Contacts of the helix formed by residues 65 - 81 (chain B) in PDB entry 1PR1
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 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLY 4.6 0.2 - - - +
64B MET* 1.3 74.2 - - - +
66B ILE* 1.3 65.9 + - - -
67B PRO* 3.3 7.9 - - - -
68B SER 3.2 2.5 + - - -
69B CYS* 3.1 24.9 + - - +
156B ALA 5.6 0.4 - - - -
180B MET* 3.5 26.9 + - - +
181B GLU* 2.8 14.7 + - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY* 1.3 71.2 - - - -
67B PRO* 1.3 69.9 - - + +
69B CYS* 3.4 7.1 - - - -
70B SER* 2.6 38.3 + - - +
111B THR* 3.7 11.2 - - - +
113B SER* 3.7 25.4 - - - +
115B VAL* 3.9 27.4 - - + -
155B SER* 4.1 12.1 - - - +
156B ALA 5.4 0.4 + - - +
157B ASP* 4.4 9.7 + - - +
180B MET 3.1 16.5 + - - +
181B GLU* 3.8 3.8 - - - -
183B ALA* 4.2 2.9 - - + -
184B GLY* 3.6 38.4 - - - +
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Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY* 3.5 7.0 - - - -
66B ILE* 1.3 98.7 - - + +
68B SER* 1.3 62.4 + - - +
70B SER* 3.7 5.7 - - - -
71B ILE* 3.5 25.1 + - - +
115B VAL* 5.7 5.4 - - + -
157B ASP* 4.8 9.9 - - - +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B MET* 4.8 1.2 - - - +
62B HIS 2.7 21.5 + - - -
63B GLY* 3.6 8.1 - - - -
64B MET 3.7 17.9 + - - -
65B GLY 3.2 7.7 + - - -
66B ILE 3.2 0.6 - - - -
67B PRO* 1.3 76.5 - - - +
69B CYS* 1.3 66.4 + - - +
70B SER 3.0 1.1 - - - -
71B ILE* 3.0 24.5 + - - +
72B TYR* 3.5 18.6 + - - -
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Residues in contact with CYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B HIS* 3.3 35.8 + - + +
65B GLY 3.1 11.6 + - - +
66B ILE* 3.4 9.2 - - - -
68B SER* 1.3 78.8 - - - +
70B SER* 1.3 63.3 + - - +
72B TYR* 3.5 1.5 + - - -
73B THR* 2.9 31.9 + - - +
181B GLU* 3.1 34.5 - - + -
185B ILE* 3.2 27.4 - - + -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 2.6 37.2 + - - +
67B PRO* 3.7 8.1 - - - -
68B SER 3.0 0.4 + - - -
69B CYS* 1.3 78.5 - - - +
71B ILE* 1.3 61.8 + - - +
73B THR* 3.6 5.9 + - - -
74B LYS* 3.1 25.8 + - - +
115B VAL* 5.7 1.2 - - - +
119B ARG* 4.8 6.7 + - - -
184B GLY* 4.1 7.4 + - - -
188B VAL* 3.9 19.4 - - - +
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Residues in contact with ILE 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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4B HIS* 3.5 53.4 - - + +
67B PRO 3.5 14.8 + - - +
68B SER* 3.0 11.7 + - - +
70B SER* 1.3 79.2 - - - +
72B TYR* 1.3 69.9 + - + +
74B LYS* 3.7 2.7 - - - +
75B GLU* 3.2 29.8 + - - +
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Residues in contact with TYR 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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4B HIS* 3.8 33.6 - + + +
5B ILE* 4.3 10.2 - - + +
18B MET* 3.9 18.2 - - + -
40B ASN* 5.1 0.7 - - - -
43B ARG* 4.1 19.2 + - - +
45B MET* 3.5 50.3 - - + +
60B MET* 3.8 20.6 - - + -
61B GLY 4.3 1.1 - - - -
62B HIS* 3.6 19.1 - - - -
68B SER* 3.5 26.7 + - - -
69B CYS* 4.1 3.4 - - - +
71B ILE* 1.3 78.8 - - + +
73B THR* 1.3 65.1 + - - +
75B GLU* 3.3 5.2 + - - +
76B LEU* 3.0 29.9 + - - +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 3.8 17.9 - - - -
69B CYS* 2.9 22.5 + - + +
70B SER* 3.6 3.5 + - - -
72B TYR* 1.3 74.9 - - - +
74B LYS* 1.3 62.9 + - - +
76B LEU* 3.4 3.7 + - - +
77B ILE* 3.1 32.9 + - - +
85B ILE* 3.4 31.4 - - + -
185B ILE* 3.4 27.4 - - + +
188B VAL* 3.5 22.2 - - - +
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Residues in contact with LYS 74 (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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70B SER 3.1 18.1 + - - +
