Contacts of the strand formed by residues 66 - 72 (chain F) in PDB entry 3P1M
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 LYS 66 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64F GLU 5.2 0.2 - - - +
65F ASP* 1.3 86.5 - - - +
67F ILE* 1.3 68.6 + - - +
82F LYS* 4.5 39.3 + - + +
83F GLY 3.3 16.8 - - - +
84F LYS* 4.2 34.4 - - + +
161F ASP* 4.9 0.3 - - - +
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Residues in contact with ILE 67 (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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65F ASP* 5.3 1.3 - - - +
66F LYS* 1.3 79.7 - - - +
68F THR* 1.3 60.1 + - - +
69F VAL* 3.9 6.6 + - + +
82F LYS* 3.2 8.0 - - - +
83F GLY 2.7 46.2 + - - +
85F VAL* 3.9 18.8 - - + -
156F LEU* 4.0 28.0 - - + -
157F THR 3.7 6.7 - - - +
158F LYS* 4.4 16.2 - - + +
160F MET* 3.7 40.8 - - + +
161F ASP* 3.2 24.0 - - + +
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Residues in contact with THR 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 ILE* 1.3 73.0 - - - +
69F VAL* 1.3 66.6 + - - +
70F HIS* 3.9 8.3 - - + +
80F THR* 3.7 23.6 - - + -
81F THR 3.4 11.7 - - - +
82F LYS* 3.8 19.3 - - + +
160F MET 3.8 1.2 - - - +
161F ASP* 2.7 18.5 + - - -
162F ASN* 2.6 50.4 + - - +
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Residues in contact with VAL 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 ILE* 3.9 12.3 + - + +
68F THR* 1.3 79.9 - - - +
70F HIS* 1.3 72.8 + - - +
71F PHE* 3.6 25.5 + - + -
79F LEU 3.8 0.5 - - - +
80F THR* 3.8 0.5 - - - -
81F THR* 3.0 38.5 + - + +
83F GLY 5.3 1.8 - - - +
89F LEU* 4.1 7.0 - - + -
92F VAL* 5.3 2.7 - - + -
156F LEU* 3.8 32.3 - - + -
163F MET* 3.7 28.9 - - + +
165F VAL* 4.4 3.8 - - + -
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Residues in contact with HIS 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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68F THR* 3.9 7.4 - - + +
69F VAL* 1.3 79.2 - - - +
71F PHE* 1.3 60.5 + - - +
78F THR* 4.3 13.0 - - + +
79F LEU 3.4 4.3 - - - +
80F THR* 2.7 41.4 + - + +
162F ASN* 3.2 44.0 + - - -
163F MET 2.9 11.1 + - - +
164F THR* 3.2 20.1 - - + +
165F VAL* 2.9 25.6 + - - +
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Residues in contact with PHE 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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69F VAL* 3.6 21.8 - - + -
70F HIS* 1.3 76.9 - - - +
72F ILE* 1.3 66.3 + - - +
73F ASN 3.8 0.6 + - - +
77F GLU 3.6 0.7 - - - +
78F THR* 3.3 5.1 - - - +
79F LEU* 2.8 56.2 + - + +
81F THR* 3.9 19.1 - - + -
89F LEU* 3.9 22.2 - - + -
92F VAL* 4.1 7.4 - - + -
93F VAL* 3.7 29.4 - - + -
98F LEU* 3.9 14.1 - - + -
100F ILE* 4.3 13.0 - - + -
117F LEU* 4.6 9.4 - - + -
165F VAL* 3.4 22.7 - - + -
167F VAL* 4.5 11.0 - - + -
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Residues in contact with ILE 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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183C THR* 3.9 23.8 - - + +
184C SER* 4.6 9.6 - - - +
71F PHE* 1.3 72.6 - - - +
73F ASN* 1.3 71.0 + - - +
76F GLY* 4.3 17.5 - - - +
77F GLU 3.6 3.4 - - - -
78F THR* 4.2 15.3 - - + +
164F THR* 3.7 26.2 - - + -
165F VAL 2.9 11.0 + - - +
166F ARG* 3.9 18.2 - - + +
167F VAL* 2.9 30.0 + - - +
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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