Contacts of the helix formed by residues 46 - 61 (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 ASN 46 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127I T 3.0 18.2 + - - -
128I G 2.7 51.2 + - + +
129I T 5.6 0.7 - - - +
22J A 3.7 9.5 + - - -
44L PRO 3.8 2.0 + - - +
45L MET* 1.3 75.3 - - - +
47L ALA* 1.3 64.4 + - - +
48L PHE* 2.9 6.8 + - - +
49L MET* 2.7 27.8 + - - +
50L VAL* 2.9 19.8 + - - +
94L ALA* 3.4 3.4 - - - -
98L ARG* 3.5 22.9 - - - +
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Residues in contact with ALA 47 (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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128I G 4.2 14.0 - - - +
46L ASN* 1.3 75.8 - - - +
48L PHE* 1.3 63.7 + - - +
50L VAL* 3.5 0.7 + - - +
51L TRP* 3.3 17.0 + - - +
79L TRP* 3.7 12.0 - - + -
90L PHE* 3.5 24.4 - - - +
91L ILE* 3.6 37.9 - - + +
94L ALA* 3.3 5.4 - - + +
98L ARG* 4.4 2.0 - - - +
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Residues in contact with PHE 48 (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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126I T 3.4 37.0 - + + -
127I T 3.3 42.0 - + - +
128I G 4.0 7.9 - - - -
46L ASN* 2.9 10.3 + - - +
47L ALA* 1.3 75.4 - - - +
49L MET* 1.3 59.6 + - - +
51L TRP* 3.3 23.2 + + - +
52L SER* 2.7 53.2 + - - -
72L SER* 5.8 0.2 - - - -
75L LEU* 3.6 14.6 - - + -
76L GLY* 3.8 23.6 - - - -
79L TRP* 3.7 28.2 - + + -
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Residues in contact with MET 49 (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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126I T 4.7 1.6 - - - +
127I T 4.0 1.3 - - - +
22J A 3.4 43.3 - - + +
23J A 3.4 64.6 - - + +
45L MET* 3.7 14.4 - - + +
46L ASN* 2.7 35.2 + - - +
48L PHE* 1.3 85.7 - - - +
50L VAL* 1.3 63.9 + - - +
52L SER* 3.1 10.4 + - - +
53L ARG* 3.0 23.6 + - - +
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Residues in contact with VAL 50 (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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45L MET* 3.6 18.8 - - + +
46L ASN 2.9 19.1 + - - +
47L ALA 3.9 4.0 - - - +
49L MET* 1.3 76.0 - - - +
51L TRP* 1.3 62.8 + - - +
53L ARG* 3.3 34.4 + - - +
54L GLY* 3.6 4.0 + - - -
90L PHE* 3.9 21.9 - - + +
93L GLU* 3.7 23.3 - - + -
94L ALA* 4.1 11.4 - - - +
97L LEU* 3.5 28.7 - - + -
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Residues in contact with TRP 51 (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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47L ALA 3.3 2.8 + - - +
48L PHE* 3.3 23.5 + + - +
50L VAL* 1.3 77.4 - - - +
52L SER* 1.3 86.2 + - - +
53L ARG 3.1 2.0 - - - -
54L GLY* 3.0 5.0 + - - -
55L GLN* 3.0 37.4 + - + +
75L LEU* 3.1 48.9 - - + -
78L GLU* 3.5 31.1 + - + -
79L TRP* 3.4 43.7 - + + -
82L LEU* 3.5 21.3 - - + +
90L PHE* 3.5 40.2 - + + -
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Residues in contact with SER 52 (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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126I T 5.4 0.4 + - - -
23J A 5.6 2.3 + - - -
48L PHE* 2.7 43.9 + - - -
49L MET* 3.1 19.9 + - - +
51L TRP* 1.3 88.5 - - - +
53L ARG* 1.3 55.0 + - - +
55L GLN* 4.3 0.7 - - - +
56L ARG* 2.4 43.8 + - - +
75L LEU* 3.6 13.3 - - - +
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Residues in contact with ARG 53 (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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23J A 5.0 19.1 - - - +
24J A 5.4 3.1 - - - +
45L MET* 3.7 33.4 - - - +
49L MET 3.0 13.2 + - - +
50L VAL* 3.3 28.2 + - - +
52L SER* 1.3 79.2 + - - +
54L GLY* 1.3 64.9 + - - +
56L ARG* 3.4 7.9 + - - +
