Contacts of the helix formed by residues 65 - 80 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLY 4.4 0.2 - - - +
64A MET* 1.3 76.1 - - - +
66A ILE* 1.3 66.3 + - - -
67A PRO* 3.4 7.0 - - - -
68A SER 3.4 2.4 + - - -
69A CYS* 3.1 25.0 + - - +
157A ASP* 6.0 0.4 - - - -
180A MET* 3.5 26.4 - - - +
181A GLU* 2.7 16.4 + - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY* 1.3 68.9 - - - -
67A PRO* 1.3 74.7 - - + +
69A CYS* 3.3 6.2 - - - -
70A SER* 2.6 43.9 + - - +
111A THR* 3.8 22.2 - - + +
113A SER* 3.8 16.2 - - - +
115A VAL* 4.0 26.5 - - + -
155A SER* 4.3 10.5 - - - +
156A ALA 5.8 0.2 - - - +
157A ASP* 4.3 10.8 + - - +
180A MET 3.2 14.8 + - - +
181A GLU* 3.9 3.1 - - - -
183A ALA* 4.5 2.5 - - + -
184A GLY* 3.7 32.5 - - - +
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET 5.5 0.2 - - - +
65A GLY* 3.5 5.8 - - - -
66A ILE* 1.3 98.6 - - + +
68A SER* 1.3 61.6 + - - +
70A SER* 3.8 5.6 - - - +
71A ILE* 3.4 26.4 + - + +
157A ASP* 4.7 9.6 - - - +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A MET* 4.5 1.4 - - - +
62A HIS 2.6 22.2 + - - -
63A GLY* 3.6 9.0 - - - -
64A MET 3.7 21.5 - - - -
65A GLY 3.4 1.9 + - - -
66A ILE 3.2 0.8 - - - -
67A PRO* 1.3 77.2 - - - +
69A CYS* 1.3 66.1 + - - +
71A ILE* 3.2 19.4 + - - +
72A TYR* 3.3 24.1 - - - -
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Residues in contact with CYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 3.5 37.1 + - + +
65A GLY 3.1 13.6 + - - +
66A ILE* 3.3 11.2 - - - -
68A SER* 1.3 78.9 - - - +
70A SER* 1.3 59.9 + - - +
72A TYR* 3.4 0.9 + - - +
73A THR* 2.8 36.7 + - - +
181A GLU* 3.2 33.0 - - + -
185A ILE* 3.8 24.9 - - + -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 2.6 38.9 + - - +
67A PRO* 3.8 7.2 - - - -
69A CYS* 1.3 79.6 - - - +
71A ILE* 1.3 62.5 + - - +
73A THR* 4.1 0.4 - - - -
74A LYS* 3.1 27.0 + - - +
115A VAL* 5.2 2.7 - - - +
119A ARG* 4.7 7.2 + - - -
184A GLY* 4.2 7.0 + - - -
188A VAL* 4.0 24.1 - - - +
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A HIS* 3.3 55.6 - - + +
67A PRO* 3.4 17.7 + - + +
68A SER* 3.2 12.2 + - - +
70A SER* 1.3 79.1 - - - +
72A TYR* 1.3 68.1 + - + +
74A LYS* 3.7 2.9 - - - +
75A GLU* 3.1 29.4 + - - +
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A HIS* 3.7 36.4 + + + +
5A ILE* 4.2 9.6 - - + -
18A MET* 4.0 18.8 - - + -
43A ARG* 4.2 20.6 - - - +
45A MET* 3.5 50.0 - - + +
60A MET* 4.2 17.7 - - + -
61A GLY 4.4 3.4 - - - -
62A HIS* 3.5 17.5 - - - -
68A SER* 3.3 25.4 - - - -
69A CYS 3.4 5.0 + - - +
71A ILE* 1.3 76.7 - - + +
73A THR* 1.3 67.4 + - - +
75A GLU* 3.4 4.5 + - - +
76A LEU* 3.0 31.3 + - - +
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 4.6 7.9 - - - -
