Contacts of the helix formed by residues 64 - 77 (chain A) in PDB entry 1PN9
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 GLU 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 4.7 8.7 + - - +
51A CYS* 5.3 1.6 - - - -
53A PRO 4.0 3.8 + - - -
63A TRP* 1.3 88.2 - - + +
65A SER* 1.3 66.3 + - - +
66A ARG* 3.2 2.9 + - - +
67A ALA* 2.9 20.4 + - + +
68A ILE* 3.1 10.5 + - - +
101A MET* 3.8 2.6 - - - +
301A GTX 2.9 40.9 + - - +
95B GLN* 3.7 33.7 - - + +
98B TYR* 3.5 26.4 - - + +
99B PHE* 4.2 12.1 + - - -
102B GLY* 5.8 0.9 - - - -
103B THR* 4.7 6.9 + - - -
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 3.4 41.0 - - - +
14A ALA* 5.0 4.2 - - - +
15A VAL* 3.8 5.8 - - - +
53A PRO* 3.8 13.7 - - - +
64A GLU* 1.3 71.2 - - - +
66A ARG* 1.3 70.6 + - - +
68A ILE* 3.2 5.7 + - - +
69A GLN* 2.8 31.9 + - - +
301A GTX 2.6 28.9 + - - -
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Residues in contact with ARG 66 (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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11A PRO* 5.4 6.9 - - - +
64A GLU* 3.2 1.8 + - - -
65A SER* 1.3 81.2 + - - +
67A ALA* 1.3 63.6 + - - +
69A GLN* 3.4 20.9 + - - +
70A ILE* 3.1 29.6 + - - +
97A LEU* 3.2 36.0 + - + +
100A ASP* 2.8 25.8 + - - -
101A MET* 3.4 32.2 - - - +
105A TYR* 4.4 12.7 - - - +
158A SER* 3.1 14.6 + - - +
162A THR* 4.5 1.4 + - - -
301A GTX 2.9 28.9 + - - -
98B TYR* 3.4 36.6 - - + +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.1 6.0 - - + +
63A TRP 3.9 5.4 - - - +
64A GLU* 2.9 13.0 + - + +
66A ARG* 1.3 78.6 - - - +
68A ILE* 1.3 59.0 + - - +
70A ILE* 3.3 4.3 + - - +
71A TYR* 2.9 28.9 + - - +
91B ALA* 4.1 8.1 - - - +
94B ASN* 4.1 16.3 - - + +
95B GLN* 3.7 36.6 - - + +
98B TYR* 4.1 5.3 - - + -
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Residues in contact with ILE 68 (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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3A PHE* 5.3 0.2 - - + -
15A VAL* 3.9 24.9 - - + -
53A PRO* 3.7 35.7 - - + +
54A THR 4.6 0.2 - - - -
55A LEU* 4.1 26.9 - - + +
62A LEU* 3.4 44.6 - - + +
63A TRP* 4.0 3.4 - - - -
64A GLU 3.1 12.7 + - - +
65A SER* 3.4 6.7 - - - +
67A ALA* 1.3 75.3 - - - +
69A GLN* 1.3 65.5 + - - +
71A TYR* 3.3 2.7 + - + +
72A LEU* 3.0 31.3 + - + +
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Residues in contact with GLN 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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14A ALA* 3.7 17.3 + - - +
15A VAL* 4.4 7.4 - - + -
18A THR* 2.7 42.1 + - - +
65A SER 2.8 16.0 + - - +
66A ARG* 3.5 20.2 + - - +
67A ALA 3.2 0.4 - - - -
68A ILE* 1.3 78.4 - - - +
70A ILE* 1.3 62.3 + - - +
72A LEU* 3.4 1.5 + - - -
73A ALA* 3.1 22.7 + - - +
97A LEU* 4.1 0.3 - - - +
154A ILE* 2.9 44.2 + - + +
157A LEU* 3.7 9.3 - - - +
158A SER* 3.4 23.9 + - - +
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Residues in contact with ILE 70 (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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66A ARG 3.1 19.4 + - - +
67A ALA* 3.7 5.2 - - - +
69A GLN* 1.3 74.6 - - + +
71A TYR* 1.3 62.4 + - - +
73A ALA* 3.2 5.7 + - - +
74A GLU* 2.9 52.0 + - - +
83A TYR* 3.5 48.2 - - + +
94A ASN* 4.0 9.6 - - - +
97A LEU* 4.2 13.5 - - + -
154A ILE* 5.4 2.0 - - + -
70B ILE* 6.1 1.6 - - + -