57L ARG* 3.4 58.5 + - - +
93L GLU* 5.7 2.6 + - - +
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Residues in contact with GLY 54 (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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50L VAL 3.6 4.5 + - - -
51L TRP 3.0 7.1 + - - -
53L ARG* 1.3 86.3 - - - +
55L GLN* 1.3 61.3 + - - +
57L ARG* 3.5 8.0 + - - +
58L LYS* 3.1 24.4 + - - +
90L PHE* 6.2 2.5 - - - -
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Residues in contact with GLN 55 (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* 3.0 47.5 + - + +
52L SER 4.1 0.9 - - - +
54L GLY* 1.3 75.5 - - - +
56L ARG* 1.3 65.0 + - - +
57L ARG 3.2 0.7 - - - -
58L LYS* 3.4 26.9 - - - +
59L MET* 2.9 37.4 + - - +
75L LEU* 3.4 22.7 - - + -
78L GLU* 3.5 16.7 + - - +
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Residues in contact with ARG 56 (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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126I T 4.3 3.4 + - - -
23J A 4.1 18.0 + - - -
24J A 3.8 37.7 + - - +
52L SER* 2.4 35.8 + - - +
53L ARG* 3.5 9.6 - - - +
54L GLY 3.3 0.2 - - - -
55L GLN* 1.3 69.2 - - - +
57L ARG* 1.3 56.6 + - + +
59L MET* 4.0 0.7 - - - +
60L ALA* 2.8 42.5 + - + +
68L ASN* 3.0 52.8 + - - +
71L ILE* 3.4 21.4 - - - +
72L SER* 2.7 32.5 + - - +
75L LEU* 3.7 12.6 - - - +
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Residues in contact with ARG 57 (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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24J A 3.7 26.4 + - - -
53L ARG* 3.4 48.0 + - - +
54L GLY* 3.9 7.0 - - - +
55L GLN 3.2 0.2 - - - -
56L ARG* 1.3 81.7 - - + +
58L LYS* 1.3 56.7 + - - +
59L MET 3.2 0.9 - - - -
60L ALA* 4.5 4.5 - - - -
61L GLN* 3.2 34.7 + - + +
62L GLU 3.9 0.3 + - - -
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Residues in contact with LYS 58 (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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54L GLY 3.1 17.8 + - - +
55L GLN* 3.1 32.4 + - - +
57L ARG* 1.3 75.5 - - - +
59L MET* 1.3 65.3 + - - +
62L GLU* 3.3 34.1 - - + +
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Residues in contact with MET 59 (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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55L GLN* 2.9 28.7 + - - +
56L ARG 4.0 1.1 - - - +
58L LYS* 1.3 87.4 - - - +
60L ALA* 1.3 59.8 + - - +
61L GLN 3.3 0.9 - - - -
62L GLU* 4.7 2.9 - - - +
63L ASN* 2.8 47.0 + - + +
66L MET* 4.3 8.2 - - + +
71L ILE* 4.3 18.6 - - + -
74L ARG* 4.1 37.9 - - + +
75L LEU* 3.8 19.3 - - + -
78L GLU* 4.5 13.0 - - - +
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Residues in contact with ALA 60 (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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24J A 6.2 0.2 - - - +
25J G 5.8 8.3 - - - -
56L ARG* 2.8 31.0 + - + +
57L ARG* 4.5 2.7 - - - -
59L MET* 1.3 73.9 - - - +
61L GLN* 1.3 59.1 + - - +
63L ASN 3.4 15.1 - - - +
64L PRO* 3.8 7.1 - - - +
65L LYS 4.9 0.9 + - - -
66L MET 5.4 3.0 + - - +
68L ASN* 5.1 2.7 - - - +
71L ILE* 3.7 22.3 - - + +
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Residues in contact with GLN 61 (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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57L ARG* 3.2 20.2 + - + +
60L ALA* 1.3 80.5 - - + +
62L GLU* 1.3 66.5 + - - +
63L ASN 3.4 0.6 + - - -
64L PRO* 3.9 12.1 - - - +
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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
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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