69A CYS* 2.8 26.4 + - - +
70A SER* 4.1 1.6 - - - -
72A TYR* 1.3 78.2 - - - +
74A LYS* 1.3 63.8 + - - +
76A LEU* 3.5 2.7 + - - +
77A ILE* 3.1 33.9 + - + +
85A ILE* 3.4 29.3 - - + +
185A ILE* 4.0 27.3 - - + +
188A VAL* 3.2 32.5 - - + -
189A ALA* 5.4 0.7 - - + -
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER 3.1 17.9 + - - +
71A ILE* 3.7 4.0 - - - +
73A THR* 1.3 80.3 - - - +
75A GLU* 1.3 67.2 + - + +
77A ILE* 3.3 3.2 + - - +
78A THR* 2.9 61.9 + - - +
79A ASP* 4.1 5.9 + - - -
188A VAL* 3.7 13.9 - - + +
192A PHE* 3.4 34.5 - - + -
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A THR* 2.7 39.5 + - + +
3A PRO* 3.5 12.7 - - + +
4A HIS* 2.6 46.9 + - - +
5A ILE* 3.6 10.7 - - + +
71A ILE* 3.1 20.0 + - + +
72A TYR* 3.9 3.9 - - - +
74A LYS* 1.3 80.6 - - + +
76A LEU* 1.3 61.2 + - - +
78A THR* 4.1 4.9 - - - -
79A ASP* 2.9 36.4 + - - +
80A PHE* 3.5 3.9 - - - -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.8 21.5 - - + -
12A PHE* 3.8 39.0 - - + -
16A VAL* 4.1 18.8 - - + -
18A MET* 4.0 33.0 - - + -
60A MET* 4.0 3.6 - - + -
72A TYR 3.0 21.3 + - - +
73A THR 3.8 2.9 - - - +
75A GLU* 1.3 75.5 - - - +
77A ILE* 1.3 59.3 + - + +
80A PHE* 2.9 29.6 + - + +
82A VAL* 3.2 28.9 + - + -
85A ILE* 4.6 6.3 - - + -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A THR* 3.1 37.1 + - + +
74A LYS* 3.7 3.8 - - - +
76A LEU* 1.3 80.1 - - - +
78A THR* 1.3 63.4 + - + +
81A GLY* 3.7 14.9 + - - -
82A VAL* 3.8 21.2 + - + +
85A ILE* 4.2 13.9 - - + -
188A VAL* 4.1 11.7 - - + +
189A ALA* 4.4 8.7 - - + -
192A PHE* 3.8 32.3 - - + +
193A GLY 5.2 0.4 - - - +
194A ALA* 3.6 25.6 - - + -
195A LYS 5.9 0.2 - - - +
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A MET* 5.5 1.7 - - - +
74A LYS* 2.9 47.3 + - - +
77A ILE* 1.3 75.3 - - + +
79A ASP* 1.3 82.4 + - - +
81A GLY 4.9 0.4 - - - -
192A PHE* 3.4 38.4 - - + -
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A THR* 3.5 30.9 - - + +
9A MET* 3.3 19.9 + - - +
74A LYS* 4.1 6.9 + - - -
75A GLU* 2.9 15.9 + - - +
78A THR* 1.3 103.7 + - - +
80A PHE* 1.3 70.5 + - + +
81A GLY 3.6 1.3 - - - -
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA* 4.6 1.3 - - - -
2A THR* 3.9 28.5 - - + -
5A ILE* 3.9 32.8 - - + -
7A ALA* 3.3 40.6 - - + -
8A GLU 3.6 21.8 - - - -
9A MET* 3.5 19.0 - - - +
10A GLY 5.0 1.3 + - - -
12A PHE* 4.0 35.2 - + + +
13A ALA 4.8 0.5 - - - +
14A ASP* 5.8 0.2 - - - -
75A GLU 3.5 12.8 - - - -
76A LEU* 2.9 25.3 + - + +
79A ASP* 1.3 82.2 - - + +
81A GLY* 1.3 63.8 + - - +
82A VAL* 3.1 6.7 + - + +
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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