Contacts of the helix formed by residues 154 - 163 (chain E) 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 THR 154 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152E GLU* 2.8 16.4 + - - +
153E PRO* 1.3 75.1 - - + +
155E ASN* 1.3 56.0 + - - +
156E PRO* 4.4 5.6 - - - +
157E SER* 2.8 42.3 + - - -
158E LYS* 3.5 3.2 + - - +
144F GLU 4.3 4.5 - - - +
147F GLN* 3.0 13.7 - - - +
148F ALA* 2.6 54.7 - - + +
151F ALA* 6.0 0.4 - - + -
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Residues in contact with ASN 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ILE 4.9 0.4 - - - -
126E VAL 3.9 7.8 + - - +
127E THR* 3.4 38.0 + - - +
129E VAL* 3.3 23.9 + - - +
130E GLU* 5.4 2.9 + - - +
153E PRO 3.3 5.8 + - - +
154E THR* 1.3 69.4 - - - +
156E PRO* 1.4 60.1 - - + +
157E SER 3.4 0.5 + - - -
158E LYS* 3.4 21.7 + - - +
159E MET* 3.7 12.0 + - - +
147F GLN* 3.1 26.3 + - - +
164I SER* 4.8 6.8 + - - +
165I PHE* 5.6 2.4 - - - -
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Residues in contact with PRO 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ILE* 3.3 37.9 - - + +
124E ALA* 4.4 9.9 - - - +
126E VAL 5.9 0.2 - - - +
154E THR* 3.7 8.1 - - - +
155E ASN* 1.4 76.1 - - + +
157E SER* 1.3 56.5 + - - +
159E MET* 3.3 2.1 + - - +
160E ARG* 3.1 31.8 + - - +
143F ASP* 4.9 1.8 - - + +
144F GLU* 3.7 33.0 - - + +
147F GLN* 2.4 36.8 - - + +
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Residues in contact with SER 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ARG* 4.2 14.0 + - - -
151E ALA 5.0 0.9 - - - -
152E GLU* 3.3 30.5 + - - +
154E THR* 2.8 31.7 + - - -
156E PRO* 1.3 72.6 - - - +
158E LYS* 1.3 61.3 + - - +
160E ARG* 3.6 15.4 - - - +
161E LYS* 3.1 25.8 + - - +
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Residues in contact with LYS 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E VAL* 3.8 23.2 - - + +
130E GLU* 5.6 10.5 + - - +
133E LEU* 5.9 1.1 - - + -
149E VAL* 3.3 38.9 - - + +
150E ARG* 4.5 11.3 - - + +
151E ALA 3.7 20.4 - - - +
153E PRO* 4.5 19.5 + - - +
154E THR 3.5 6.2 + - - +
155E ASN* 3.4 21.6 + - - +
156E PRO 3.2 0.6 - - - -
157E SER* 1.3 80.2 - - - +
159E MET* 1.3 57.5 + - - +
161E LYS* 3.6 0.8 + - - +
162E LEU* 3.1 20.6 + - - +
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Residues in contact with MET 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E LEU* 3.3 31.9 - - + +
123E ILE* 3.8 12.8 - - + +
126E VAL* 3.9 19.7 - - + +
129E VAL* 3.7 36.8 - - + -
132E LEU* 5.8 4.0 - - + -
155E ASN 3.7 5.5 + - - +
156E PRO 3.3 8.8 + - - +
157E SER 3.3 0.4 - - - -
158E LYS* 1.3 77.6 - - - +
160E ARG* 1.3 54.4 + - - +
161E LYS 3.2 0.4 - - - -
162E LEU* 3.5 23.6 - - + +
163E PHE* 2.7 63.7 + - + -
177E LEU* 5.5 5.8 - - + -
181E LEU* 5.6 3.1 - - + -
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Residues in contact with ARG 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 3.1 27.5 + - - +
131B TRP* 3.6 27.7 - - - +
134B ASP* 0.7 128.3 + - - +
146B TYR* 3.8 15.1 + - - +
150B ARG* 4.3 19.8 + - - +
119E ARG* 4.6 5.2 + - - +
123E ILE* 3.7 31.1 - - + +
156E PRO* 3.1 18.4 + - - +
157E SER* 3.8 17.8 - - - +
158E LYS 3.4 0.4 - - - -
159E MET* 1.3 76.3 - - - +
161E LYS* 1.3 59.9 + - - +
163E PHE* 3.8 4.0 + - - +
164E SER* 3.2 20.3 + - - -
144F GLU* 4.3 8.7 - - - +
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Residues in contact with LYS 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ARG* 5.1 16.5 - - - +
148E ALA* 3.4 32.9 - - + +
149E VAL* 3.7 17.5 - - + +
152E GLU* 4.1 23.5 + - - +
157E SER 3.1 16.9 + - - +
158E LYS* 4.0 5.4 - - - +
159E MET 3.2 0.2 - - - -
160E ARG* 1.3 77.4 - - - +
162E LEU* 1.3 62.3 + - - +
164E SER* 3.3 18.3 + - - +
165E PHE* 3.2 36.7 - - + -
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Residues in contact with LEU 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ILE* 6.5 0.2 - - + -
129E VAL* 4.7 3.8 - - + -
132E LEU* 5.1 11.0 - - + +
133E LEU* 3.7 27.6 - - + -
136E LEU* 5.8 0.4 - - + -
141E LEU* 4.9 9.0 - - + -
149E VAL* 4.3 8.7 - - + +
158E LYS 3.1 16.5 + - - +
159E MET* 3.0 36.2 + - + +
161E LYS* 1.3 77.5 - - - +
163E PHE* 1.3 72.2 + - + +
164E SER 3.4 0.5 + - - -
165E PHE* 3.4 15.5 + - - +
166E THR* 3.7 7.4 + - - -
169E TRP* 4.3 12.6 - - + -
177E LEU* 3.7 33.0 - - + -
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Residues in contact with PHE 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TYR* 5.5 1.0 + - - -
143B ASP* 5.4 0.2 - - - +
115E ILE* 3.6 35.7 - - + -
116E ASP* 5.4 2.0 - - - -
119E ARG* 3.7 45.7 + - + +
122E LEU* 3.7 31.4 - - + -
123E ILE* 3.8 25.4 - - + -
159E MET* 2.7 52.1 + - + +
160E ARG 4.0 0.7 - - - +
162E LEU* 1.3 76.4 - - + +
164E SER* 1.3 63.4 + - - +
165E PHE 3.2 1.1 - - - -
166E THR* 3.2 26.7 + - - -
167E PRO* 3.4 12.1 - - - +
169E TRP* 6.3 0.7 - + - -
177E LEU* 5.9 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