Contacts of the helix formed by residues 96 - 112 (chain C) in PDB entry 1O97
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 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C GLY 3.3 2.6 + - - +
95C SER* 1.3 73.4 - - - +
97C ALA* 1.3 59.8 + - - +
98C ILE* 3.1 8.4 + - - +
99C VAL* 3.0 22.9 + - - +
100C VAL* 2.9 28.5 + - - +
127C TYR* 5.4 13.0 - - + +
225C SER* 3.0 27.4 + - - +
226C MET* 2.7 35.9 + - - +
227C SER* 4.3 4.0 + - - -
114D PHE 5.6 0.3 - - - +
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASP* 1.3 78.4 - - - +
98C ILE* 1.3 61.3 + - + +
100C VAL* 3.8 3.9 - - - -
101C GLY* 2.9 24.6 + - - -
127C TYR* 4.0 23.5 - - + -
129C SER* 3.7 26.7 - - - -
130C THR* 3.3 32.6 - - - +
133C SER* 4.0 0.7 + - - -
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASP* 3.1 10.1 + - - +
97C ALA* 1.3 89.9 - - + +
99C VAL* 1.3 58.1 + - + +
101C GLY* 3.3 1.0 + - - -
102C ARG* 3.1 21.1 + - - +
129C SER* 4.3 0.4 - - - -
133C SER* 3.6 10.3 - - - -
137C TYR* 3.5 25.5 + - - +
226C MET* 3.9 30.5 - - + -
104D SER* 3.9 30.7 - - - +
107D ALA* 4.9 1.1 - - + -
108D SER* 3.7 28.3 - - - +
114D PHE* 4.1 18.6 - - + -
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C SER* 3.4 28.7 - - - +
96C ASP* 3.0 19.3 + - - +
98C ILE* 1.3 76.1 - - + +
100C VAL* 1.3 65.8 + - - +
102C ARG* 3.1 9.6 + - + +
103C ILE* 3.0 26.9 + - + +
219C ASP 4.0 5.8 - - - +
220C VAL* 3.8 22.0 - - + -
221C GLY 4.0 0.7 - - - +
224C GLN* 3.7 27.8 - - + +
225C SER* 3.6 13.5 - - - +
226C MET* 6.2 0.2 - - + -
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 4.3 14.6 - - + -
95C SER* 3.7 22.2 - - - +
96C ASP 2.9 20.9 + - - +
97C ALA* 3.9 5.8 - - - +
99C VAL* 1.3 74.1 - - - +
101C GLY* 1.3 63.0 + - - +
103C ILE* 3.2 7.2 + - + +
104C LEU* 2.9 37.3 + - + +
130C THR* 3.8 6.1 - - + -
1262C AMP 3.7 44.9 - - + +
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Residues in contact with GLY 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ALA 2.9 16.2 + - - -
98C ILE 3.3 5.6 + - - -
99C VAL 3.2 0.2 - - - -
100C VAL* 1.3 77.7 - - - +
102C ARG* 1.3 58.3 + - - +
104C LEU 3.5 0.2 + - - -
105C THR* 2.9 29.1 + - - -
130C THR* 4.3 2.7 - - - +
133C SER* 3.7 11.2 - - - -
134C VAL* 3.8 22.6 - - - +
137C TYR* 4.0 6.5 - - - -
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Residues in contact with ARG 102 (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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98C ILE 3.1 12.2 + - - +
99C VAL* 3.1 13.0 + - + +
101C GLY* 1.3 76.6 - - - +
103C ILE* 1.3 63.8 + - + +
105C THR* 3.2 4.9 + - - -
106C GLU* 3.1 41.9 + - - +
109C LYS* 4.8 3.8 - - - +
137C TYR* 3.5 48.3 - - + +
215C LEU* 3.4 35.2 - - - +
219C ASP* 5.6 9.1 - - - +
220C VAL* 6.3 0.2 - - - -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 3.7 30.1 - - + -
87C VAL* 3.7 30.7 - - + -
92C ALA* 4.6 7.4 - - + -
95C SER* 4.3 9.2 - - - +
99C VAL* 3.0 24.2 + - + +
100C VAL* 3.7 7.4 - - - +
102C ARG* 1.3 76.4 - - + +
104C LEU* 1.3 63.7 + - - +
106C GLU* 3.1 13.2 + - - +
107C VAL* 3.4 12.3 + - - +
210C LEU* 4.7 3.6 - - + -
213C ILE* 3.9 6.6 - - + +
215C LEU* 3.9 14.4 - - + -
220C VAL* 3.8 31.4 - - + -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 5.8 0.7 - - + -
6C ALA* 4.0 17.5 - - + -
62C VAL* 3.8 25.1 - - + -
64C VAL* 3.8 21.3 - - + -
100C VAL* 2.9 29.5 + - + +
101C GLY 3.9 3.8 - - - +
103C ILE* 1.3 76.4 - - - +
105C THR* 1.3 59.4 + - - +
107C VAL* 3.1 8.5 + - - +
108C ILE* 2.9 39.6 + - + +
130C THR* 4.1 7.2 - - + -
134C VAL* 3.9 22.4 - - + -
