Contacts of the helix formed by residues 67 - 75 (chain F) in PDB entry 5SV1
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 67 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65F ALA* 3.2 2.6 - - - +
66F ARG* 1.3 79.8 - - - +
68F LEU* 1.3 64.2 + - - +
69F ASN* 3.6 7.5 + - - +
70F GLN* 2.9 37.5 + - - +
71F ALA* 2.9 12.1 + - - +
219F LEU* 4.0 7.6 - - - -
223F ASP* 4.0 14.1 - - - -
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Residues in contact with LEU 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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67F SER* 1.3 70.7 - - - +
69F ASN* 1.3 56.5 + - - +
71F ALA* 3.3 3.4 + - + +
72F ASN* 3.0 40.5 + - - +
88F LEU* 4.0 23.3 - - + -
91F ALA* 5.7 4.7 - - + -
92F GLN* 5.2 5.6 - - - +
95F LEU* 4.6 15.7 - - + -
216F VAL* 4.4 12.6 - - + +
219F LEU* 3.8 29.2 - - + +
220F GLN* 3.9 31.9 - - + -
223F ASP* 2.9 23.3 + - + +
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Residues in contact with ASN 69 (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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67F SER* 3.1 6.3 + - - +
68F LEU* 1.3 75.1 - - - +
70F GLN* 1.3 60.7 + - - +
72F ASN* 3.2 9.4 + - - +
73F ASP* 2.9 43.6 + - - +
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Residues in contact with GLN 70 (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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64F GLU* 4.3 7.9 + - - +
65F ALA* 4.1 8.3 - - + +
66F ARG* 3.3 49.3 + - - +
67F SER* 2.9 24.4 + - - +
69F ASN* 1.3 75.2 - - - +
71F ALA* 1.3 57.0 + - - +
73F ASP* 3.3 9.8 + - + +
74F ILE* 2.9 46.4 + - + +
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Residues in contact with ALA 71 (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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62F LEU* 3.9 18.4 - - + +
65F ALA* 3.6 21.7 - - + +
67F SER 2.9 8.5 + - - +
68F LEU* 3.5 9.0 - - - +
69F ASN 3.1 0.2 - - - -
70F GLN* 1.3 74.5 - - - +
72F ASN* 1.3 60.7 + - - +
74F ILE* 3.0 2.9 + - - +
75F ALA* 2.8 32.2 + - - +
88F LEU* 4.5 15.7 - - + -
215F GLN* 6.4 0.2 - - + -
216F VAL* 6.2 0.9 - - + -
219F LEU* 4.0 13.0 - - + -
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Residues in contact with ASN 72 (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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68F LEU* 3.0 28.2 + - - +
69F ASN* 3.2 16.4 + - - +
71F ALA* 1.3 75.2 - - - +
73F ASP* 1.3 60.2 + - - +
75F ALA* 3.8 1.1 - - - -
76F ALA* 3.0 28.9 + - - +
85F LEU* 5.8 4.2 - - - +
88F LEU* 4.1 35.5 + - - +
89F ASN* 5.1 5.9 + - - -
92F GLN* 4.2 20.5 + - - +
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Residues in contact with ASP 73 (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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69F ASN* 2.9 32.5 + - - +
70F GLN* 3.6 11.8 - - + +
71F ALA 3.1 0.2 - - - -
72F ASN* 1.3 78.7 - - - +
74F ILE* 1.3 66.7 + - + +
76F ALA* 3.4 16.4 + - - +
77F ASP* 4.8 2.9 - - - +
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Residues in contact with ILE 74 (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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61F LEU* 3.9 48.7 - - + +
62F LEU* 4.1 11.7 - - + -
64F GLU* 5.0 8.3 - - + +
65F ALA* 4.6 13.2 - - + +
70F GLN* 2.9 39.3 + - + +
71F ALA 3.7 3.4 - - - +
73F ASP* 1.3 77.3 - - + +
75F ALA* 1.3 59.3 + - - +
76F ALA 3.3 1.0 + - - -
77F ASP* 4.6 5.7 - - - +
78F PHE* 3.9 11.7 - - + -
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Residues in contact with ALA 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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62F LEU* 4.0 12.6 - - + -
71F ALA 2.8 19.1 + - - +
72F ASN* 3.8 2.5 - - - +
74F ILE* 1.3 71.0 - - - +
76F ALA* 1.3 65.4 + - - +
77F ASP* 3.2 4.1 + - - -
78F PHE* 3.5 38.2 + - + -
84F SER* 5.4 2.0 - - - -
85F LEU* 3.5 19.0 - - + +
88F LEU* 4.1 17.5 - - + -
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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
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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