Contacts of the helix formed by residues 69 - 80 (chain A) in PDB entry 1S89
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.4 0.9 - - - -
66A GLY 3.1 6.8 + - - -
67A PRO 3.3 2.0 + - - -
68A MET* 1.3 81.6 - - - +
70A GLY* 1.3 64.2 + - - +
71A ASP 3.3 3.1 - - - -
72A GLN* 3.2 8.3 + - - +
73A GLN* 3.0 29.4 + - - +
101A ASP* 5.1 2.0 - - - -
76F ALA* 5.0 0.2 - - - -
79F SER* 4.1 6.3 + - - -
108F LEU* 3.8 23.5 - - - +
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Residues in contact with GLY 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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45A THR* 3.8 8.7 - - - +
63A MET* 4.5 1.0 - - - +
64A LEU* 3.2 26.0 + - - +
65A SER 2.9 12.3 + - - -
66A GLY 3.4 0.4 + - - -
68A MET 3.8 0.4 - - - -
69A GLY* 1.3 77.6 - - - +
71A ASP* 1.3 61.6 + - - +
73A GLN* 3.2 12.3 + - - +
74A VAL* 2.9 28.2 + - - +
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Residues in contact with ASP 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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17A VAL* 4.1 5.0 - - - +
45A THR* 3.9 8.4 - - - +
66A GLY* 3.7 10.7 + - - +
69A GLY 3.3 0.6 - - - -
70A GLY* 1.3 75.6 - - - +
72A GLN* 1.3 59.3 + - - +
74A VAL* 3.3 4.3 + - - +
75A GLY* 2.8 24.3 + - - -
88A PHE* 4.9 1.2 - - - -
98A ASN* 2.9 28.2 + - - -
101A ASP* 3.6 34.7 - - + +
102A VAL* 4.1 8.2 - - - +
105A LEU* 3.7 23.0 - - + +
201A PGA 2.8 22.2 - - - +
72F GLN* 3.9 1.8 - - - +
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Residues in contact with GLN 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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69A GLY 3.2 8.8 + - - +
71A ASP* 1.3 75.1 - - - +
73A GLN* 1.3 61.2 + - - +
75A GLY* 3.6 0.5 - - - -
76A ALA* 2.8 29.1 + - - +
101A ASP* 3.3 22.6 + - + +
104A ALA* 6.1 0.2 - - + -
71F ASP 3.8 2.3 - - - +
72F GLN* 3.5 44.7 - - + +
75F GLY* 3.3 19.6 - - - -
76F ALA* 4.3 3.1 - - - +
101F ASP 5.3 0.6 - - - +
104F ALA* 2.9 42.6 + - + +
105F LEU* 3.8 3.9 - - - +
108F LEU* 3.0 24.8 - - + +
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Residues in contact with GLN 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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63A MET* 3.0 24.8 - - + +
64A LEU* 2.7 51.3 + - - +
69A GLY 3.0 14.7 + - - +
70A GLY* 3.2 8.3 + - - +
72A GLN* 1.3 74.7 - - - +
74A VAL* 1.3 65.5 + - - +
76A ALA* 3.3 3.7 + - - +
77A LEU* 3.1 29.1 + - + +
76F ALA* 3.9 21.3 - - + -
79F SER* 4.2 3.1 - - - +
80F GLU* 3.4 31.5 + - - +
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Residues in contact with VAL 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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15A ALA* 4.0 26.2 - - + -
17A VAL* 4.5 9.2 - - + -
43A TYR* 6.1 1.8 - - + -
44A ALA* 5.2 2.5 - - - +
45A THR* 4.3 17.0 - - + +
63A MET* 4.5 14.1 - - + -
70A GLY 2.9 18.9 + - - +
71A ASP* 3.6 7.9 - - - +
73A GLN* 1.3 75.4 - - - +
75A GLY* 1.3 65.0 + - - +
77A LEU* 3.0 12.0 + - + +
78A ILE* 2.9 32.0 + - + +
83A ILE* 4.8 2.9 - - + -
86A LEU* 4.4 7.4 - - + -
105A LEU* 4.0 17.3 - - + -
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Residues in contact with GLY 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 ASP 2.8 11.7 + - - -
73A GLN 3.2 0.4 - - - -
74A VAL* 1.3 75.6 - - - +
76A ALA* 1.3 61.4 + - - +
78A ILE* 3.1 7.5 + - - +
79A SER* 3.0 18.5 + - - -
105A LEU* 3.6 15.1 - - - +
108A LEU* 3.6 18.0 - - - +
72F GLN* 3.3 21.8 - - - -
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Residues in contact with ALA 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 GLN 2.8 19.7 + - - +
73A GLN 3.6 5.6 - - - +
74A VAL 3.2 0.2 - - - -
75A GLY* 1.3 70.7 - - - +
77A LEU* 1.3 64.0 + - + +
79A SER* 2.9 24.4 + - - -
80A GLU* 3.0 20.4 + - - +
69F GLY 5.0 0.2 - - - -
72F GLN* 4.3 5.2 - - - +
73F GLN* 3.9 32.5 - - + +
76F ALA* 4.5 7.2 - - + -
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Residues in contact with LEU 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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43A TYR* 4.5 16.6 - - + -
63A MET* 4.2 24.5 - - + -
73A GLN 3.1 16.9 + - - +
74A VAL* 3.0 13.1 + - + +
76A ALA* 1.3 76.7 - - + +
78A ILE* 1.3 61.4 + - - +
80A GLU* 3.3 15.3 + - - +
82A LYS* 2.8 55.1 + - + +
83A ILE* 3.6 25.8 - - + -
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Residues in contact with ILE 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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6A ARG* 5.5 0.9 + - - -
74A VAL* 2.9 20.8 + - + +
75A GLY* 3.1 7.6 + - - +
77A LEU* 1.3 78.0 - - - +
79A SER* 1.3 59.0 + - - +
81A GLY* 2.9 21.0 + - - -
83A ILE* 3.6 29.9 - - + +
86A LEU* 4.1 12.8 - - + -
105A LEU* 3.8 29.2 - - + +
108A LEU* 4.2 12.6 - - + +
109A ALA* 4.4 6.7 - - + +
112A TRP* 4.0 28.3 - - + +
114A ILE* 4.1 28.1 - - + +
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Residues in contact with SER 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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75A GLY 3.0 11.8 + - - -
76A ALA* 2.9 19.4 + - - -
78A ILE* 1.3 76.0 - - - +
80A GLU* 1.3 59.7 + - - +
81A GLY 3.2 1.3 + - - -
108A LEU* 4.5 1.6 - - - -
112A TRP* 3.4 33.1 - - - +
64F LEU* 3.3 24.0 - - - +
68F MET 3.3 26.2 - - - -
69F GLY* 4.1 12.2 + - - -
73F GLN* 4.3 1.7 - - - +
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Residues in contact with GLU 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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76A ALA* 3.0 26.3 + - - +
77A LEU* 3.8 12.8 - - - +
78A ILE 3.0 0.4 - - - -
79A SER* 1.3 77.8 - - - +
81A GLY* 1.3 62.3 + - - +
82A LYS* 3.2 34.6 + - + +
64F LEU* 4.9 2.7 - - + -
73F GLN* 2.9 37.2 + - - +
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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