Contacts of the helix formed by residues 128 - 137 (chain C) in PDB entry 6N1H
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 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C VAL* 3.6 3.5 - - + +
127C THR* 1.3 78.3 - - - +
129C VAL* 1.3 63.9 + - - +
130C GLU* 3.3 15.9 - - - +
131C TRP* 3.3 22.1 + - - +
132C LEU* 3.2 23.6 + - + +
184C SER* 2.5 25.1 + - - +
185C GLN* 3.3 18.3 + - - +
142G THR* 3.8 22.4 + - - +
144G GLU* 5.0 2.8 + - - +
145G GLN* 3.5 23.0 + - - +
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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
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126C VAL* 3.7 14.4 - - + +
127C THR 3.7 0.6 - - - -
128C ASN* 1.3 76.8 - - - +
130C GLU* 1.3 62.5 + - - +
132C LEU* 3.0 7.4 + - + +
133C LEU* 2.9 46.2 + - + +
149C VAL* 4.5 1.3 - - + -
155C ASN* 3.3 25.6 - - - +
158C LYS* 3.8 30.1 - - + +
159C MET* 3.7 36.1 - - + -
162C LEU* 4.7 3.4 - - + -
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Residues in contact with GLU 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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127C THR 4.5 3.0 - - - +
128C ASN* 3.8 18.5 - - - +
129C VAL* 1.3 82.1 + - - +
131C TRP* 1.3 56.5 + - + +
133C LEU* 4.0 12.4 + - + +
134C ASP* 3.0 6.8 + - - +
150C ARG* 5.8 4.3 - - + +
155C ASN* 5.4 3.1 + - - +
158C LYS* 5.6 9.3 + - - +
160F ARG* 2.4 54.2 + - - +
144G GLU* 4.7 17.5 - - + +
145G GLN* 5.1 1.2 - - - +
148G ALA* 5.7 1.9 - - - +
165G PHE* 4.7 13.7 - - - -
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Residues in contact with TRP 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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128C ASN* 3.3 24.1 + - - +
129C VAL 3.2 0.4 - - - -
130C GLU* 1.3 82.1 - - + +
132C LEU* 1.3 66.7 + - + +
133C LEU 3.2 0.2 - - - -
134C ASP* 3.2 17.2 + - + +
135C ALA* 3.3 19.5 + - + +
180C ALA* 3.3 30.7 - - + -
183C GLU* 3.4 34.1 - - + -
184C SER* 3.5 24.5 - - - -
120F ALA* 5.2 8.9 + - + +
123F ILE* 6.3 0.2 - - + -
124F ALA* 4.9 7.7 - - + +
160F ARG* 3.6 10.8 - - - +
144G GLU* 3.8 33.6 + - + +
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Residues in contact with LEU 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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126C VAL* 5.0 5.6 - - + -
128C ASN* 3.2 24.3 + - + +
129C VAL* 3.0 14.7 + - - +
131C TRP* 1.3 80.9 - - + +
133C LEU* 1.3 61.6 + - - +
135C ALA* 3.5 2.6 + - - +
136C LEU* 3.2 30.0 + - + +
159C MET* 5.8 3.6 - - + -
162C LEU* 5.1 11.0 - - + -
177C LEU* 4.2 18.2 - - + -
180C ALA* 3.7 27.1 - - + +
181C LEU* 3.8 32.3 - - + -
184C SER* 3.7 28.9 - - - +
185C GLN* 5.5 0.4 - - - +
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Residues in contact with LEU 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 VAL* 2.9 24.9 + - + +
130C GLU* 4.2 11.2 - - - +
131C TRP 3.2 0.2 - - - -
132C LEU* 1.3 77.6 - - - +
134C ASP* 1.3 59.3 + - - +
136C LEU* 3.7 1.0 - - - +
137C TYR* 3.0 29.8 + - - +
141C LEU* 3.7 25.3 - - + +
146C TYR* 3.5 22.2 - - + +
149C VAL* 3.7 38.6 - - + -
150C ARG* 3.7 28.3 - - + -
158C LYS* 5.9 1.8 - - + -
162C LEU* 3.7 17.3 - - + -
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Residues in contact with ASP 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 GLU 3.4 1.3 - - - -
131C TRP* 3.2 12.1 + - + +
132C LEU 3.2 0.8 - - - -
133C LEU* 1.3 76.5 - - - +
135C ALA* 1.3 63.1 + - - +
137C TYR* 3.5 17.6 + - - +
146C TYR* 2.9 19.8 + - - -
119F ARG* 3.9 4.7 + - - +
120F ALA* 3.8 31.0 + - + +
123F ILE* 3.4 22.0 - - + +
160F ARG* 1.8 51.8 + - - -
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Residues in contact with ALA 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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131C TRP* 3.3 24.5 + - + +
132C LEU 3.9 4.3 - - - +
133C LEU 3.3 0.2 - - - -
134C ASP* 1.3 80.5 - - - +
136C LEU* 1.3 60.6 + - - +
137C TYR 3.6 2.3 + - - +
139C LYS* 4.0 22.0 + - - +
176C LEU* 4.4 4.2 - - + +
180C ALA* 3.9 28.0 - - + -
183C GLU* 5.6 1.6 - - - +
120F ALA* 4.8 5.6 - - - +
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Residues in contact with LEU 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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132C LEU* 3.2 28.6 + - + +
133C LEU* 3.7 0.7 - - - -
134C ASP 3.3 0.2 - - - -
135C ALA* 1.3 76.7 - - - +
137C TYR* 1.3 58.9 + - - +
139C LYS* 4.3 0.9 - - - -
140C VAL* 3.0 34.8 + - + +
141C LEU* 2.9 45.6 + - + -
162C LEU* 5.8 0.9 - - + -
169C TRP* 4.8 3.4 - - + -
173C CYS 4.6 2.5 - - - +
176C LEU* 3.8 23.3 - - + +
177C LEU* 3.8 46.7 - - + +
180C ALA* 3.9 20.4 - - + -
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Residues in contact with TYR 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 LEU 3.0 16.9 + - - +
134C ASP* 3.7 15.4 - - - +
135C ALA 3.3 6.4 - - - +
136C LEU* 1.3 78.1 - - - +
138C GLY* 1.3 63.5 + - - +
139C LYS* 3.1 8.7 + - - +
141C LEU* 3.6 16.4 - - - -
143C ASP* 3.7 43.3 + - + +
146C TYR* 3.7 26.0 - + + -
116F ASP 5.6 3.6 - - - -
119F ARG* 3.2 47.2 + - + -
167F PRO* 5.0 4.0 - - - +
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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