Contacts of the helix formed by residues 64 - 81 (chain F) in PDB entry 6TYF
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 PRO 64 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ALA 4.3 3.8 - - - +
63F ARG* 1.3 88.8 - - + +
65F ALA* 1.3 63.6 + - - +
66F ARG* 3.2 8.1 + - + +
67F ALA* 3.7 16.7 + - + +
68F TRP 4.2 2.4 + - - -
5H G 3.9 13.4 + - + +
6H T 3.5 29.2 - - + +
7H C 3.4 18.6 - - - +
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F HIS* 4.9 11.8 - - + +
57F VAL* 4.0 29.8 - - + +
58F ILE* 5.8 4.0 - - + -
60F ASP 5.5 0.9 - - - +
63F ARG 3.0 8.0 + - - +
64F PRO* 1.3 71.4 - - - +
66F ARG* 1.3 63.6 + - - +
67F ALA 3.3 0.2 - - - -
68F TRP* 3.4 6.0 + - - +
69F LEU* 3.2 29.2 + - + +
5H G 4.3 7.4 - - - +
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Residues in contact with ARG 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C GLU* 5.4 0.2 + - - -
286C PRO* 5.3 7.3 - - - +
21F GLU 3.9 9.3 + - - -
22F HIS* 3.3 38.5 + - + +
25F VAL* 3.4 41.0 - - + +
64F PRO* 3.2 6.3 - - + -
65F ALA* 1.3 78.4 - - - +
67F ALA* 1.3 62.5 + - - +
69F LEU* 3.1 8.9 + - + +
70F PHE* 3.0 54.4 + - + -
7H C 5.8 1.8 - - - +
8H A 3.3 26.9 + - - +
9H G 4.4 15.8 + - - -
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Residues in contact with ALA 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F PRO* 3.7 13.5 + - + +
65F ALA 3.3 0.8 - - - -
66F ARG* 1.3 79.0 - - - +
68F TRP* 1.3 60.2 + - - +
70F PHE 3.4 1.0 + - - -
71F THR* 3.0 27.5 + - - -
5H G 3.8 16.4 - - + +
6H T 3.8 20.0 - - - +
7H C 4.9 2.0 + - - +
8H A 3.1 38.6 + - - +
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Residues in contact with TRP 68 (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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47F THR 4.3 2.7 - - - -
50F ARG* 3.8 29.2 - - + -
51F ALA* 3.8 16.6 - - + -
54F HIS* 3.6 23.6 - + - -
56F GLU* 4.6 5.1 + - - -
57F VAL* 3.6 32.1 - - + +
64F PRO 4.2 1.2 + - - -
65F ALA 3.4 9.2 + - - +
66F ARG 3.3 0.4 - - - -
67F ALA* 1.3 78.3 - - - +
69F LEU* 1.3 86.3 + - + +
71F THR* 3.5 4.9 + - - -
72F VAL* 3.2 44.2 + - + +
4H T 3.5 39.3 + + + +
5H G 3.9 41.8 - + - +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F LEU* 5.7 2.2 - - + -
22F HIS* 3.7 38.6 - - + +
26F LEU* 4.0 14.4 - - + -
47F THR* 3.6 22.8 - - + +
48F LEU* 4.2 20.4 - - + -
51F ALA* 4.2 10.1 - - + -
57F VAL* 5.7 0.7 - - + -
65F ALA* 3.2 18.1 + - + +
66F ARG* 3.1 10.8 + - + +
68F TRP* 1.3 102.0 - - + +
70F PHE* 1.3 60.0 + - + +
72F VAL 3.2 0.7 + - - -
73F ALA* 2.9 31.2 + - - +
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Residues in contact with PHE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F VAL* 4.0 25.1 - - + -
26F LEU* 3.9 13.7 - - + -
29F TYR* 3.4 59.7 + + + +
66F ARG* 3.0 56.8 + - + -
67F ALA 3.4 5.3 + - - +
69F LEU* 1.3 75.6 - - - +
71F THR* 1.3 57.1 + - - +
73F ALA* 4.6 0.2 - - - -
74F ARG* 3.0 27.0 + - - +
8H A 3.6 45.8 - + + +
9H G 5.5 6.7 - + - -
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Residues in contact with THR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ALA 3.0 16.8 + - - -
68F TRP* 3.9 6.5 - - - -
69F LEU 3.1 0.2 - - - -
70F PHE* 1.3 75.9 - - - +
72F VAL* 1.3 64.0 + - - +
74F ARG* 3.4 8.7 + - + +
75F ASN* 3.1 32.4 + - - +
4H T 3.8 33.4 - - - +
5H G 4.8 11.0 + - - +
8H A 3.4 15.4 + - - -
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Residues in contact with VAL 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F THR* 3.9 19.1 - - + -
50F ARG* 4.3 14.1 - - + +
68F TRP* 3.2 49.8 + - + +
69F LEU 3.2 3.8 + - - +
71F THR* 1.3 75.1 - - - +
73F ALA* 1.3 63.2 + - - +
75F ASN* 3.4 2.9 + - - +
