Contacts of the helix formed by residues 88 - 96 (chain B) 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 SER 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLY 3.9 1.6 + - - -
87B ASP* 1.3 75.0 - - - +
89B LEU* 1.3 60.9 + - - +
90B LEU* 3.3 10.4 + - - +
91B ASP* 2.9 53.4 + - - +
92B VAL* 3.1 11.8 + - - +
152B CYS* 3.6 23.5 + - - +
154B ILE 3.3 9.6 - - - -
155B CYS* 4.2 10.9 - - - +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 4.1 9.4 - - + -
71B PHE* 3.9 26.5 - - + -
88B SER* 1.3 71.9 - - - +
90B LEU* 1.3 61.0 + - - +
92B VAL* 3.2 9.8 + - + +
93B VAL* 3.0 27.9 + - - +
103B PHE* 5.0 0.7 - - - -
117B LEU* 4.0 17.9 - - + -
119B PHE* 3.7 37.0 - - + -
151B GLY 3.2 10.8 + - - +
154B ILE* 3.0 30.3 + - + +
156B LEU* 4.2 14.6 - - + -
163B MET* 3.9 23.3 - - + -
165B VAL* 4.6 2.2 - - + -
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B FES 3.9 5.6 - - - -
88B SER* 3.1 8.2 + - - +
89B LEU* 1.3 77.7 - - - +
91B ASP* 1.3 65.6 + - - +
93B VAL* 3.1 3.3 + - + +
94B VAL* 3.0 40.1 + - + +
103B PHE* 3.8 33.4 - - + +
104B GLY* 3.9 14.8 - - - +
107B GLU* 3.8 10.8 - - - +
108B GLY* 3.5 35.4 - - - +
151B GLY 3.6 5.5 + - - -
152B CYS* 3.6 19.7 - - + +
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASP* 4.0 17.6 - - + +
88B SER* 2.9 44.8 + - - +
90B LEU* 1.3 79.0 - - - +
92B VAL* 1.3 52.3 + - - +
94B VAL* 4.7 4.0 - - - -
95B GLU* 2.7 58.4 + - - +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 5.3 4.3 - - + -
71B PHE* 4.1 13.7 - - + -
81B THR* 3.6 30.1 - - + -
82B LYS 4.7 2.5 - - - +
83B GLY* 4.2 10.5 - - - -
87B ASP* 4.5 7.6 - - + +
88B SER 3.1 12.6 + - - +
89B LEU* 3.5 13.0 - - + +
90B LEU 3.1 0.2 - - - -
91B ASP* 1.3 75.9 - - - +
93B VAL* 1.3 63.7 + - - +
95B GLU* 5.0 2.5 - - - -
96B ASN* 3.2 32.8 + - - +
98B LEU* 4.4 0.2 - - - +
156B LEU* 3.8 30.3 - - + -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.7 26.9 - - + -
89B LEU 3.0 16.3 + - - +
90B LEU* 3.5 6.7 - - + +
92B VAL* 1.3 75.7 - - - +
94B VAL* 1.3 64.3 + - + +
97B ASN* 3.2 16.8 + - - -
98B LEU* 3.2 26.3 + - + +
100B ILE* 3.9 28.3 - - + +
103B PHE* 3.7 35.9 - - + +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.0 37.5 + - + +
91B ASP* 4.0 4.3 - - - +
93B VAL* 1.3 77.3 - - + +
95B GLU* 1.3 70.4 + - + +
96B ASN 3.1 2.0 - - - -
97B ASN* 3.1 21.8 + - - +
103B PHE 5.5 3.6 - - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LYS* 4.3 15.2 + - - +
87B ASP* 3.1 25.6 - - - +
91B ASP* 2.7 41.6 + - - +
92B VAL* 4.5 2.2 - - - +
94B VAL* 1.3 77.5 - - + +
96B ASN* 1.3 68.3 + - - +
97B ASN* 3.5 5.4 + - - -
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B THR* 3.0 27.2 + - - +
82B LYS 3.0 20.1 + - - +
92B VAL* 3.2 23.6 + - - +
94B VAL 3.1 0.6 - - - -
95B GLU* 1.3 85.7 + - - +
97B ASN* 1.3 71.9 + - - +
98B LEU* 3.3 14.1 + - + +
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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