Contacts of the helix formed by residues 69 - 80 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ALA* 5.0 0.3 - - - -
79A SER* 4.1 6.5 + - - -
107A ARG* 5.2 0.7 - - - -
108A LEU* 3.7 24.7 - - - +
64F LEU* 4.5 0.7 - - - -
66F GLY 3.0 7.4 + - - -
67F PRO 3.3 2.2 + - - -
68F MET* 1.3 79.9 - - - +
70F GLY* 1.3 64.0 + - - +
71F ASP 3.3 2.7 - - - -
72F GLN* 3.4 7.4 + - - +
73F GLN* 3.1 29.4 + - - +
101F ASP* 5.4 0.4 - - - -
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Residues in contact with GLY 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F THR* 3.9 8.7 - - - -
63F MET* 4.6 1.2 - - - +
64F LEU* 3.2 25.0 + - - +
65F SER 2.9 11.2 + - - -
66F GLY 3.5 0.2 + - - -
68F MET 3.7 0.2 - - - -
69F GLY* 1.3 78.5 - - - +
71F ASP* 1.3 62.6 + - - +
73F GLN* 3.1 15.6 + - - +
74F VAL* 3.0 27.0 + - - +
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Residues in contact with ASP 71 (chain F).
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* 3.8 1.2 - - - +
17F VAL* 4.0 11.3 - - - +
45F THR* 4.1 1.9 - - - +
66F GLY* 3.7 12.2 + - - +
69F GLY 3.3 0.4 - - - -
70F GLY* 1.3 74.8 - - - +
72F GLN* 1.3 59.2 + - + +
74F VAL* 3.2 6.9 + - - +
75F GLY* 2.9 23.0 + - - -
88F PHE* 4.4 4.0 - - - -
98F ASN* 2.6 32.6 + - - -
101F ASP* 3.8 30.5 - - + +
102F VAL* 4.6 0.9 - - - +
105F LEU* 3.5 24.4 - - + +
206F PGA 2.8 21.3 - - - +
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Residues in contact with GLN 72 (chain F).
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 3.9 2.3 - - - +
72A GLN* 3.5 43.2 - - + +
75A GLY* 3.3 19.9 - - - -
76A ALA* 4.3 3.6 - - - +
101A ASP 5.2 0.5 - - - +
104A ALA* 2.9 35.8 + - + +
105A LEU* 4.3 4.7 + - - -
108A LEU* 2.9 30.2 - - + +
69F GLY 3.4 8.2 + - - +
70F GLY 3.2 0.6 - - - -
71F ASP* 1.3 74.3 - - - +
73F GLN* 1.3 60.8 + - - +
75F GLY* 3.7 0.3 - - - -
76F ALA* 2.9 31.2 + - - +
101F ASP* 3.2 24.7 + - + +
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Residues in contact with GLN 73 (chain F).
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* 3.9 15.5 - - + -
79A SER* 4.3 3.1 - - - +
80A GLU* 2.9 40.1 + - - +
63F MET* 3.3 23.4 - - - +
64F LEU* 2.8 49.7 + - - +
69F GLY 3.1 15.4 + - - +
70F GLY* 3.1 9.1 + - - +
72F GLN* 1.3 76.6 - - - +
74F VAL* 1.3 62.8 + - - +
76F ALA* 3.5 3.0 + - - +
77F LEU* 3.1 30.1 + - + +
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Residues in contact with VAL 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ALA* 3.9 27.8 - - + -
17F VAL* 4.7 8.7 - - + -
43F TYR* 6.3 1.8 - - + -
44F ALA* 5.4 3.8 - - - +
45F THR* 4.5 13.5 - - + -
63F MET* 4.5 14.8 - - + -
70F GLY 3.0 15.8 + - - +
71F ASP* 3.5 7.9 - - - +
73F GLN* 1.3 76.2 - - - +
75F GLY* 1.3 65.1 + - - +
77F LEU* 3.1 11.1 + - + +
78F ILE* 3.0 36.8 + - + +
83F ILE* 4.7 3.8 - - + -
86F LEU* 4.3 6.5 - - + -
105F LEU* 4.1 15.7 - - + -
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Residues in contact with GLY 75 (chain F).
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* 3.3 20.2 - - - -
71F ASP 2.9 11.3 + - - -
72F GLN 3.2 0.4 + - - -
74F VAL* 1.3 76.7 - - - +
76F ALA* 1.3 55.2 + - - +
78F ILE* 3.1 8.6 + - - +
79F SER* 2.9 24.4 + - - -
105F LEU* 3.6 13.9 - - - +
108F LEU* 3.6 20.2 - - - +
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Residues in contact with ALA 76 (chain F).
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 5.0 0.2 - - - -
72A GLN* 4.1 5.0 + - - +
73A GLN* 3.9 27.4 - - + -
76A ALA* 4.5 6.7 - - + -
72F GLN 2.9 17.3 + - - +
73F GLN 3.7 5.4 - - - +
75F GLY* 1.3 77.3 - - - +
77F LEU* 1.3 58.6 + - + +
79F SER* 2.7 23.8 + - - -
80F GLU* 2.9 32.0 + - - +
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F TYR* 4.7 13.7 - - + -
63F MET* 4.1 26.0 - - + -
73F GLN* 3.1 17.8 + - + +
74F VAL* 3.1 12.4 + - + +
76F ALA* 1.3 77.7 - - + +
78F ILE* 1.3 57.5 + - - +
80F GLU* 3.3 10.1 + - - +
81F GLY 3.1 3.8 + - - -
82F LYS* 2.8 60.9 + - + +
83F ILE* 3.6 24.9 - - + -
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Residues in contact with ILE 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ARG* 5.6 0.5 + - - -
74F VAL* 3.0 32.1 + - + +
75F GLY* 3.1 7.6 + - - +
77F LEU* 1.3 74.1 - - - +
79F SER* 1.3 61.0 + - - +
81F GLY* 2.9 19.9 + - - -
83F ILE* 3.6 31.3 - - + +
86F LEU* 4.3 13.2 - - + -
105F LEU* 4.1 15.7 - - + +
108F LEU* 4.2 11.7 - - + +
109F ALA* 4.4 8.1 - - + +
112F TRP* 4.1 27.0 - - + +
114F ILE* 3.8 30.3 - - + +
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Residues in contact with SER 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.2 20.8 - - - +
68A MET 3.4 24.2 - - - -
69A GLY* 4.1 8.4 - - - -
73A GLN* 4.2 4.9 - - - +
75F GLY 2.9 12.7 + - - -
76F ALA* 2.7 24.3 + - - -
78F ILE* 1.3 77.7 - - - +
80F GLU* 1.3 59.8 + - - +
81F GLY 3.2 1.3 + - - -
108F LEU* 4.5 1.6 - - - -
112F TRP* 3.4 37.3 - - - +
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Residues in contact with GLU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 5.0 3.1 - - + -
73A GLN* 3.4 28.7 + - - +
76F ALA* 2.9 32.8 + - - +
77F LEU* 3.7 11.9 - - - +
78F ILE 3.1 0.4 - - - -
79F SER* 1.3 76.6 + - - +
81F GLY* 1.3 61.9 + - - +
82F LYS* 3.1 41.0 + - + +
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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