Contacts of the helix formed by residues 62 - 77 (chain A) in PDB entry 1PME
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 GLN 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A HIS* 1.3 72.7 - - - +
63A THR* 1.3 68.4 + - + +
65A CYS* 3.4 2.6 + - - -
66A GLN* 2.9 43.2 + - - +
338A LEU 2.7 40.9 + - - +
339A PRO* 4.3 1.3 - - + -
340A LYS* 4.0 24.1 - - + +
343A LEU* 3.5 11.9 - - + +
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Residues in contact with THR 63 (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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36A TYR* 4.9 0.4 - - - -
61A HIS* 4.2 4.9 - - - +
62A GLN* 1.3 86.4 - - + +
64A TYR* 1.3 87.5 + - - +
66A GLN* 3.0 33.5 - - - +
67A ARG* 3.1 15.9 + - - +
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Residues in contact with TYR 64 (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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36A TYR* 3.3 48.5 - + + -
57A SER 5.3 2.0 - - - -
58A PRO* 3.7 17.9 - - + +
61A HIS* 3.3 41.0 + + + +
63A THR* 1.3 93.9 - - - +
65A CYS* 1.3 58.1 + - - +
67A ARG 3.5 0.3 + - - -
68A THR* 3.0 31.5 + - - -
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Residues in contact with CYS 65 (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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58A PRO* 3.3 28.7 - - - -
59A PHE* 3.6 31.0 - - - -
61A HIS 3.0 14.8 + - - +
62A GLN* 3.6 5.8 - - - +
64A TYR* 1.3 75.8 - - - +
66A GLN* 1.3 60.7 + - - +
68A THR* 3.4 1.1 + - - -
69A LEU* 2.9 31.5 + - - +
340A LYS* 4.2 16.6 - - - -
343A LEU* 3.8 21.0 - - + +
344A LYS 4.7 0.4 - - - -
347A ILE* 3.7 10.1 - - + +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 2.9 35.6 + - - +
63A THR* 3.0 23.2 + - - +
65A CYS* 1.3 73.5 - - - +
67A ARG* 1.3 82.6 + - - +
69A LEU* 4.0 4.3 - - - +
70A ARG* 3.0 64.6 + - - +
343A LEU* 4.1 14.6 - - + +
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.3 30.5 - - + +
63A THR* 3.1 11.4 + - - +
64A TYR 3.7 0.7 - - - +
66A GLN* 1.3 101.6 - - - +
68A THR* 1.3 58.7 + - - +
70A ARG* 3.3 24.5 - - - +
71A GLU* 2.9 30.0 + - - +
169A GLY* 3.1 41.2 + - - +
170A LEU* 3.5 34.4 + - + +
171A ALA 5.5 0.2 + - - -
172A ARG* 5.7 4.8 - - - +
188A VAL* 4.1 19.6 - - - +
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Residues in contact with THR 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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36A TYR* 3.3 20.9 - - - -
56A ILE* 3.5 27.9 - - + +
58A PRO* 3.5 10.7 - - + +
64A TYR 3.0 17.3 + - - -
65A CYS 3.7 4.0 - - - -
66A GLN 3.3 0.2 - - - -
67A ARG* 1.3 75.1 - - - +
69A LEU* 1.3 59.3 + - - +
71A GLU* 3.5 5.1 + - - +
72A ILE* 3.0 53.2 + - + +
101A VAL* 5.9 2.0 - - + -
347A ILE* 3.9 16.2 - - + -
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Residues in contact with LEU 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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65A CYS 2.9 18.2 + - - +
66A GLN* 4.0 5.2 - - - +
68A THR* 1.3 73.9 - - - +
70A ARG* 1.3 59.0 + - - +
72A ILE* 3.3 3.7 + - + -
73A LYS* 2.8 71.7 + - + +
343A LEU* 4.7 14.6 - - + +
346A LEU* 4.0 38.1 - - + +
347A ILE* 3.9 25.6 - - + -
350A GLU* 4.2 10.1 - - + +
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLN* 3.0 61.6 + - - +
67A ARG* 3.3 31.2 - - - +
69A LEU* 1.3 81.3 - - - +
71A GLU* 1.3 61.6 + - - +
73A LYS* 3.7 5.6 - - - +
