Contacts of the helix formed by residues 123 - 138 (chain C) in PDB entry 1S1Q
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 ASP 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C GLU* 3.2 27.0 - - + +
80C TYR* 3.9 0.2 - - - -
113C TYR* 3.0 12.8 + - - -
117C TRP* 3.8 9.6 - - - -
120C PRO 4.8 6.0 - - - +
121C GLN 4.8 4.1 - - - +
122C SER* 1.3 74.7 - - - +
124C LEU* 1.3 58.7 + - - +
125C LEU* 4.1 12.8 - - - +
126C GLY* 3.1 18.5 + - - -
127C LEU* 3.0 23.9 + - - +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU* 3.0 22.3 + - + +
25C THR* 4.0 17.3 - - - +
28C VAL* 3.4 19.1 - - + -
55C LEU* 4.0 24.5 - - + -
74C LEU* 4.7 8.5 - - + -
76C LEU* 4.0 17.9 - - + -
80C TYR* 3.2 26.2 - - + +
85C PRO* 3.9 24.7 - - + -
117C TRP* 4.6 1.8 - - + -
123C ASP* 1.3 71.0 - - - +
125C LEU* 1.3 65.6 + - - +
127C LEU* 3.3 8.5 + - + +
128C ILE* 3.0 29.8 + - + +
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU 5.2 0.7 - - - +
27C ASN* 3.7 35.0 - - + +
28C VAL* 3.7 19.0 - - + +
31C LEU* 3.4 35.7 - - + -
32C TYR* 4.0 15.7 + - + -
123C ASP* 3.4 12.1 + - - +
124C LEU* 1.3 77.8 - - - +
126C GLY* 1.3 58.3 + - - +
128C ILE* 3.3 5.4 + - - +
129C GLN* 2.9 43.8 + - - +
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Residues in contact with GLY 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TYR* 3.5 23.0 - - - -
123C ASP* 3.1 12.3 + - - -
125C LEU* 1.3 74.7 - - - +
127C LEU* 1.3 63.3 + - - +
129C GLN* 3.4 17.8 + - - +
130C VAL* 3.1 28.4 + - - +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 4.7 7.6 - - + -
85C PRO* 3.6 32.3 - - + -
87C CYS* 3.9 13.7 - - - -
111C LEU* 3.7 18.2 - - + -
113C TYR* 3.5 21.7 - - + -
114C LEU* 3.9 18.8 - - + -
117C TRP* 4.3 3.1 - - + -
123C ASP 3.0 17.0 + - - +
124C LEU* 3.6 11.2 - - + +
125C LEU 3.2 0.4 - - - -
126C GLY* 1.3 73.7 - - - +
128C ILE* 1.3 62.8 + - + +
130C VAL* 3.3 2.3 + - - +
131C MSE 3.0 47.3 + - + +
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL* 3.7 33.2 - - + -
32C TYR* 3.5 36.6 - - + -
35C LEU* 3.7 17.0 - - + -
59C ILE* 4.0 15.0 - - + -
72C ILE* 5.3 0.2 - - + -
74C LEU* 4.3 20.9 - - + -
124C LEU 3.0 18.5 + - - +
125C LEU 3.8 3.6 - - - +
127C LEU* 1.3 75.1 - - + +
129C GLN* 1.3 64.7 + - - +
131C MSE 3.2 11.7 + - - +
132C ILE* 2.9 33.0 + - + +
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Residues in contact with GLN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 5.6 3.6 - - - +
32C TYR* 4.4 13.6 + - - +
125C LEU* 2.9 40.5 + - - +
126C GLY* 3.4 15.4 - - - +
128C ILE* 1.3 76.9 - - - +
130C VAL* 1.3 62.9 + - + +
132C ILE* 3.4 4.6 + - - +
133C VAL* 3.2 28.7 + - + +
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 4.2 18.6 - - + -
112C PRO* 5.6 3.1 - - + -
113C TYR* 3.9 30.5 - - + +
126C GLY 3.1 13.7 + - - +
127C LEU 3.7 7.4 - - - +
128C ILE 3.3 0.2 - - - -
129C GLN* 1.3 73.6 - - + +
131C MSE 1.3 56.1 + - - +
133C VAL* 3.1 7.1 + - - +
134C VAL* 2.8 49.6 + - + +
