Contacts of the helix formed by residues 73 - 82 (chain N) in PDB entry 1PP9
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 ASN 73 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64N PHE 5.9 0.4 - - - -
71N PRO 4.8 0.7 - - - +
72N GLY* 1.3 69.2 - - - -
74N ALA* 1.3 60.9 + - - +
75N LEU 3.4 0.9 - - - -
76N GLU* 3.1 14.6 - - - +
77N LYS* 2.9 59.4 + - - +
289O SER* 4.1 19.9 + - - +
291O ALA* 4.1 13.4 - - + +
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Residues in contact with ALA 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N ARG* 3.6 24.0 - - + -
71N PRO* 3.0 20.5 + - + +
72N GLY 3.0 2.4 + - - -
73N ASN* 1.3 78.0 + - - +
75N LEU* 1.3 67.4 + - - +
77N LYS* 3.2 11.6 + - - +
78N GLU* 3.1 22.8 + - - +
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Residues in contact with LEU 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N ALA 4.2 1.1 - - - +
64N PHE* 3.8 32.1 - - - +
66N GLY* 5.0 3.6 - - - +
67N THR* 4.8 7.4 - - + -
70N ARG* 3.8 27.6 + - + +
72N GLY 4.0 2.2 + - - +
73N ASN 3.4 0.2 - - - -
74N ALA* 1.3 77.0 - - - +
76N GLU* 1.3 64.3 + - - +
78N GLU* 3.1 5.4 + - - +
79N VAL* 3.0 24.1 + - + +
86N LEU* 4.2 11.2 - - + -
112N LEU* 3.7 33.9 - - + +
115N ASP* 4.9 4.3 - - - +
116N ILE* 3.5 42.2 - - + -
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Residues in contact with GLU 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64N PHE 4.5 13.4 + - - +
65N LYS* 5.3 6.2 - - - +
73N ASN* 3.1 20.2 - - - +
75N LEU* 1.3 79.5 - - - +
77N LYS* 1.3 61.8 + - - +
79N VAL* 3.2 5.0 + - - +
80N GLU* 2.9 47.1 + - - +
86N LEU* 6.2 0.4 - - - -
285O VAL* 4.4 23.9 - - + +
288O GLY* 3.6 8.2 - - - -
289O SER* 2.3 50.1 + - - -
290O ASN 3.1 8.1 + - - -
291O ALA* 3.1 9.3 + - + +
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Residues in contact with LYS 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N ASN* 2.9 49.1 + - - +
74N ALA* 3.2 11.2 + - - +
76N GLU* 1.3 74.0 - - - +
78N GLU* 1.3 50.7 + - - +
80N GLU* 4.0 0.3 - - - +
81N SER* 2.7 39.4 + - - -
291O ALA* 3.5 20.0 - - + -
292O THR* 4.2 19.5 - - + +
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Residues in contact with GLU 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N ARG* 2.9 32.9 + - - +
74N ALA 3.1 11.3 + - - +
75N LEU* 3.5 9.0 - - - +
77N LYS* 1.3 75.6 - - - +
79N VAL* 1.3 66.5 + - - +
81N SER* 3.2 16.2 + - - +
82N MET* 3.3 24.2 + - + +
108N LYS* 3.0 39.4 + - + +
112N LEU* 4.2 9.0 - - + -
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Residues in contact with VAL 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N LEU* 3.0 19.7 + - + +
76N GLU 3.7 6.1 - - - +
78N GLU* 1.3 77.8 - - - +
80N GLU* 1.3 60.3 - - - +
82N MET* 3.4 13.2 + - + +
84N ALA* 3.0 55.9 + - + +
85N HIS 4.1 0.4 - - - +
86N LEU* 4.0 32.8 - - + +
99N ILE* 5.0 7.2 - - + -
112N LEU* 3.9 19.5 - - + -
285O VAL* 4.0 19.3 - - + -
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Residues in contact with GLU 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N GLU* 2.9 45.1 + - - +
77N LYS 4.0 2.9 - - - +
79N VAL* 1.3 77.9 - - - +
81N SER* 1.3 58.6 + - - +
83N GLY* 2.8 19.9 + - - -
284O HIS* 3.8 32.9 - - + -
285O VAL* 4.7 4.3 - - + +
290O ASN* 3.8 8.6 - - - -
291O ALA* 3.3 10.7 + - - -
292O THR* 2.5 54.2 + - + +
363O LYS* 3.4 18.9 - - - +
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Residues in contact with SER 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77N LYS 2.7 23.2 + - - -
78N GLU* 3.2 13.5 + - - +
80N GLU* 1.3 75.9 - - - +
82N MET* 1.3 55.7 + - - +
83N GLY 3.2 1.1 - - - -
292O THR* 4.8 6.2 + - - -
359O ALA* 4.0 25.0 - - - -
362O ASN* 2.9 28.0 + - - +
363O LYS* 4.8 0.7 - - - +
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Residues in contact with MET 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N GLU* 3.3 23.3 + - + +
79N VAL* 3.5 15.9 - - + +
80N GLU 3.2 1.0 - - - -
81N SER* 1.3 77.0 - - - +
83N GLY* 1.3 60.5 + - - +
84N ALA* 3.4 16.2 + - + +
99N ILE* 6.1 1.6 - - + -
101N ALA* 5.3 2.1 - - + +
102N LEU* 4.6 5.5 + - - +
105N ASP* 3.9 39.4 - - - +
108N LYS* 3.9 22.7 - - + -
109N ALA* 5.3 3.8 - - - +
112N LEU* 3.4 32.3 - - + -
362O ASN* 4.1 18.3 - - - +
366O ALA* 4.5 4.9 - - - +
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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