74A ILE* 3.1 39.3 + - + +
168A PHE 4.5 3.4 - - - +
169A GLY 4.2 9.9 - - - -
171A ALA 2.9 28.5 + - - +
172A ARG* 5.0 11.8 - - - +
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Residues in contact with GLU 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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54A LYS* 2.7 31.1 + - - -
56A ILE* 4.7 2.9 - - - +
67A ARG 2.9 17.6 + - - +
68A THR* 3.9 5.4 - - - +
70A ARG* 1.3 75.8 - - - +
72A ILE* 1.3 61.7 + - + +
74A ILE* 3.3 1.5 + - - +
75A LEU* 2.9 52.2 + - + +
103A LEU* 3.9 9.3 - - + +
167A ASP* 3.6 11.3 + - - +
168A PHE* 2.9 45.4 + - + +
169A GLY* 3.7 5.0 + - - +
1001A SB2 6.1 0.4 - - - -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 5.2 0.7 - - + -
68A THR* 3.0 39.4 + - + +
69A LEU* 3.8 5.6 - - - +
71A GLU* 1.3 75.7 - - + +
73A LYS* 1.3 62.3 + - - +
76A LEU* 3.1 53.0 + - + +
86A ILE* 4.8 3.6 - - - -
89A ILE* 4.3 2.7 - - + -
101A VAL* 4.7 5.2 - - + -
103A LEU* 4.1 30.7 - - + -
347A ILE* 4.4 11.0 - - + -
350A GLU* 3.9 14.1 - - + -
351A THR* 4.1 27.1 - - + -
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Residues in contact with LYS 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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69A LEU* 2.8 48.0 + - + +
70A ARG* 3.7 6.3 - - - +
72A ILE* 1.3 73.5 - - - +
74A ILE* 1.3 61.5 + - + +
76A LEU* 3.6 2.2 + - - +
77A ARG* 3.3 23.9 + - - +
329A PHE* 3.6 20.4 - - + -
346A LEU* 6.1 2.8 - - - +
350A GLU* 3.4 38.2 + - - +
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Residues in contact with ILE 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 ARG* 3.1 32.0 + - + +
71A GLU* 3.8 3.8 - - - +
73A LYS* 1.3 80.3 - - + +
75A LEU* 1.3 59.2 + - + +
77A ARG* 3.3 2.3 + - - +
78A PHE* 3.0 60.6 + - + -
145A VAL* 4.2 13.5 - - + -
168A PHE* 3.8 20.9 - - + +
171A ALA* 3.8 29.2 - - + +
172A ARG* 5.7 1.3 - - - -
329A PHE* 3.8 23.3 - - + -
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Residues in contact with LEU 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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71A GLU* 2.9 49.8 + - + +
72A ILE 4.2 0.2 - - - +
74A ILE* 1.3 74.9 - - + +
76A LEU* 1.3 58.7 + - - +
78A PHE* 3.2 21.8 - - + +
83A ILE* 4.2 6.7 - - + -
84A ILE* 3.3 41.8 - - + +
85A GLY* 4.7 1.0 - - - -
86A ILE* 3.8 39.5 + - + -
103A LEU* 5.0 3.4 - - + -
167A ASP 5.9 1.8 - - - +
168A PHE* 3.7 32.5 - - + -
1001A SB2 5.1 3.4 - - + -
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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
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72A ILE* 3.1 39.5 + - + +
73A LYS* 4.0 3.8 - - - +
74A ILE 3.3 0.2 - - - -
75A LEU* 1.3 75.0 - - - +
77A ARG* 1.3 61.5 + - - +
78A PHE 4.3 2.9 - - - +
79A ARG* 5.8 1.7 + - - -
86A ILE* 3.5 37.2 - - + +
89A ILE* 4.3 6.5 - - + -
350A GLU* 3.5 23.6 - - + +
353A ARG* 3.4 46.2 + - - +
354A PHE* 4.3 11.7 - - + -
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Residues in contact with ARG 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 LYS* 3.3 15.1 + - - +
74A ILE 3.3 3.9 + - - +
76A LEU* 1.3 77.4 - - - +
78A PHE* 1.3 67.0 + - + +
79A ARG* 3.7 4.7 + - - +
139A TYR* 4.0 5.2 + - - -
327A ALA* 3.4 27.6 + - + +
328A PRO 2.9 33.5 + - - -
329A PHE* 3.4 44.3 - - + +
353A ARG* 5.8 0.2 - - - +
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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