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Residues in contact with MSE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ILE* 4.0 20.4 - - + -
72C ILE* 4.2 14.8 - - - -
74C LEU* 4.0 14.8 - - + -
87C CYS* 4.2 7.9 - - + -
109C ILE* 4.2 20.4 - - + -
111C LEU* 4.2 17.5 - - + +
127C LEU* 3.0 52.3 + - + +
128C ILE* 3.4 13.7 - - - +
130C VAL* 1.3 77.4 - - - +
132C ILE* 1.3 55.1 + - - +
134C VAL* 4.7 2.5 - - - -
135C PHE* 2.7 65.2 + - + +
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Residues in contact with ILE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TYR* 3.5 40.8 - - + +
59C ILE* 4.0 20.0 - - + -
60C PRO* 3.6 26.9 - - + +
61C VAL* 3.9 11.4 - - + +
62C PRO* 4.0 16.8 - - + +
128C ILE* 2.9 23.9 + - + +
129C GLN* 3.9 4.9 - - - +
131C MSE 1.3 75.4 - - - +
133C VAL* 1.3 65.1 + - + +
136C GLY* 3.1 20.4 + - - -
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C GLN* 3.2 14.6 + - + +
130C VAL* 3.1 10.8 + - - +
132C ILE* 1.3 79.2 - - + +
134C VAL* 1.3 70.0 + - + +
136C GLY* 3.5 2.1 + - - -
137C ASP* 3.4 22.2 + - - +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C HIS* 2.9 46.2 - - + +
111C LEU* 4.0 13.2 - - + -
112C PRO* 6.1 2.0 - - + -
130C VAL* 2.8 38.3 + - + +
131C MSE 4.0 1.6 - - - +
133C VAL* 1.3 79.5 - - + +
135C PHE* 1.3 62.5 + - + +
137C ASP* 3.1 7.1 + - - +
138C GLU* 2.9 29.6 + - + +
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Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ILE* 4.5 13.7 - - + -
61C VAL* 3.7 22.9 - - + +
70C ILE* 4.8 7.6 - - + -
72C ILE* 4.8 1.3 - - + -
89C VAL* 4.0 16.6 - - + -
102C HIS* 4.6 11.7 - - + -
103C VAL* 3.9 14.1 - - + -
109C ILE* 4.0 24.9 - - + -
111C LEU* 5.5 1.1 - - + -
131C MSE 2.7 54.6 + - + +
134C VAL* 1.3 80.0 - - + +
136C GLY* 1.3 60.7 + - - +
138C GLU 3.7 8.1 - - - -
139C PRO* 3.2 25.8 - - - +
140C PRO* 3.7 31.4 - - + -
510C ACY 4.0 1.7 - - - +
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Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 3.5 3.8 - - - +
62C PRO* 3.5 23.3 - - - +
63C TYR* 3.3 25.9 - - - -
132C ILE 3.1 17.8 + - - -
133C VAL 3.5 2.9 + - - -
134C VAL 3.3 0.6 - - - -
135C PHE* 1.3 74.6 - - - +
137C ASP* 1.3 57.9 + - - +
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Residues in contact with ASP 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C TYR* 5.2 2.5 - - - -
133C VAL* 3.4 12.0 + - - +
134C VAL* 3.1 10.0 + - - +
136C GLY* 1.3 80.0 - - - +
138C GLU* 1.3 70.4 + - + +
139C PRO* 3.6 8.0 - - - +
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Residues in contact with GLU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LYS* 2.6 39.6 + - - +
102C HIS* 3.2 20.3 + - + +
103C VAL* 5.9 0.3 - - - +
134C VAL* 2.9 12.1 + - - +
135C PHE* 3.5 13.0 - - - +
137C ASP* 1.3 88.1 - - + +
139C PRO* 1.3 68.3 - - - +
140C PRO* 3.4 8.1 - - - +
9001C CU 2.0 28.8 - - - -
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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