Contacts of the strand formed by residues 66 - 73 (chain L) in PDB entry 6AHU
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 TYR 66 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122H VAL* 4.7 19.4 - - + +
124H ASP* 5.3 3.2 + - - -
65L PRO* 1.3 75.8 - - - +
67L TYR* 1.3 70.9 + - - +
180L LEU* 4.6 17.9 - - + -
181L LEU 3.7 9.0 - - - +
182L ALA* 4.3 1.8 - - + -
205L HIS* 2.9 66.5 + + + +
206L GLN 3.9 19.1 + - - -
207L PRO* 4.0 7.4 - - + -
208L LYS* 5.9 2.3 - - - +
282L THR 4.8 1.4 + - - -
283L GLY* 3.8 12.9 - - - -
284L PHE* 3.6 57.9 - - + +
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Residues in contact with TYR 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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65L PRO* 4.6 15.2 - - + +
66L TYR* 1.3 80.9 - - - +
68L PHE* 1.3 59.5 + - - +
69L VAL 4.3 0.4 - - - -
180L LEU* 3.6 5.0 - - - -
181L LEU* 2.6 45.0 + - + +
182L ALA* 4.9 3.4 - - - -
183L TRP 5.9 0.9 - - - -
192L THR* 3.7 16.5 + - - -
193L MET* 3.6 36.6 - - + -
194L MET* 3.6 26.5 - - + +
202L ILE* 3.8 32.1 - - + -
203L GLN 3.4 1.3 - - - -
204L GLU* 3.6 41.8 + - + -
205L HIS* 4.7 0.2 - - - -
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Residues in contact with PHE 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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124H ASP* 4.4 17.5 - - + +
67L TYR* 1.3 75.3 - - - +
69L VAL* 1.3 62.2 + - - +
70L LYS* 3.6 36.1 - - + -
97L TYR* 3.7 39.0 - + + -
178L ASP* 3.7 28.7 - - + -
179L PHE 3.4 14.4 - - - -
180L LEU* 3.6 17.5 - - + -
201L GLN 3.2 6.6 - - - +
202L ILE* 3.4 0.2 - - - -
203L GLN* 3.1 33.7 + - - +
205L HIS* 3.6 24.9 - - + +
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Residues in contact with VAL 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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68L PHE* 1.3 78.7 - - - +
70L LYS* 1.3 64.1 - - - +
71L ASN 3.8 0.2 + - - -
72L LEU* 3.7 29.1 + - + -
177L PHE 3.9 1.2 - - - +
178L ASP* 3.4 6.9 - - - +
179L PHE* 3.3 29.2 + - + +
181L LEU* 3.8 28.9 - - + -
197L PHE* 4.7 7.6 - - + -
200L TYR* 3.8 26.7 - - + -
201L GLN 3.6 3.8 - - - +
202L ILE* 3.8 28.9 - - + -
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Residues in contact with LYS 70 (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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68L PHE* 3.6 31.2 - - + -
69L VAL* 1.3 74.9 - - - +
71L ASN* 1.3 78.0 + - - +
72L LEU 3.6 0.2 + - - -
178L ASP* 3.4 9.9 - - - +
200L TYR* 4.0 13.0 - - - +
201L GLN* 3.5 37.0 + - + +
203L GLN* 4.6 19.3 - - - +
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Residues in contact with ASN 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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70L LYS* 1.3 78.3 - - - +
72L LEU* 1.3 62.1 + - - +
73L PRO* 3.6 2.9 - - - +
176L LYS* 3.4 48.4 - - + +
177L PHE* 3.2 6.7 + - - -
178L ASP* 2.9 18.2 + - - +
200L TYR* 3.4 21.8 - - + -
201L GLN* 5.8 1.7 + - - +
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Residues in contact with LEU 72 (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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69L VAL* 3.7 17.3 - - + -
70L LYS 4.5 0.2 - - - -
71L ASN* 1.3 75.3 - - - +
73L PRO* 1.3 78.4 - - + +
74L LEU 4.0 0.2 + - - -
76L GLU* 4.0 9.4 - - + -
77L LEU* 4.1 18.2 - - + -
175L LEU 4.1 0.2 - - - +
176L LYS* 3.4 1.0 - - - -
177L PHE 2.8 27.8 + - - +
179L PHE* 3.2 33.9 - - + -
181L LEU* 4.2 14.1 - - + -
197L PHE* 3.7 35.2 - - + -
200L TYR* 3.7 26.5 - - + -
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Residues in contact with PRO 73 (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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71L ASN 3.6 5.8 - - - +
72L LEU* 1.3 96.5 - - + +
74L LEU* 1.3 65.5 + - - +
75L HIS* 3.5 37.0 - - + +
76L GLU* 3.6 17.5 + - + +
77L LEU* 4.3 5.2 + - - +
175L LEU 3.3 13.5 - - - +
176L LYS* 3.9 7.4 - - + -
179L PHE* 4.5 1.1 - - - -
200L TYR* 3.4 30.3 - - + +
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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