* 3.0 40.6 + - + +
76F ALA* 4.0 11.2 - - - +
78F VAL* 1.3 79.5 - - + +
80F LEU* 1.3 58.5 + - - +
82F GLU* 3.6 7.3 - - - +
83F LEU* 2.9 28.4 + - - +
86F ARG* 5.0 1.4 + - - -
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 3.7 40.6 - - + +
18F SER* 4.6 7.2 - - - +
19F LEU* 3.8 35.7 - - + -
22F LEU* 5.8 0.7 - - + -
61F MET* 3.9 18.6 - - - -
65F MET* 6.0 0.2 - - + -
76F ALA* 3.1 25.1 - - + +
77F ILE* 3.1 15.3 + - + +
79F GLN* 1.3 75.5 - - - +
81F GLN* 1.3 56.0 + - - +
83F LEU* 3.5 14.3 - - + +
84F SER* 2.6 37.1 + - - -
121F PHE* 4.5 13.1 - - + -
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Residues in contact with GLN 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.2 32.5 - - + +
58F GLN* 4.3 7.0 + - - +
61F MET* 3.7 26.5 + - + +
62F GLU* 3.5 41.2 + - - +
77F ILE* 2.8 34.9 + - - +
78F VAL* 3.6 12.5 - - - +
80F LEU* 1.3 75.0 - - - +
82F GLU* 1.3 64.4 + - - +
84F SER* 3.2 4.7 + - - -
85F LEU* 2.9 28.9 + - + +
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Residues in contact with GLU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 2.8 38.1 - - - +
85B LEU* 3.9 7.9 - - + +
86B ARG* 2.6 42.6 + - - +
78F VAL* 2.8 23.9 + - + +
79F GLN* 3.6 8.3 - - - +
81F GLN* 1.3 73.0 - - - +
83F LEU* 1.3 66.8 + - - +
85F LEU* 2.9 19.2 + - - +
86F ARG* 3.2 33.8 + - - +
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Residues in contact with LEU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F MET* 2.9 44.6 - - + +
11F ILE* 3.9 20.4 - - + +
15F HIS* 3.9 28.5 - - + +
79F GLN 2.9 19.3 + - - +
80F LEU* 3.5 18.2 - - + +
82F GLU* 1.3 74.7 - - - +
84F SER* 1.3 56.8 + - - +
86F ARG* 3.1 26.7 + - - +
87F LEU* 3.0 30.9 + - + +
121F PHE* 4.3 14.8 - - + -
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Residues in contact with SER 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F PHE* 3.9 17.5 - - - -
58F GLN* 2.8 39.4 + - - -
61F MET* 3.7 4.7 - - - +
80F LEU 2.6 23.3 + - - -
81F GLN 3.5 3.1 - - - -
82F GLU 3.1 0.2 - - - -
83F LEU* 1.3 76.1 - - - +
85F LEU* 1.3 60.8 + - - +
87F LEU* 3.3 12.6 + - - +
88F LYS* 3.4 17.0 + - - +
121F PHE* 4.0 14.7 - - - -
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Residues in contact with LEU 85 (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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78B VAL* 4.4 24.2 - - + +
81B GLN* 3.3 46.4 - - + +
82B GLU* 3.6 35.4 - - + +
85B LEU* 4.6 6.5 - - + -
58F GLN* 5.0 5.2 - - - +
81F GLN* 2.9 18.7 + - + +
82F GLU* 2.9 14.4 + - - +
84F SER* 1.3 78.0 - - - +
86F ARG* 1.3 63.1 + - + +
87F LEU 3.7 0.2 + - - -
88F LYS* 3.7 34.1 - - + +
89F SER* 5.5 0.9 + - - -
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Residues in contact with ARG 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 5.5 5.7 + - - +
6F TYR* 4.6 1.7 + - - -
10F MET* 2.9 35.3 + - + +
15F HIS* 5.7 3.0 + - - -
79F GLN 5.0 1.4 + - - -
82F GLU* 3.2 29.7 + - - +
83F LEU* 3.1 43.4 + - - +
85F LEU* 1.3 76.2 - - + +
87F LEU* 1.3 63.9 + - - +
88F LYS 3.2 1.2 + - - -
89F SER* 3.8 15.1 + - - -
90F CYS* 4.9 0.2 - - - -
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Residues in contact with LEU 87 (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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10F MET* 3.7 32.5 - - + -
11F ILE* 3.8 25.6 - - + -
54F PHE* 3.6 32.5 - - + -
83F LEU* 3.0 23.3 + - + +
84F SER* 3.3 9.8 + - - +
86F ARG* 1.3 75.8 - - - +
88F LYS* 1.3 57.4 + - - +
89F SER 3.1 3.4 - - - -
90F CYS* 2.8 30.5 + - - +
91F PHE* 3.2 19.2 - - + -
121F PHE* 5.2 1.1 - - + -
124F THR* 4.9 2.0 - - + -
128F LEU* 3.9 21.8 - - + -
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Residues in contact with LYS 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B MET 5.2 1.4 + - - -
62B GLU* 3.3 34.0 + - - +
69B ASP* 3.9 12.1 - - - +
77B ILE* 5.9 0.8 - - - +
78B VAL* 5.5 7.4 - - + +
81B GLN* 3.6 18.8 + - - +
54F PHE* 5.0 7.2 - - + -
55F LEU* 6.1 7.0 - - + -
58F GLN* 4.6 7.4 - - - +
84F SER 3.5 13.9 - - - +
85F LEU* 3.7 27.8 - - + +
86F ARG 3.2 0.8 - - - -
87F LEU* 1.3 77.9 - - - +
89F SER* 1.3 59.0 + - - +
91F PHE* 3.0 33.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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