76F MET* 3.0 43.7 + - + +
4H T 3.6 32.0 + - + +
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Residues in contact with ALA 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 3.9 18.2 - - + -
29F TYR* 4.5 8.5 - - + -
30F ALA* 5.1 3.8 - - + -
43F VAL* 3.7 21.7 - - + +
47F THR* 3.8 12.7 + - - +
69F LEU 2.9 16.6 + - - +
70F PHE 4.1 3.1 - - - +
72F VAL* 1.3 75.5 - - - +
74F ARG* 1.3 64.9 + - - +
76F MET* 3.3 2.6 + - - +
77F ILE* 3.0 30.8 + - + +
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C VAL* 5.9 6.7 - - - +
402C GLU* 4.1 34.2 + - - +
403C ARG* 6.2 2.0 - - - +
29F TYR* 3.7 20.0 + - - +
33F LEU* 4.4 16.2 - - + -
70F PHE 3.0 20.1 + - - +
71F THR* 3.7 10.1 - - - +
72F VAL 3.3 0.2 - - - -
73F ALA* 1.3 76.6 - - - +
75F ASN* 1.3 72.9 + - - +
77F ILE* 3.2 3.5 + - - +
78F ILE* 3.2 36.5 + - - +
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Residues in contact with ASN 75 (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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71F THR* 3.1 21.3 + - - +
72F VAL* 3.9 3.6 - - - +
73F ALA 3.3 0.2 - - - -
74F ARG* 1.3 87.1 + - - +
76F MET* 1.3 65.4 + - + +
78F ILE* 3.2 12.7 - - + +
79F ASP* 2.9 28.5 - - - +
3H G 3.4 37.6 + - - +
4H T 2.4 37.0 + - + +
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Residues in contact with MET 76 (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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43F VAL* 4.4 15.3 - - + +
46F GLU* 3.5 46.7 - - + +
47F THR* 4.1 13.9 - - - +
50F ARG* 3.3 44.4 - - + +
72F VAL* 3.0 25.0 + - + +
73F ALA* 3.6 6.3 - - - +
75F ASN* 1.3 77.6 - - + +
77F ILE* 1.3 62.9 + - - +
79F ASP* 3.4 7.5 + - - +
80F GLU* 3.2 24.7 + - - +
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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
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30F ALA* 3.8 21.3 - - + -
33F LEU* 3.5 48.2 - - + +
34F THR* 3.7 31.6 - - + -
39F GLN* 5.2 2.7 - - - +
43F VAL* 4.1 14.1 - - + -
73F ALA 3.0 17.3 + - - +
74F ARG* 3.2 5.8 + - - +
76F MET* 1.3 76.3 - - - +
78F ILE* 1.3 65.9 + - - +
80F GLU* 3.3 10.0 + - - +
81F ARG* 3.2 27.0 + - + +
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Residues in contact with ILE 78 (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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74F ARG* 3.2 26.2 + - - +
75F ASN* 3.2 25.4 - - + +
77F ILE* 1.3 78.4 - - - +
79F ASP* 1.3 70.5 + - - +
81F ARG* 3.0 36.3 + - + +
82F ARG* 3.8 9.7 + - + +
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Residues in contact with ASP 79 (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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75F ASN* 2.9 20.0 + - - +
76F MET* 3.7 7.9 - - - +
77F ILE 3.2 0.8 - - - -
78F ILE* 1.3 83.1 - - - +
80F GLU* 1.3 63.8 + - - +
81F ARG 3.2 0.5 + - - -
82F ARG* 3.3 25.3 + - - +
3H G 4.6 10.1 - - - +
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Residues in contact with GLU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D ARG* 6.0 0.2 + - - -
39F GLN* 4.1 25.5 + - + +
43F VAL* 6.3 2.5 - - + -
76F MET 3.2 13.8 + - - +
77F ILE* 3.3 10.7 + - - +
79F ASP* 1.3 79.1 - - - +
81F ARG* 1.3 57.4 + - + +
82F ARG 3.0 6.3 + - - +
84F ALA* 5.5 0.9 + - - +
85F ARG* 3.4 30.0 + - - +
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU 4.9 12.9 + - - -
34F THR* 5.6 3.2 + - - +
77F ILE* 3.2 20.2 + - + +
78F ILE* 3.0 32.7 + - + +
80F GLU* 1.3 75.8 - - + +
82F ARG* 1.3 61.7 + - - +
85F ARG* 3.7 43.4 - - - +
86F PHE* 3.7 19.1 - - - -
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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