Contacts of the helix formed by residues 128 - 146 (chain C) in PDB entry 6O81
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 GLN 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU* 4.0 20.5 - - + +
126C TYR 3.5 19.4 + - - +
127C ALA* 1.3 81.8 + - - +
129C LEU* 1.3 62.3 + - - +
130C GLN 3.3 2.6 + - - -
131C SER* 3.6 16.1 + - - +
132C ASN* 2.9 28.9 + - - +
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TRP* 4.1 30.3 - - + +
54C ALA* 4.8 18.4 - - + +
92C GLU* 5.7 3.8 - - + -
93C TYR* 5.6 10.3 - - + +
96C LEU* 3.8 24.1 - - + +
126C TYR 3.3 26.5 - - - +
127C ALA* 3.2 10.0 - - - +
128C GLN* 1.3 77.7 - - - +
130C GLN* 1.3 66.7 + - + +
132C ASN* 3.2 5.3 + - - +
133C ILE* 3.0 38.1 + - + +
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Residues in contact with GLN 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.4 24.4 + - + +
47C THR* 3.5 25.3 + - - +
49C HIS 5.6 0.6 + - - -
51C TRP* 3.8 31.1 - - + -
127C ALA 4.4 5.3 + - - +
128C GLN 3.3 0.6 - - - -
129C LEU* 1.3 84.8 - - + +
131C SER* 1.3 58.0 + - - +
133C ILE* 3.2 7.3 + - - +
134C ILE* 2.9 39.8 + - + +
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLN* 3.6 15.9 + - - +
129C LEU 3.4 0.2 - - - -
130C GLN* 1.3 78.4 - - - +
132C ASN* 1.3 63.6 + - - +
134C ILE* 3.4 8.3 + - - +
135C GLU* 2.9 31.3 + - - +
91L PRO* 6.0 1.5 - - - +
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Residues in contact with ASN 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 3.6 29.2 + - + +
96C LEU* 3.9 16.2 - - - +
128C GLN* 2.9 29.7 + - - +
129C LEU* 3.2 8.5 + - - +
130C GLN 3.2 0.6 - - - -
131C SER* 1.3 85.8 + - - +
133C ILE* 1.3 57.8 + - - +
135C GLU* 3.3 15.2 - - - +
136C ALA* 2.9 29.5 + - - +
52L ARG* 3.3 26.9 + - - +
53L ARG* 3.7 1.8 + - - -
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.7 24.7 - - + -
85C VAL* 5.2 2.9 - - + -
88C ILE* 3.9 14.4 - - + -
89C ILE* 3.7 36.3 - - + -
92C GLU* 3.7 34.5 - - + -
129C LEU* 3.0 22.6 + - + +
130C GLN* 3.8 6.7 - - - +
132C ASN* 1.3 73.3 - - - +
134C ILE* 1.3 61.3 + - - +
136C ALA* 3.7 2.5 - - - +
137C ILE* 2.9 38.8 + - + +
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Residues in contact with ILE 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 4.2 21.0 + - + +
46C ILE* 3.9 21.3 - - + -
47C THR* 3.7 29.4 - - + -
130C GLN* 2.9 29.5 + - + +
131C SER* 3.7 8.5 - - - +
133C ILE* 1.3 76.6 - - - +
135C GLU* 1.3 56.6 + - - +
137C ILE* 3.4 5.0 + - + +
138C ASN* 2.8 45.1 + - - +
91L PRO* 4.7 11.9 - - + -
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Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C SER 2.9 21.8 + - - +
132C ASN* 3.3 13.6 - - - +
134C ILE* 1.3 74.3 - - - +
136C ALA* 1.3 60.1 + - - +
138C ASN* 3.5 11.1 - - + +
139C GLU* 2.9 39.2 + - - +
52L ARG* 4.0 23.3 + - - +
53L ARG* 2.4 41.2 + - - -
91L PRO* 5.3 12.3 - - + -
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ILE* 3.9 30.9 - - + +
132C ASN 2.9 18.6 + - - +
133C ILE* 3.7 4.3 - - - +
134C ILE 3.3 0.2 - - - -
135C GLU* 1.3 75.8 - - - +
137C ILE* 1.3 60.7 + - - +
139C GLU* 3.3 15.0 - - - +
140C LEU* 2.9 28.9 + - - +
53L ARG* 3.6 19.7 - - - +
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Residues in contact with ILE 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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39C LEU* 3.8 32.7 - - + +
42C LEU* 4.8 2.0 - - + -
43C ARG* 3.5 41.1 - - + +
46C ILE* 3.8 26.0 - - + -
85C VAL* 4.7 20.4 - - + -
88C ILE* 5.4 6.1 - - + -
133C ILE* 2.9 29.2 + - + +
134C ILE* 3.8 4.7 - - - +
136C ALA* 1.3 76.5 - - + +
138C ASN* 1.3 57.0 + - - +
140C LEU* 3.3 7.3 + - - +
141C LEU* 2.9 29.2 + - + +
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Residues in contact with ASN 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 2.5 35.6 + - - +
