Contacts of the helix formed by residues 57 - 69 (chain L) in PDB entry 6T9L
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 57 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99K CYS 4.1 2.9 - - - +
100K GLU* 2.8 33.7 - - - +
101K ASP* 4.0 6.4 - - - +
55L SER* 3.0 16.2 + - - +
56L THR* 1.3 75.6 - - - +
58L PHE* 1.3 65.3 + - - +
59L THR* 3.4 18.0 + - - -
60L GLN* 3.5 23.9 + - + +
61L ILE* 3.0 26.4 + - - +
32M THR* 5.3 0.2 - - - -
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Residues in contact with PHE 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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56K ALA* 6.0 1.3 - - + -
58K PHE* 5.8 1.6 - + - -
69K TRP* 4.6 11.0 - + - -
95K PHE* 3.6 29.4 - + + -
100K GLU 4.0 1.1 - - - +
101K ASP* 3.5 17.4 + - - +
102K TYR* 3.5 37.5 - + + -
56L THR 3.3 4.6 + - - -
57L ASN* 1.3 73.7 + - - +
59L THR* 1.3 62.3 + - + +
61L ILE* 3.3 3.5 + - - +
62L LEU* 2.7 62.6 + - + +
25M GLN* 4.5 11.9 - - + -
28M VAL* 3.8 30.7 - - + -
29M ALA* 3.8 9.6 - - - -
32M THR* 4.1 15.7 - - + -
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Residues in contact with THR 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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69K TRP* 4.4 15.3 - - + -
95K PHE* 4.2 8.5 - - + -
100K GLU* 3.2 48.7 + - + +
57L ASN* 3.4 12.9 + - - -
58L PHE* 1.3 77.4 - - + +
60L GLN* 1.3 53.6 + - - +
62L LEU* 4.4 5.4 - - - -
63L SER* 2.7 36.0 + - - -
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Residues in contact with GLN 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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53L ASN* 3.7 34.2 + - - +
55L SER* 2.8 30.9 + - - -
57L ASN* 3.4 24.8 + - + +
58L PHE 3.2 0.6 - - - -
59L THR* 1.3 82.3 + - - +
61L ILE* 1.3 62.2 + - + +
63L SER* 2.8 17.2 + - - -
64L THR* 3.4 14.9 - - + +
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Residues in contact with ILE 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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46L THR* 4.5 9.0 - - - +
49L GLU* 3.9 12.3 - - + +
50L MET* 3.9 28.0 - - + -
53L ASN* 3.4 29.6 - - + +
55L SER 4.3 9.9 - - - +
56L THR 5.1 0.7 - - - -
57L ASN 3.0 18.8 + - - +
58L PHE* 3.9 3.8 - - - +
60L GLN* 1.3 78.4 - - + +
62L LEU* 1.3 60.6 + - - +
64L THR* 2.5 29.8 + - - +
65L VAL* 3.0 22.3 + - + +
28M VAL* 3.8 24.7 - - + -
32M THR* 6.0 3.6 - - - +
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Residues in contact with LEU 62 (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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69K TRP* 4.0 17.0 - - + +
58L PHE* 2.7 50.1 + - + +
59L THR* 4.3 3.4 - - - +
61L ILE* 1.3 74.1 - - - +
63L SER* 1.3 60.9 + - - +
64L THR 3.1 1.1 + - - -
65L VAL* 3.8 7.9 - - + -
66L GLU* 3.2 44.7 + - + +
24M ILE* 4.5 2.2 - - + -
25M GLN* 3.7 42.0 - - + +
28M VAL* 3.8 21.3 - - + -
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Residues in contact with SER 63 (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 THR 2.7 25.1 + - - -
60L GLN* 2.8 17.8 + - - -
62L LEU* 1.3 74.2 - - - +
64L THR* 1.3 61.0 + - - +
67L PRO* 3.2 22.8 - - - +
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Residues in contact with THR 64 (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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49L GLU* 3.4 33.5 + - - +
53L ASN* 5.0 4.0 - - - +
60L GLN* 3.4 17.0 - - + +
61L ILE* 2.5 21.7 + - - -
63L SER* 1.3 83.5 - - - +
65L VAL* 1.3 66.3 + - - +
66L GLU 3.4 0.7 - - - -
67L PRO* 3.5 2.8 - - - +
68L LYS* 3.3 23.0 + - - +
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Residues in contact with VAL 65 (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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42L VAL 5.8 0.4 - - - +
45L LEU* 3.8 29.0 - - + +
46L THR* 4.6 10.5 - - - -
49L GLU* 3.8 26.0 - - + +
61L ILE* 3.2 24.5 - - + +
62L LEU* 3.8 15.9 - - + -
64L THR* 1.3 77.8 + - - +
66L GLU* 1.3 63.9 + - - +
68L LYS* 3.3 0.3 + - - +
69L ALA* 2.9 35.0 + - + +
24M ILE* 5.0 5.2 - - + -
28M VAL* 4.3 15.0 - - + -
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Residues in contact with GLU 66 (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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62L LEU* 3.2 32.8 + - + +
65L VAL* 1.3 80.6 - - - +
67L PRO* 1.3 70.8 - - + +
69L ALA 3.6 3.3 + - - -
70L LEU* 3.3 28.3 + - - +
20M LEU* 5.5 0.3 - - - +
21M THR* 3.8 30.2 + - - +
24M ILE* 3.8 35.4 - - + +
25M GLN* 5.2 2.2 - - + +
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Residues in contact with PRO 67 (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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63L SER* 3.2 29.2 - - - +
64L THR 3.5 5.8 - - - +
66L GLU* 1.3 98.5 - - + +
68L LYS* 1.3 55.9 + - - +
70L LEU* 3.7 21.6 - - + +
71L GLU* 3.1 15.8 - - - +
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Residues in contact with LYS 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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45L LEU* 4.0 23.0 - - + +
64L THR 3.3 18.4 + - - +
65L VAL* 3.3 7.3 + - - +
66L GLU 3.2 0.6 - - - -
67L PRO* 1.3 76.9 - - - +
69L ALA* 1.3 60.3 + - - +
70L LEU 3.1 4.7 - - - -
71L GLU* 2.9 48.4 + - - +
72L MET* 3.3 29.5 - - + +
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Residues in contact with ALA 69 (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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38L TRP* 3.8 10.0 - - + -
42L VAL* 4.6 7.0 - - + -
45L LEU* 5.3 3.4 - - + -
65L VAL* 2.9 17.9 + - + +
66L GLU 3.6 0.2 + - - -
67L PRO 3.5 0.4 - - - -
68L LYS* 1.3 76.0 - - - +
70L LEU* 1.3 62.4 + - - +
71L GLU 3.4 0.4 - - - -
72L MET* 3.1 35.8 - - - +
73L VAL* 3.3 13.2 - - - +
24M ILE* 3.8 27.7 - - + +
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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