71B ILE* 3.7 4.3 - - - +
72B TYR 3.2 0.6 - - - -
73B THR* 1.3 83.4 + - - +
75B GLU* 1.3 66.2 + - + +
77B ILE* 3.4 2.4 + - - +
78B THR* 3.0 54.0 + - - +
79B ASP* 4.6 7.9 + - - -
188B VAL* 4.0 12.8 - - + -
192B PHE* 3.6 43.5 - - + -
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Residues in contact with GLU 75 (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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2B THR* 2.4 44.9 + - + +
3B PRO* 3.9 4.3 - - - +
4B HIS* 2.7 40.5 + - - +
5B ILE* 3.6 14.0 - - + +
71B ILE* 3.2 21.4 + - + +
72B TYR* 3.3 4.0 + - - +
74B LYS* 1.3 83.7 - - + +
76B LEU* 1.3 60.9 + - - +
78B THR* 4.0 5.4 - - - -
79B ASP* 2.8 38.1 + - - +
80B PHE* 3.3 4.6 - - - -
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Residues in contact with LEU 76 (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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5B ILE* 4.0 9.4 - - + -
12B PHE* 3.9 46.0 - - + -
16B VAL* 4.3 16.2 - - + -
18B MET* 4.0 22.9 - - + -
60B MET* 3.8 20.0 - - + -
72B TYR 3.0 22.4 + - - +
73B THR* 3.7 6.5 - - - +
74B LYS 3.3 0.2 - - - -
75B GLU* 1.3 76.5 - - - +
77B ILE* 1.3 61.7 + - - +
80B PHE* 3.1 18.0 + - + -
81B GLY 3.3 0.2 + - - -
82B VAL* 3.1 37.7 + - + +
85B ILE* 4.6 2.9 - - + -
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Residues in contact with ILE 77 (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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73B THR* 3.1 20.2 + - - +
74B LYS* 3.8 3.4 - - - +
76B LEU* 1.3 80.3 - - - +
78B THR* 1.3 62.4 + - + +
81B GLY* 3.6 15.4 + - - -
82B VAL* 3.6 17.4 + - + +
85B ILE* 4.2 19.1 - - + -
188B VAL* 3.9 23.6 - - + +
189B ALA* 4.5 7.4 - - + +
192B PHE* 3.9 29.8 - - + +
193B GLY 5.2 0.7 - - - +
194B ALA* 3.5 30.3 - - + -
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Residues in contact with THR 78 (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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74B LYS* 3.0 39.8 + - - +
77B ILE* 1.3 77.8 - - + +
79B ASP* 1.3 77.7 + - - +
81B GLY 4.8 0.7 - - - -
192B PHE* 3.5 39.3 - - + -
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Residues in contact with ASP 79 (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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1B ALA 5.8 1.1 - - - +
2B THR* 3.0 29.6 - - + +
9B MET* 3.8 16.0 + - - +
74B LYS* 4.6 5.9 + - - -
75B GLU* 2.8 25.5 + - - +
78B THR* 1.3 94.0 + - - +
80B PHE* 1.3 73.6 + - + +
81B GLY 3.7 1.1 - - - -
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Residues in contact with PHE 80 (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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1B ALA 3.7 11.7 - - - -
2B THR* 4.0 21.1 - - + -
5B ILE* 3.8 31.6 - - + -
7B ALA* 3.5 40.4 - - + -
8B GLU* 3.6 20.0 - - - -
9B MET* 3.5 19.2 - - - +
10B GLY 5.0 1.8 + - - -
12B PHE* 3.6 34.3 - + + +
13B ALA 5.1 0.9 - - - +
75B GLU 3.3 15.7 - - - -
76B LEU* 3.1 20.4 + - + +
79B ASP* 1.3 83.2 - - + +
81B GLY* 1.3 63.9 + - - +
82B VAL* 3.2 9.4 + - + +
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Residues in contact with GLY 81 (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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9B MET* 3.9 11.3 - - - -
14B ASP* 4.1 9.7 - - - +
76B LEU 3.3 1.6 + - - -
77B ILE 3.6 10.6 + - - -
78B THR 4.8 0.8 - - - -
79B ASP 3.7 1.2 - - - -
80B PHE* 1.3 77.7 - - - +
82B VAL* 1.3 63.8 + - - +
83B LYS* 3.2 29.6 + - - +
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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