Contacts of the helix formed by residues 119 - 128 (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 ASN 119 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C ALA 3.3 19.4 + - - -
110C THR* 3.9 16.9 - - + +
113C ASN* 3.2 15.4 - - - +
114C ILE 2.9 28.4 + - - +
116C VAL* 4.4 4.2 - - - +
89F PHE* 3.6 12.3 - - - -
117F ALA* 3.5 1.5 - - - +
118F THR* 1.3 83.8 + - - +
120F VAL* 1.3 62.2 + - - +
122F THR* 2.7 31.3 + - - -
123F ALA* 3.0 18.7 + - - +
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Residues in contact with VAL 120 (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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113C ASN* 3.3 12.9 + - - +
139C LEU* 6.3 5.2 - - + -
25F MET* 4.8 19.5 - - + +
29F TRP* 4.2 16.6 - - + -
32F ARG* 4.4 11.2 - - - +
89F PHE* 3.7 28.0 - - + -
119F ASN* 1.3 71.8 - - - +
121F ALA* 1.3 60.6 + - - +
123F ALA* 3.0 3.4 + - - +
124F ASP* 2.8 48.2 + - - +
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Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ASN* 2.9 47.3 + - - +
114C ILE 4.1 8.7 - - - -
115C PRO* 4.1 6.7 - - + -
138C ILE* 4.2 15.9 - - + -
119F ASN* 3.9 1.1 - - - +
120F VAL* 1.3 74.5 - - - +
122F THR* 1.3 61.7 + - - +
124F ASP* 3.4 5.5 + - - +
125F PHE* 3.0 33.5 + - + -
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Residues in contact with THR 122 (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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114C ILE 3.4 0.7 + - - -
115C PRO* 3.3 7.2 - - - +
116C VAL* 3.0 42.0 + - - +
122C THR* 4.6 0.2 - - + -
126C ILE* 4.3 9.4 - - + -
116F VAL 3.7 18.6 - - - +
117F ALA* 3.7 11.4 - - + -
118F THR* 4.6 1.7 + - - +
119F ASN* 2.7 25.8 + - - -
121F ALA* 1.3 75.1 - - - +
123F ALA* 1.3 66.0 + - - +
125F PHE* 3.3 5.5 + - - +
126F ILE* 3.0 38.1 + - + +
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Residues in contact with ALA 123 (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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29F TRP* 3.5 30.7 - - + +
87F ILE* 4.6 5.4 - - + +
89F PHE* 4.0 15.3 - - + -
117F ALA* 3.6 15.6 - - + +
119F ASN 3.0 14.4 + - - +
120F VAL 3.0 7.4 + - - +
122F THR* 1.3 77.3 - - - +
124F ASP* 1.3 57.4 + - - +
126F ILE* 3.7 3.3 - - - +
127F ILE* 3.1 30.5 + - - +
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Residues in contact with ASP 124 (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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29F TRP* 2.9 21.8 + - - -
32F ARG* 3.4 16.0 + - - -
33F HIS* 3.1 17.8 + - - -
120F VAL* 2.8 26.4 + - - +
121F ALA* 3.6 7.0 - - - +
123F ALA* 1.3 74.7 - - - +
125F PHE* 1.3 68.0 + - + +
127F ILE* 3.4 4.3 + - - +
128F GLN* 2.9 44.7 + - - +
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Residues in contact with PHE 125 (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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8C LEU* 4.9 6.1 - - + -
12C LYS* 5.0 3.8 - - - -
85C VAL* 6.0 1.1 - - + -
115C PRO* 3.7 26.9 - - + -
125C PHE 3.8 1.8 - - - +
126C ILE* 3.7 28.5 - - + -
129C SER* 3.0 43.0 + - - -
131C HIS* 3.9 19.5 - - + -
132C PHE* 3.9 32.5 - + - -
136C VAL* 4.2 20.6 - - + -
138C ILE* 5.8 2.0 - - + -
121F ALA* 3.0 29.3 + - + +
122F THR* 3.3 5.6 + - - +
124F ASP* 1.3 82.1 - - + +
126F ILE* 1.3 61.0 + - - +
128F GLN* 4.5 3.8 - - - -
129F SER* 3.2 13.0 + - - -
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Residues in contact with ILE 126 (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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122C THR* 4.3 8.1 - - + -
125C PHE* 3.8 19.6 - - + -
126C ILE* 4.8 4.3 - - + -
85F VAL* 4.8 6.5 - - + -
87F ILE* 5.4 5.2 - - + -
115F PRO* 4.4 16.8 - - + -
116F VAL 3.8 34.3 - - - +
117F ALA* 3.8 13.7 - - + -
122F THR* 3.0 27.3 + - + +
123F ALA* 3.7 5.2 - - - +
125F PHE* 1.3 77.6 - - - +
127F ILE* 1.3 63.6 + - + +
129F SER* 3.2 20.8 + - - -
132F PHE* 3.4 30.4 - - + -
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Residues in contact with ILE 127 (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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29F TRP* 3.9 15.3 - - + -
33F HIS* 3.9 46.0 - - + +
36F LEU* 3.3 38.6 - - + +
37F LEU* 3.9 23.6 - - + -
123F ALA 3.1 20.7 + - - +
124F ASP* 3.5 8.7 - - - +
126F ILE* 1.3 76.7 - - + +
128F GLN* 1.3 63.2 + - + +
129F SER 3.3 1.9 + - - +
132F PHE* 4.0 29.7 - - + +
133F ASN* 5.8 0.7 + - - -
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Residues in contact with GLN 128 (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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129C SER* 4.1 11.2 + - - +
130C PRO* 3.1 24.3 - - + +
131C HIS* 3.7 34.6 + - - +
33F HIS* 5.1 10.5 - - + -
124F ASP* 2.9 39.9 + - - +
125F PHE* 3.9 4.2 + - - -
127F ILE* 1.3 81.8 - - + +
129F SER* 1.3 66.2 + - - +
130F PRO* 3.5 0.9 - - - +
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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