83B TYR* 5.6 0.2 - - - +
90B ARG* 5.3 0.2 - - - -
91B ALA* 6.4 0.2 - - - -
94B ASN* 4.0 29.6 - - - +
98B TYR* 4.6 9.9 - - + +
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Residues in contact with TYR 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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55A LEU* 4.7 7.6 - - + -
57A ASP* 2.6 41.3 + - + +
60A PHE* 3.9 25.1 - + - -
62A LEU* 3.8 17.3 - - + -
67A ALA 2.9 17.3 + - - +
68A ILE* 3.5 5.8 - - + +
70A ILE* 1.3 78.1 - - - +
72A LEU* 1.3 68.8 + - + +
74A GLU* 4.1 7.1 - - - +
75A LYS* 2.8 67.8 + - + +
76A TYR* 4.2 6.7 - + - -
87B PRO* 3.7 20.1 - - + +
88B GLN* 4.0 18.0 + - + -
91B ALA* 3.9 11.6 - - + +
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Residues in contact with LEU 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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1A MET* 4.4 13.7 - - - -
15A VAL* 4.3 18.4 - - + -
18A THR* 4.2 11.2 - - + -
19A ALA* 3.9 35.7 - - + +
22A VAL* 3.9 10.5 - - + +
24A VAL* 4.7 8.1 - - + -
26A LEU* 5.4 3.8 - - + -
55A LEU* 5.3 4.5 - - + -
68A ILE* 3.0 26.0 + - + +
69A GLN 3.7 4.0 - - - +
71A TYR* 1.3 86.2 - - + +
73A ALA* 1.3 56.6 + - - +
76A TYR* 2.8 56.9 + - + +
77A GLY 3.1 4.5 + - - -
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Residues in contact with ALA 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 THR* 4.9 0.6 - - + +
22A VAL* 4.1 12.1 - - - +
69A GLN 3.1 16.3 + - - +
70A ILE* 3.2 5.4 + - - +
72A LEU* 1.3 76.5 - - - +
74A GLU* 1.3 58.2 + - - +
77A GLY* 2.8 30.1 + - - +
79A ASP 5.6 0.2 - - - +
82A LEU* 4.9 5.2 - - + -
83A TYR* 3.9 28.7 - - + -
154A ILE* 3.9 18.2 - - + -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 2.9 41.7 + - + +
71A TYR* 4.1 3.6 - - - +
73A ALA* 1.3 74.5 - - - +
75A LYS* 1.3 59.9 + - - +
77A GLY 4.7 4.3 + - - +
83A TYR* 3.7 16.8 - - + -
90A ARG* 3.5 23.6 + - - +
85B LYS 5.5 2.9 - - - -
87B PRO* 4.2 27.4 - - + +
90B ARG* 3.5 33.9 + - - +
91B ALA* 5.5 0.3 + - - -
94B ASN* 5.0 0.2 + - - -
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Residues in contact with LYS 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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57A ASP* 3.1 10.3 + - - -
58A ASN* 6.4 0.2 - - - +
71A TYR* 2.8 61.0 + - + +
74A GLU* 1.3 75.1 - - - +
76A TYR* 1.3 90.1 + - + +
77A GLY 5.2 0.4 - - - -
78A LYS* 5.4 4.7 + - - -
87B PRO* 4.1 19.3 - - + -
88B GLN* 4.8 8.7 + - - +
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Residues in contact with TYR 76 (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 MET* 3.5 24.4 - - + +
22A VAL* 4.0 15.5 - - + +
24A VAL* 3.6 31.0 - - + -
57A ASP* 2.5 34.5 + - - -
71A TYR* 4.2 2.9 - + - -
72A LEU* 2.8 30.6 + - + +
75A LYS* 1.3 110.4 + - + +
77A GLY* 1.3 64.8 + - - +
78A LYS* 3.4 19.0 + - - +
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Residues in contact with GLY 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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22A VAL* 3.8 18.2 - - - -
72A LEU 3.1 3.4 + - - -
73A ALA* 2.8 24.9 + - - +
74A GLU 4.7 4.7 - - - +
75A LYS 3.7 0.5 - - - -
76A TYR* 1.3 77.8 - - - +
78A LYS* 1.3 65.6 + - - +
79A ASP 3.5 8.0 - - - -
82A LEU* 5.9 1.6 - - - -
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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