Contacts of the helix formed by residues 63 - 72 (chain B) in PDB entry 1PR9
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 ASP 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 3.0 18.5 + - + +
61B LEU 3.1 1.3 - - - -
62B GLY* 1.3 77.5 - - - +
64B TRP* 1.3 57.5 + - - +
65B GLU* 3.1 17.9 + - - +
66B ALA* 3.0 31.6 + - + +
67B THR* 2.9 35.0 + - - -
109B ARG* 4.8 0.2 - - - +
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Residues in contact with TRP 64 (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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61B LEU 5.4 0.7 - - - -
62B GLY 3.8 4.4 + - - -
63B ASP* 1.3 72.1 + - - +
65B GLU* 1.3 88.3 + - + +
67B THR 3.4 0.2 + - - -
68B GLU* 3.1 22.5 + - - +
109B ARG* 3.8 52.9 - - + +
110B ALA* 6.0 0.2 - - - -
112B ILE* 5.0 6.7 - - + -
113B GLN* 2.9 74.6 + - + +
116B GLN* 4.1 17.5 - - - -
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Residues in contact with GLU 65 (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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63B ASP* 3.1 12.1 + - - +
64B TRP* 1.3 102.9 + - + +
66B ALA* 1.3 60.3 + - - +
68B GLU* 3.5 7.6 + - - +
69B ARG* 3.2 33.5 + - - +
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Residues in contact with ALA 66 (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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59B VAL* 3.6 14.7 - - + +
60B ASP 4.9 0.9 - - - +
63B ASP* 3.0 31.8 + - + +
65B GLU* 1.3 74.7 - - - +
67B THR* 1.3 60.8 + - - +
69B ARG* 3.4 9.3 + - - +
70B ALA* 3.0 29.3 + - - +
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Residues in contact with THR 67 (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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59B VAL* 4.0 7.7 - - - +
60B ASP 3.5 2.9 + - - -
61B LEU* 3.4 46.0 + - + +
63B ASP 2.9 19.9 + - - -
66B ALA* 1.3 78.3 - - - +
68B GLU* 1.3 57.8 + - - +
70B ALA* 3.1 1.3 + - - -
71B LEU* 2.8 46.2 + - + +
110B ALA* 6.3 0.4 - - + -
113B GLN* 3.3 26.7 - - + +
114B VAL* 4.5 6.5 - - + -
117B ILE* 5.2 1.3 - - + -
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Residues in contact with GLU 68 (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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64B TRP* 3.1 22.6 + - - +
65B GLU* 3.7 8.2 - - - +
67B THR* 1.3 77.1 - - - +
69B ARG* 1.3 61.2 + - + +
71B LEU 4.6 0.2 - - - +
72B GLY* 3.0 29.8 + - - +
113B GLN* 3.6 20.3 + - - +
117B ILE* 4.7 9.2 - - + -
120B ARG* 5.7 2.9 + - - -
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Residues in contact with ARG 69 (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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65B GLU* 3.2 23.8 + - - +
66B ALA* 3.4 7.8 + - - +
67B THR 3.2 0.2 - - - -
68B GLU* 1.3 81.1 - - + +
70B ALA* 1.3 60.7 + - - +
72B GLY* 4.4 2.1 + - - -
73B SER* 4.8 7.1 + - - -
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Residues in contact with ALA 70 (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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57B VAL* 4.3 19.0 - - + +
58B CYS 5.2 1.8 - - - +
59B VAL* 3.9 24.9 - - + -
66B ALA 3.0 17.7 + - - +
67B THR 3.1 2.7 + - - +
69B ARG* 1.3 79.0 - - - +
71B LEU* 1.3 65.1 + - + +
72B GLY 3.6 0.2 - - - -
73B SER* 4.1 11.1 + - - -
74B VAL* 5.0 1.7 + - - +
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Residues in contact with LEU 71 (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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11B LEU* 4.5 16.4 - - + -
13B THR* 5.9 0.2 - - + -
37B VAL* 4.3 19.1 - - + -
57B VAL* 3.9 23.6 - - + -
59B VAL* 5.3 2.0 - - + -
61B LEU* 4.7 5.8 - - + -
67B THR* 2.8 28.0 + - + +
70B ALA* 1.3 80.7 - - + +
72B GLY* 1.3 68.0 + - - +
73B SER 3.0 2.7 - - - -
74B VAL* 2.9 32.5 + - + +
114B VAL* 4.0 36.8 - - + -
117B ILE* 4.0 21.9 - - + +
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Residues in contact with GLY 72 (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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68B GLU* 3.0 20.2 + - - -
69B ARG 4.4 0.6 + - - -
70B ALA 3.6 0.4 - - - -
71B LEU* 1.3 78.7 - - - +
73B SER* 1.3 55.6 + - - +
74B VAL* 3.4 2.5 + - - +
75B GLY 4.7 2.4 + - - -
117B ILE* 4.6 14.2 - - - +
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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