134C ILE* 2.8 41.9 + - - +
135C GLU* 3.5 11.3 - - + +
136C ALA 3.2 0.2 - - - -
137C ILE* 1.3 77.6 - - - +
139C GLU* 1.3 57.9 + - - +
141C LEU* 3.1 6.3 + - - +
142C VAL* 2.9 31.7 + - + +
91L PRO* 4.2 15.4 - - - +
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Residues in contact with GLU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU* 2.9 27.9 + - - +
136C ALA* 3.3 18.0 - - - +
138C ASN* 1.3 71.8 - - - +
140C LEU* 1.3 61.2 + - + +
142C VAL* 3.4 11.3 + - + +
143C GLU* 2.9 28.1 + - - +
51L SER* 3.5 28.5 - - - -
52L ARG 4.5 1.6 + - - -
53L ARG* 3.4 34.4 + - - +
61L LEU* 5.4 7.4 - - + +
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.9 29.4 - - + -
81C MET* 4.6 11.2 - - + -
84C ARG* 4.0 51.8 - - + +
85C VAL* 5.2 2.0 - - + -
88C ILE* 4.1 14.6 - - + -
136C ALA 2.9 18.1 + - - +
137C ILE* 3.6 6.5 - - + +
138C ASN 3.2 0.2 - - - -
139C GLU* 1.3 78.4 - - + +
141C LEU* 1.3 57.4 + - - +
143C GLU* 3.3 15.2 + - + +
144C LEU* 2.9 33.1 + - + +
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 4.0 36.4 - - + +
39C LEU* 3.8 33.4 - - + -
40C GLY* 5.3 2.9 - - - +
43C ARG* 3.4 29.6 - - - +
137C ILE 2.9 13.6 + - - +
138C ASN* 3.1 8.7 + - - +
140C LEU* 1.3 76.1 - - - +
142C VAL* 1.3 60.3 + - + +
144C LEU* 3.7 9.1 - - + +
145C GLU* 2.9 30.8 + - - +
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Residues in contact with VAL 142 (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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138C ASN* 2.9 17.7 + - + +
139C GLU* 3.7 11.0 - - - +
141C LEU* 1.3 76.4 - - + +
143C GLU* 1.3 62.1 + - - +
145C GLU* 3.5 17.3 + - - +
146C GLY* 3.5 9.9 + - - -
60L LYS 4.2 3.4 - - - +
61L LEU* 3.8 32.9 - - + +
63L ARG* 5.3 4.3 - - + +
66L ARG* 4.0 24.5 - - - +
86L LYS* 5.0 3.4 - - + +
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Residues in contact with GLU 143 (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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84C ARG* 4.4 15.8 + - - -
139C GLU 2.9 17.5 + - - +
140C LEU* 3.6 15.5 - - + +
142C VAL* 1.3 78.0 - - - +
144C LEU* 1.3 60.6 + - - +
146C GLY 3.5 10.6 + - - +
147C THR* 3.7 9.0 + - - -
150C ASN* 5.5 0.2 + - - -
327C ASN* 3.9 24.7 + - - +
328C ILE* 4.9 7.3 - - - +
60L LYS* 3.4 39.7 - - - +
61L LEU* 5.3 1.5 - - + +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 3.0 51.8 - - + +
35C ALA* 3.8 25.1 - - + -
36C ARG* 3.7 19.7 - - + -
39C LEU* 4.6 14.4 - - + -
81C MET* 4.9 4.7 - - + -
140C LEU* 2.9 22.7 + - + +
141C LEU* 3.8 9.6 - - + +
142C VAL 3.3 0.2 - - - -
143C GLU* 1.3 74.8 - - - +
145C GLU* 1.3 61.4 + - - +
146C GLY 3.3 0.2 - - - -
147C THR* 3.3 14.4 - - - +
272C PHE* 4.1 25.1 - - + -
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Residues in contact with GLU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 3.6 12.8 - - - +
36C ARG* 5.5 14.6 - - - +
141C LEU 2.9 17.0 + - - +
142C VAL* 3.9 10.8 - - - +
143C GLU 3.3 0.4 - - - -
144C LEU* 1.3 79.1 - - - +
146C GLY* 1.3 58.6 + - - +
147C THR 3.6 1.0 + - - -
148C MET* 5.0 1.9 + - - +
149C GLU* 5.2 1.0 + - - +
63L ARG* 4.2 24.4 - - + +
66L ARG* 4.3 20.3 - - - -
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Residues in contact with GLY 146 (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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142C VAL 3.5 10.7 + - - -
143C GLU 3.8 6.1 - - - -
144C LEU 3.3 0.4 - - - -
145C GLU* 1.3 80.6 - - - +
147C THR* 1.3 53.2 + - - +
148C MET 3.7 0.7 - - - -
149C GLU* 3.5 21.2 - - - +
150C ASN* 2.6 37.2 + - - -
60L LYS 5.2 2.1 - - - +
63L ARG* 4.4 10.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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