Contacts of the helix formed by residues 125 - 139 (chain C) in PDB entry 6N0M
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 CYS 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C ALA* 3.4 22.9 + - + +
123C HIS 3.7 2.9 - - - +
124C GLN* 1.3 71.0 - - - +
126C SER* 1.3 68.0 + - - +
127C TYR 3.0 4.5 + - - -
128C LEU* 3.1 34.3 + - - -
129C VAL* 3.0 20.8 + - - +
208C SER* 3.7 15.9 - - - +
211C VAL* 4.2 15.5 - - - -
212C PHE* 3.8 24.2 - - + -
312C MET* 3.8 6.1 - - - -
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Residues in contact with SER 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C GLN 3.3 6.0 + - - -
125C CYS* 1.3 70.6 - - - +
127C TYR* 1.3 64.9 + - - +
129C VAL* 4.6 0.9 - - - -
130C GLY* 2.9 24.8 + - - -
212C PHE* 5.0 1.6 - - - -
218C PRO* 5.7 9.9 - - - -
312C MET* 3.8 23.2 - - - +
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Residues in contact with TYR 127 (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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77C ASP* 3.2 17.5 - - - +
78C ASN* 3.2 1.4 + - + -
79C LEU* 2.9 41.5 + - + -
125C CYS* 3.0 1.9 + - - -
126C SER* 1.3 79.1 - - - +
128C LEU* 1.3 66.4 + - + +
131C SER* 2.9 33.3 + - - -
211C VAL* 3.9 34.5 - - + -
216C ILE* 3.4 22.2 - - + +
217C LEU* 3.3 25.6 - - - -
218C PRO* 3.6 21.7 - - + +
219C GLU* 2.8 27.2 + - - -
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Residues in contact with LEU 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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79C LEU* 5.0 3.1 - - + -
97C HIS* 5.9 2.5 - - + -
120C ALA* 3.6 15.7 - - + -
125C CYS* 3.1 14.7 + - - -
127C TYR* 1.3 91.6 - - + +
129C VAL* 1.3 62.2 + - - +
131C SER* 4.0 5.6 - - - +
132C HIS* 2.9 59.6 + - + +
204C CYS* 3.7 11.0 - - + +
207C LEU* 3.7 28.0 - - + +
208C SER* 3.5 40.2 - - - +
211C VAL* 4.1 3.1 - - + -
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 3.7 25.0 - - + +
120C ALA* 3.7 20.2 - - + -
121C ALA* 3.7 14.6 - - - +
125C CYS 3.0 20.4 + - - +
126C SER* 4.0 1.8 - - - +
128C LEU* 1.3 76.7 - - - +
130C GLY* 1.3 53.4 + - - +
132C HIS* 3.1 1.7 + - - -
133C MET* 2.5 59.0 + - - +
312C MET* 3.8 35.0 - - + -
315C PHE* 4.8 3.4 - - + -
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Residues in contact with GLY 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C SER 2.9 14.3 + - - -
129C VAL* 1.3 74.1 - - - +
131C SER* 1.3 66.4 + - - +
133C MET* 3.5 12.1 - - - +
134C ALA* 2.8 26.8 + - - +
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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
----------------------------------------------------------
77C ASP* 5.1 5.2 + - - -
127C TYR* 2.9 32.4 + - - -
128C LEU* 3.6 10.6 + - - +
130C GLY* 1.3 75.1 - - - +
132C HIS* 1.3 65.1 + - - -
134C ALA* 3.1 6.4 + - - +
135C GLU* 3.1 40.3 + - - +
219C GLU* 6.1 0.7 - - - -
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Residues in contact with HIS 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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97C HIS* 5.0 5.3 - + - -
101C LEU* 3.7 33.2 - - + +
113C HIS* 3.2 32.3 + - - +
116C ALA* 3.3 29.0 - - + +
117C ILE* 3.8 8.7 - - + -
128C LEU* 2.9 50.7 + - + +
131C SER* 1.3 72.0 - - - +
133C MET* 1.3 58.1 + - - +
134C ALA 3.0 1.6 - - - -
135C GLU* 3.7 19.2 + - - -
136C PHE* 2.6 36.7 + - - +
204C CYS* 4.1 6.8 - - - -
207C LEU* 6.0 0.2 - - - +
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Residues in contact with MET 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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117C ILE* 3.7 16.2 - - + +
129C VAL* 2.5 49.7 + - + +
130C GLY* 3.5 9.6 - - - +
132C HIS* 1.3 71.7 - - - +
134C ALA* 1.3 65.6 + - - +
136C PHE* 3.2 5.5 - - - +
137C LEU* 3.2 24.1 + - + +
146C LEU* 3.8 46.9 - - + +
311C ASP* 4.2 19.3 - - - +
315C PHE* 4.3 13.7 - - + -
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Residues in contact with ALA 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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130C GLY 2.8 12.4 + - - +
131C SER* 3.2 11.9 - - - +
133C MET* 1.3 76.6 - - - +
135C GLU* 1.3 58.6 + - + +
137C LEU* 2.9 27.9 + - - +
138C GLN* 3.0 32.4 + - - +
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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
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97C HIS* 5.2 4.7 + - - -
102C HIS* 3.5 24.1 + - - -
113C HIS* 3.6 29.0 - - + +
131C SER* 3.1 26.8 + - - +
132C HIS* 3.1 19.8 + - - +
134C ALA* 1.3 73.4 - - + +
136C PHE* 1.3 61.3 + - - +
138C GLN* 3.8 12.7 - - + +
139C THR* 2.9 28.8 + - - -
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Residues in contact with PHE 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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110C SER* 3.3 24.5 - - - -
113C HIS* 3.9 12.8 - - + +
114C TYR* 4.1 11.0 - + + -
117C ILE* 4.4 3.8 - - + -
132C HIS 2.6 22.7 + - - +
133C MET* 3.2 7.6 - - - +
135C GLU* 1.3 71.7 - - - +
137C LEU* 1.3 63.6 + - + +
139C THR* 3.2 11.1 - - - +
141C GLY* 2.8 42.1 + - - -
142C ASP 3.3 39.3 - - - -
143C PRO* 4.3 1.1 - - + -
145C TRP* 3.4 32.3 - + + -
146C LEU* 3.3 35.4 - - + -
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Residues in contact with LEU 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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133C MET* 3.5 12.6 - - + +
134C ALA* 2.9 10.5 + - - +
136C PHE* 1.3 81.6 - - + +
138C GLN* 1.3 65.9 + - - +
139C THR 3.1 2.0 - - - -
140C GLY* 3.2 13.9 + - - -
141C GLY 4.1 5.3 + - - +
143C PRO* 3.8 42.6 - - + -
146C LEU* 3.9 23.6 - - + -
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Residues in contact with GLN 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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134C ALA* 3.0 36.7 + - - +
135C GLU* 3.4 14.1 + - + +
137C LEU* 1.3 77.2 - - - +
139C THR* 1.3 59.6 - - - +
140C GLY 3.3 1.0 + - - -
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Residues in contact with THR 139 (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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109C SER* 3.5 23.5 + - - -
110C SER* 3.5 34.5 + - - +
113C HIS* 4.0 5.6 - - + -
135C GLU 2.9 15.3 + - - +
136C PHE* 3.2 19.7 - - - +
137C LEU 3.1 0.8 - - - -
138C GLN* 1.3 77.8 - - - +
140C GLY* 1.3 55.4 + - - +
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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