1262C AMP 3.8 30.7 - - + +
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Residues in contact with THR 105 (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 GLY 2.9 22.1 + - - -
102C ARG* 3.5 6.7 - - - +
103C ILE 3.2 0.2 - - - -
104C LEU* 1.3 76.5 - - - +
106C GLU* 1.3 64.6 + - - +
108C ILE* 3.2 9.7 + - - +
109C LYS* 2.9 42.3 + - - +
134C VAL* 3.6 15.1 + - - +
137C TYR* 3.3 35.0 - - + +
138C LEU* 3.5 21.5 - - + -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ARG* 3.1 44.1 + - - +
103C ILE 3.1 8.5 + - - +
105C THR* 1.3 79.4 - - - +
107C VAL* 1.3 61.1 + - - +
109C LYS* 2.7 48.0 + - - +
110C LYS* 3.6 20.3 + - - +
213C ILE* 3.6 38.6 - - + +
215C LEU* 4.1 11.2 - - + -
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Residues in contact with VAL 107 (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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4C LEU* 4.6 1.6 - - + -
62C VAL* 4.0 29.8 - - + -
85C VAL* 4.5 9.2 - - + -
87C VAL* 3.6 29.8 - - + -
103C ILE 3.4 9.6 + - - +
104C LEU* 3.1 9.5 + - - +
106C GLU* 1.3 74.8 - - - +
108C ILE* 1.3 66.7 + - + +
110C LYS* 3.1 8.7 + - - +
111C GLU* 3.0 35.5 + - + +
208C VAL* 4.8 5.2 - - + -
213C ILE* 4.1 18.6 - - + -
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Residues in contact with ILE 108 (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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4C LEU* 3.8 27.8 - - + -
6C ALA* 6.2 1.1 - - + -
62C VAL* 6.5 0.2 - - + -
104C LEU* 2.9 28.5 + - + +
105C THR* 3.2 4.9 + - - +
107C VAL* 1.3 75.7 - - + +
109C LYS* 1.3 53.9 + - - +
111C GLU* 4.3 6.3 - - - -
112C ALA* 2.7 32.2 + - - -
113C PRO* 3.4 21.1 - - + +
116C VAL* 4.1 19.1 - - + -
134C VAL* 3.6 30.7 - - + -
138C LEU* 3.7 26.0 - - + -
140C TRP* 4.7 4.3 - - + -
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Residues in contact with LYS 109 (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 ARG* 4.8 5.1 - - - +
105C THR* 2.9 36.2 + - + +
106C GLU* 2.7 44.4 + - - +
107C VAL 3.2 0.4 - - - -
108C ILE* 1.3 77.9 - - - +
110C LYS* 1.3 64.1 + - + +
112C ALA* 3.8 11.1 + - - +
137C TYR 5.0 5.2 - - - -
138C LEU* 4.6 8.3 - - + +
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Residues in contact with LYS 110 (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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106C GLU 3.6 15.0 - - - +
107C VAL* 3.1 7.7 + - - +
109C LYS* 1.3 79.9 - - + +
111C GLU* 1.3 63.4 + - + +
112C ALA* 3.7 2.3 + - - +
212C ASP* 3.6 21.2 + - - -
213C ILE* 4.1 20.0 - - + +
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Residues in contact with GLU 111 (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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2C LYS* 2.8 49.2 + - + +
4C LEU* 3.9 24.5 - - + -
60C VAL* 4.4 7.2 - - - +
83C ARG* 2.8 37.7 + - - -
85C VAL* 4.5 5.5 - - - +
107C VAL* 3.0 25.4 + - + +
108C ILE 3.8 2.7 - - - +
110C LYS* 1.3 78.2 - - + +
112C ALA* 1.3 71.4 + - - +
113C PRO* 3.3 3.7 - - + -
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Residues in contact with ALA 112 (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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2C LYS* 5.0 1.7 - - - +
108C ILE 2.7 17.2 + - - -
109C LYS* 4.2 10.8 - - - +
110C LYS 3.4 2.9 - - - +
111C GLU* 1.3 76.0 - - - +
113C PRO* 1.3 70.2 - - - +
114C ASP* 4.8 3.8 - - - +
140C TRP* 6.0 1.3 - - - -
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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