Contacts of the strand formed by residues 66 - 72 (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 LYS 66 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64H GLU 3.5 5.7 + - - +
65H ASP* 1.3 75.8 - - - +
67H ILE* 1.3 62.7 + - - +
68H THR* 5.3 0.5 + - - -
82H LYS* 4.8 21.7 - - + +
83H GLY 3.4 15.3 - - - +
84H LYS* 4.7 8.3 - - + +
161H ASP* 4.8 0.7 - - - +
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Residues in contact with ILE 67 (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 4.4 1.3 + - - +
66H LYS* 1.3 76.7 - - - +
68H THR* 1.3 60.3 + - - +
69H VAL* 3.8 6.4 + - + +
82H LYS* 3.3 4.4 - - - -
83H GLY 2.8 44.8 + - - +
85H VAL* 4.0 22.0 - - + -
156H LEU* 3.8 29.2 - - + -
157H THR 3.8 6.7 - - - +
158H LYS* 4.4 15.9 - - + +
160H MET* 3.8 39.5 - - + +
161H ASP* 3.2 23.1 - - + +
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Residues in contact with THR 68 (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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67H ILE* 1.3 73.9 - - - +
69H VAL* 1.3 65.6 + - - +
70H HIS* 3.9 8.3 - - + +
80H THR* 3.7 24.2 - - + -
81H THR 3.4 13.0 - - - +
82H LYS* 4.0 14.9 - - + +
160H MET 3.8 1.0 - - - +
161H ASP* 2.6 18.3 + - - -
162H ASN* 2.6 50.8 + - - +
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Residues in contact with VAL 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H ILE* 3.8 10.9 + - + +
68H THR* 1.3 79.2 - - - +
70H HIS* 1.3 72.1 + - - +
71H PHE* 3.7 25.2 + - + -
79H LEU 3.8 1.0 - - - +
80H THR* 3.8 0.3 - - - -
81H THR* 3.0 39.1 + - + +
83H GLY 5.4 1.8 - - - +
89H LEU* 4.1 7.6 - - + -
92H VAL* 5.5 2.5 - - + -
156H LEU* 3.8 34.5 - - + -
163H MET* 3.7 28.7 - - + +
165H VAL* 4.4 3.8 - - + -
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Residues in contact with HIS 70 (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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68H THR* 3.9 7.6 - - + +
69H VAL* 1.3 74.5 - - - +
71H PHE* 1.3 62.3 + - - +
78H THR* 4.3 15.5 - - + +
79H LEU 3.4 3.1 - - - -
80H THR* 2.7 41.7 + - + +
162H ASN* 3.3 44.2 + - - +
163H MET 2.9 8.9 + - - +
164H THR* 3.2 18.1 - - + +
165H VAL* 2.9 29.1 + - - +
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Residues in contact with PHE 71 (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* 3.7 19.7 - - + -
70H HIS* 1.3 77.4 - - - +
72H ILE* 1.3 64.7 + - - +
73H ASN* 3.8 0.6 + - - +
77H GLU 3.5 1.6 - - - +
78H THR* 3.2 4.6 - - - -
79H LEU* 2.8 56.5 + - + +
81H THR* 3.9 14.4 - - + -
89H LEU* 4.0 22.9 - - + -
92H VAL* 4.0 8.1 - - + -
93H VAL* 3.7 28.9 - - + -
98H LEU* 3.9 20.2 - - + -
100H ILE* 4.3 13.5 - - + -
117H LEU* 4.5 9.4 - - + -
165H VAL* 3.4 23.3 - - + -
167H VAL* 4.4 12.1 - - + -
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Residues in contact with ILE 72 (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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183B THR* 3.6 25.1 - - - +
184B SER* 5.0 6.1 - - - +
71H PHE* 1.3 72.1 - - - +
73H ASN* 1.3 71.0 + - - +
76H GLY* 4.3 18.4 - - - +
77H GLU 3.6 2.7 - - - +
78H THR* 4.2 15.3 - - + +
164H THR* 3.8 27.1 - - + -
165H VAL 2.9 11.0 + - - +
166H ARG* 3.6 20.2 - - + +
167H VAL* 2.9 31.5 + - - +
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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