Contacts of the helix formed by residues 67 - 81 (chain L) in PDB entry 6YOV
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 HIS 67 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26J G 5.1 15.7 + - - -
27J C 4.6 23.6 + - - -
65L LYS 4.0 11.9 + - - -
66L MET* 1.3 80.4 - - - +
68L ASN* 1.3 65.8 + - - +
69L SER* 4.0 14.4 - - - +
70L GLU* 3.0 22.2 + - + +
71L ILE* 3.0 12.3 + - - +
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Residues in contact with ASN 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I T 4.4 1.6 - - - -
24J A 3.5 18.9 + - + +
25J G 2.6 71.0 + - - +
26J G 5.4 2.6 + - - -
56L ARG* 3.0 32.4 + - - +
60L ALA* 5.1 2.3 - - - +
66L MET 3.8 1.5 + - - -
67L HIS* 1.3 71.6 - - - +
69L SER* 1.3 63.1 + - - +
71L ILE* 3.8 9.5 - - - +
72L SER* 3.0 30.0 + - - -
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Residues in contact with SER 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I C 3.6 22.9 + - - -
125I T 3.5 35.3 - - - +
25J G 4.7 2.1 + - - +
26J G 5.7 0.7 + - - -
67L HIS* 3.1 11.1 - - - +
68L ASN* 1.3 80.8 - - - +
70L GLU* 1.3 60.3 + - - +
72L SER 3.7 0.2 + - - -
73L LYS* 3.3 32.7 + - - +
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Residues in contact with GLU 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L MET* 4.0 17.9 - - + -
67L HIS* 3.0 17.0 + - + +
69L SER* 1.3 76.5 - - - +
71L ILE* 1.3 66.3 + - - +
73L LYS* 3.2 25.0 + - - +
74L ARG* 3.1 59.9 + - - +
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Residues in contact with ILE 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L ARG* 3.4 30.5 - - - +
59L MET* 4.3 13.5 - - + -
60L ALA* 3.7 37.2 - - + -
66L MET* 3.4 34.8 - - - +
67L HIS 3.0 10.8 + - - +
68L ASN* 3.3 17.2 + - - +
70L GLU* 1.3 76.5 - - - +
72L SER* 1.3 57.2 + - - +
74L ARG* 3.1 6.0 + - - +
75L LEU* 2.8 47.1 + - + +
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Residues in contact with SER 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I T 2.4 48.7 + - - -
126I T 3.0 26.7 + - - +
56L ARG* 2.7 25.0 + - - +
68L ASN 3.0 8.4 + - - -
69L SER 3.8 0.9 - - - -
71L ILE* 1.3 76.6 - - - +
73L LYS* 1.3 61.6 + - - +
75L LEU* 3.9 3.2 - - - +
76L GLY 2.9 19.8 + - - -
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Residues in contact with LYS 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I T 3.6 41.1 + - - +
126I T 4.0 15.0 + - - +
69L SER* 3.3 26.2 + - - +
70L GLU* 3.2 24.7 + - - +
71L ILE 3.2 0.4 - - - -
72L SER* 1.3 77.6 - - - +
74L ARG* 1.3 65.5 + - + +
76L GLY* 3.4 1.4 + - - -
77L ALA* 3.3 20.3 + - - +
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Residues in contact with ARG 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L MET* 4.1 21.9 - - + +
63L ASN* 3.8 11.7 - - - +
66L MET* 3.2 35.5 - - - +
70L GLU* 3.1 41.4 + - - +
71L ILE* 3.1 7.9 + - + +
73L LYS* 1.3 79.4 - - + +
75L LEU* 1.3 60.9 + - + +
77L ALA* 3.2 6.8 + - - +
78L GLU* 2.8 31.3 + - - +
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Residues in contact with LEU 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L PHE* 3.8 7.2 - - + -
51L TRP* 3.1 22.8 - - + -
52L SER* 3.6 32.8 - - - +
55L GLN* 3.4 26.0 - - + -
56L ARG* 3.7 14.1 - - - +
59L MET* 3.8 17.9 - - + -
71L ILE* 2.8 39.4 + - + +
72L SER* 3.9 4.3 - - - +
74L ARG* 1.3 72.9 - - + +
76L GLY* 1.3 68.1 + - - +
78L GLU* 3.8 12.8 - - - +
79L TRP* 2.9 21.0 + - - +
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Residues in contact with GLY 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I T 4.0 19.1 - - - -
127I T 4.9 5.5 - - - +
48L PHE* 3.8 14.9 - - - -
72L SER 2.9 17.5 + - - -
73L LYS 3.8 1.8 - - - -
74L ARG 3.2 0.2 - - - -
75L LEU* 1.3 78.6 - - - +
77L ALA* 1.3 61.5 + - - +
79L TRP* 3.3 3.8 + - - +
80L LYS* 3.2 25.7 + - - +
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Residues in contact with ALA 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L LYS 3.3 10.7 + - - +
74L ARG* 3.2 9.7 + - - +
76L GLY* 1.3 77.3 - - - +
78L GLU* 1.3 62.4 + - - +
80L LYS* 3.1 18.6 + - - +
81L LEU* 3.2 24.1 + - + +
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Residues in contact with GLU 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L TRP* 3.5 22.7 + - + -
55L GLN* 3.5 21.5 - - - +
59L MET* 4.5 11.1 - - - +
74L ARG* 2.8 21.1 + - - +
75L LEU* 3.7 18.5 - - - +
77L ALA* 1.3 72.4 - - - +
79L TRP* 1.3 63.6 + - - +
81L LEU* 3.2 20.7 + - + +
82L LEU* 3.4 19.7 + - + +
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Residues in contact with TRP 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I T 3.6 12.5 + - - -
128I G 2.7 29.1 + - - -
47L ALA* 3.7 30.7 - - + -
48L PHE* 3.7 17.9 - + + -
51L TRP* 3.4 56.2 - + + -
75L LEU 2.9 18.3 + - - +
76L GLY 3.6 3.8 - - - +
78L GLU* 1.3 76.5 - - - +
80L LYS* 1.3 76.2 + - + +
82L LEU* 3.0 26.9 + - + +
87L LYS* 3.1 70.0 - - + +
90L PHE* 4.0 5.2 - - + -
91L ILE* 4.2 4.5 - - + -
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Residues in contact with LYS 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I T 4.6 22.0 - - - +
128I G 4.5 13.5 + - - -
76L GLY 3.2 15.2 + - - +
77L ALA* 3.1 11.6 + - - +
79L TRP* 1.3 92.2 - - + +
81L LEU* 1.3 64.1 + - + +
82L LEU 3.6 2.3 + - - +
87L LYS* 4.0 18.8 + - - +
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Residues in contact with LEU 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L ALA* 3.3 22.4 - - + +
78L GLU* 3.2 13.1 + - + +
79L TRP 3.1 1.2 - - - -
80L LYS* 1.3 78.7 - - + +
82L LEU* 1.3 64.9 + - - +
83L SER 3.9 0.5 + - - -
86L GLU* 4.6 1.2 - - - +
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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