Contacts of the helix formed by residues 54 - 63 (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 GLY 54 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48N GLU* 2.6 12.7 + - - -
53N ASN* 1.3 75.4 - - - +
55N ALA* 1.3 55.3 + - - +
56N GLY 3.5 2.2 - - - -
57N TYR* 3.3 6.2 + - - +
58N PHE* 2.9 28.4 + - - +
134N ILE* 5.7 0.3 - - - +
167N VAL 3.8 10.8 - - - -
168N GLU 3.4 24.4 - - - +
173N ASN* 5.7 0.2 - - - -
174N VAL* 6.0 1.2 - - - +
177N LEU* 3.9 9.0 - - - +
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Residues in contact with ALA 55 (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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48N GLU* 3.6 0.2 + - - -
52N ASN* 2.9 24.4 + - + +
53N ASN 3.4 0.2 - - - -
54N GLY* 1.3 74.8 - - - +
56N GLY* 1.3 55.7 + - - +
58N PHE* 2.8 4.2 + - - +
59N VAL* 2.7 39.0 + - - +
177N LEU* 3.9 7.9 - - + +
181N ASP 4.9 1.6 - - - +
182N LEU* 3.8 19.0 - - + +
185N TYR* 3.8 30.7 - - + -
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Residues in contact with GLY 56 (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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44N GLY* 6.4 0.2 - - - -
48N GLU* 3.0 14.1 + - - -
55N ALA* 1.3 75.9 - - - +
57N TYR* 1.3 58.3 + - - +
59N VAL* 3.2 5.4 + - - +
60N GLU* 2.9 27.0 + - - +
90N SER* 4.3 7.6 + - - -
95N THR* 5.7 4.3 - - - +
97N TYR* 4.9 1.9 + - - -
185N TYR* 3.6 31.0 - - - -
190N TYR* 5.3 1.8 + - - -
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Residues in contact with TYR 57 (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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48N GLU* 4.5 1.2 + - - -
54N GLY 3.3 9.7 + - - +
55N ALA 3.1 0.6 - - - -
56N GLY* 1.3 76.1 - - - +
58N PHE* 1.3 62.8 + - - +
60N GLU* 3.3 23.3 + - - +
61N HIS* 3.1 43.5 + + - -
90N SER* 4.5 5.3 + - - -
134N ILE* 4.0 21.5 - - + -
137N GLU* 2.8 26.8 + - + +
138N LEU* 5.7 0.2 - - + -
141N ASN* 5.0 3.3 + - - -
167N VAL* 3.6 33.9 + - + +
168N GLU* 3.7 42.7 + - + +
287O ARG* 3.4 19.0 + - - -
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Residues in contact with PHE 58 (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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54N GLY 2.9 12.6 + - - +
55N ALA* 2.8 8.7 + - - +
57N TYR* 1.3 75.5 - - - +
59N VAL* 1.3 65.9 + - - +
61N HIS* 2.9 16.1 + - - +
62N LEU* 3.4 9.7 + - + +
127N ILE* 3.5 47.6 - - + -
130N GLU* 3.9 13.5 - - + -
131N ARG* 3.9 22.4 - - + -
134N ILE* 3.8 22.4 - - + -
174N VAL* 3.8 25.1 - - + -
177N LEU* 3.9 24.5 - - + -
182N LEU* 3.8 23.6 - - + -
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Residues in contact with VAL 59 (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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55N ALA 2.7 19.5 + - - +
56N GLY* 3.5 9.9 - - - +
58N PHE* 1.3 72.7 - - - +
60N GLU* 1.3 54.7 + - - +
62N LEU* 2.7 29.2 + - - +
63N ALA* 2.8 17.7 + - + +
97N TYR* 3.6 18.2 - - + +
120N CYS* 5.7 2.2 - - - -
122N LEU* 5.4 6.5 - - + -
182N LEU* 4.4 16.4 - - + -
185N TYR* 4.4 9.2 - - + -
186N LEU* 4.0 38.1 - - + -
190N TYR* 4.0 10.8 - - + +
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Residues in contact with GLU 60 (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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56N GLY 2.9 14.1 + - - +
57N TYR* 3.4 18.0 - - - +
58N PHE 3.2 0.4 - - - -
59N VAL* 1.3 77.6 - - - +
61N HIS* 1.3 60.5 + - - +
62N LEU 3.3 0.7 + - - -
63N ALA* 3.7 11.9 + - - +
64N PHE* 4.8 8.1 + - - -
88N ALA* 4.0 23.1 - - + -
89N TYR* 3.6 1.2 - - - -
90N SER* 2.5 39.9 + - - +
95N THR* 6.0 0.9 - - + -
97N TYR* 4.1 12.3 - - + +
286O LYS* 2.6 31.9 + - - +
287O ARG* 2.7 26.4 + - - +
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Residues in contact with HIS 61 (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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57N TYR* 3.1 38.2 - + - -
58N PHE 2.9 10.9 + - - +
60N GLU* 1.3 77.9 - - + +
62N LEU* 1.3 59.1 + - - +
64N PHE 5.0 0.4 + - - -
65N LYS* 3.4 28.9 + - - +
130N GLU* 3.3 35.2 + - + +
133N VAL* 4.0 5.5 - - + +
134N ILE* 3.4 24.3 - - + +
137N GLU* 2.8 34.9 + - - -
287O ARG* 3.3 40.6 - - - +
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Residues in contact with LEU 62 (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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58N PHE* 3.7 14.8 - - + +
59N VAL* 2.7 9.2 + - - +
61N HIS* 1.3 78.9 - - - +
63N ALA* 1.3 54.4 + - - +
64N PHE 3.2 2.9 - - - -
65N LYS* 2.7 31.7 + - + +
120N CYS* 3.7 8.0 - - - -
122N LEU* 3.4 38.1 - - + +
126N GLN* 3.6 33.2 - - + -
127N ILE* 3.8 22.2 - - + +
130N GLU* 3.8 15.5 - - + -
182N LEU* 3.6 27.4 - - + -
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Residues in contact with ALA 63 (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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59N VAL* 2.8 15.6 + - + +
60N GLU 3.8 7.6 - - - +
61N HIS 3.7 0.4 - - - -
62N LEU* 1.3 73.7 - - - +
64N PHE* 1.3 67.8 + - + +
65N LYS 3.9 0.2 + - - -
66N GLY 4.8 2.8 + - - +
67N THR* 5.2 1.0 - - - +
75N LEU* 4.2 1.6 - - - +
97N TYR* 3.4 36.1 - - + -
116N ILE* 3.4 29.6 - - + +
120N CYS* 3.8 17.6 - - - +
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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