Contacts of the strand formed by residues 78 - 84 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H HIS* 4.3 23.1 - - + +
71H PHE 3.2 11.2 - - - +
72H ILE* 4.2 15.8 - - + +
76H GLY 3.9 4.9 + - - -
77H GLU* 1.3 78.4 - - - +
79H LEU* 1.3 68.2 + - - +
80H THR* 4.1 7.3 + - - +
164H THR* 5.6 0.9 - - + -
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Residues in contact with LEU 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H VAL 3.8 1.0 - - - +
70H HIS* 3.4 1.3 - - - -
71H PHE* 2.8 54.0 + - + +
73H ASN* 4.0 24.0 - - + +
77H GLU* 4.2 26.5 - - + +
78H THR* 1.3 79.0 - - - +
80H THR* 1.3 62.9 + - - +
98H LEU* 4.2 28.9 - - + -
99H ASP* 4.1 25.8 - - + +
100H ILE* 4.6 6.7 - - + -
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Residues in contact with THR 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H THR* 3.7 15.0 - - + -
69H VAL 3.8 3.1 - - - -
70H HIS* 2.7 38.1 + - + +
78H THR* 4.1 7.4 + - - +
79H LEU* 1.3 72.6 - - - +
81H THR* 1.3 66.8 + - - +
82H LYS* 6.3 0.4 - - + -
98H LEU* 5.4 1.6 - - - +
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Residues in contact with THR 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H THR* 3.4 8.2 - - - +
69H VAL* 3.0 40.5 + - + +
71H PHE* 3.9 12.8 - - + -
80H THR* 1.3 76.9 - - - +
82H LYS* 1.3 69.0 + - - +
92H VAL* 3.6 29.8 - - + -
96H ASN* 3.0 25.2 + - - +
98H LEU* 4.2 18.5 - - + +
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Residues in contact with LYS 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H LYS* 4.8 19.7 - - + +
67H ILE 3.3 7.0 - - - +
68H THR* 4.0 17.9 - - + +
80H THR* 6.3 0.4 - - + -
81H THR* 1.3 83.9 + - - +
83H GLY* 1.3 59.8 + - - +
96H ASN* 3.0 22.4 + - - +
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Residues in contact with GLY 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H LYS* 3.4 6.3 - - - -
67H ILE* 2.8 36.6 + - - +
69H VAL* 5.3 2.0 - - - +
82H LYS* 1.3 73.9 - - - +
84H LYS* 1.3 65.3 + - - -
87H ASP* 5.2 0.7 - - - -
92H VAL* 4.2 13.4 - - - +
96H ASN* 5.0 0.2 - - - -
156H LEU* 3.8 16.5 - - - +
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Residues in contact with LYS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H ASP 4.6 5.4 - - - +
66H LYS* 4.7 7.6 - - + +
67H ILE* 5.3 0.2 - - - -
83H GLY* 1.3 73.6 - - - -
85H VAL* 1.3 68.7 + - - +
86H GLY 3.4 0.2 + - - -
87H ASP* 3.1 44.4 + - - +
156H LEU* 3.4 9.6 - - - +
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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