Contacts of the strand formed by residues 78 - 84 (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 THR 78 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F HIS* 4.3 22.0 - - + +
71F PHE 3.3 12.1 - - - +
72F ILE* 4.2 15.8 - - + +
76F GLY 4.0 4.5 + - - -
77F GLU* 1.3 79.3 - - - +
79F LEU* 1.3 69.9 + - - +
80F THR* 4.1 7.3 + - - +
164F THR* 5.6 1.1 - - + -
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Residues in contact with LEU 79 (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 3.8 1.4 - - - +
70F HIS* 3.4 1.2 - - - -
71F PHE* 2.8 52.5 + - + +
73F ASN* 4.0 22.9 - - + +
77F GLU* 3.9 31.2 - - + +
78F THR* 1.3 76.5 - - - +
80F THR* 1.3 61.0 + - - +
81F THR* 5.4 0.2 - - - -
98F LEU* 4.1 28.7 - - + -
99F ASP* 4.1 25.8 - - + +
100F ILE* 4.6 7.4 - - + -
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Residues in contact with THR 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F THR* 3.7 14.6 - - + -
69F VAL 3.8 3.1 - - - -
70F HIS* 2.7 38.1 + - + +
78F THR* 4.1 6.9 + - - +
79F LEU* 1.3 72.3 - - - +
81F THR* 1.3 66.7 + - - +
82F LYS* 6.3 0.4 - - + -
98F LEU* 5.5 1.2 - - - +
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Residues in contact with THR 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F THR* 3.4 9.1 - - - +
69F VAL* 3.0 38.9 + - + +
71F PHE* 3.9 13.2 - - + -
79F LEU 5.4 0.2 - - - -
80F THR* 1.3 77.3 - - - +
82F LYS* 1.3 70.7 + - - +
92F VAL* 3.6 28.9 - - + -
96F ASN* 2.8 25.2 + - - +
98F LEU* 4.3 18.7 - - + +
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Residues in contact with LYS 82 (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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66F LYS* 4.5 40.8 + - + +
67F ILE* 3.2 8.7 - - - +
68F THR* 3.8 20.6 - - + +
80F THR* 6.3 0.4 - - + -
81F THR* 1.3 88.7 + - - +
83F GLY* 1.3 58.8 + - - +
96F ASN* 3.1 21.7 + - - +
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Residues in contact with GLY 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F LYS* 3.3 6.7 - - - -
67F ILE* 2.7 40.2 + - - +
69F VAL* 5.3 1.8 - - - +
81F THR* 5.2 0.4 - - - +
82F LYS* 1.3 74.5 - - - +
84F LYS* 1.3 64.5 + - - -
87F ASP* 5.3 0.2 - - - -
92F VAL* 4.2 14.3 - - - +
96F ASN* 5.0 0.2 - - - -
156F LEU* 3.8 16.5 - - - +
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Residues in contact with LYS 84 (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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64F GLU 4.9 9.2 - - - +
65F ASP 4.4 0.2 - - - -
66F LYS* 4.2 37.5 - - + +
83F GLY* 1.3 74.9 - - - -
85F VAL* 1.3 71.1 + - - +
86F GLY 3.4 0.2 + - - -
87F ASP* 3.1 41.5 + - - +
95F GLU* 2.6 34.2 + - - +
156F LEU* 3.5 7.9 - - - +
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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