Contacts of the helix formed by residues 167 - 177 (chain E) in PDB entry 1XFV
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 LYS 167 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E PHE* 3.1 39.9 - - + -
160E ALA* 3.1 30.9 + - - +
161E ILE* 3.5 23.8 - - + +
164E GLU* 2.8 37.3 + - - +
165E GLN 2.5 9.7 + - - -
166E SER* 1.3 75.6 - - - +
168E GLU* 1.3 60.7 + - - +
169E VAL 3.5 0.2 - - - -
170E TYR* 3.9 8.2 - - - +
171E TYR 4.3 0.2 + - - -
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Residues in contact with GLU 168 (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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84E ASP 4.9 0.3 - - - +
85E LEU* 2.9 26.9 - - + +
88E LYS* 2.7 34.9 + - - +
141E PHE* 5.5 0.2 - - - -
161E ILE* 3.0 33.8 - - + +
162E ASN* 4.9 1.7 - - - +
165E GLN 2.5 14.8 + - - +
167E LYS* 1.3 72.0 - - - +
169E VAL* 1.3 52.6 + - - +
170E TYR 2.5 18.8 + - - -
171E TYR* 2.7 19.9 + - + +
172E GLU* 3.0 20.3 + - - +
251E PRO* 3.3 26.7 - - + +
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Residues in contact with VAL 169 (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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131E ARG* 4.4 22.0 - - - +
165E GLN 3.2 7.0 + - - +
166E SER* 3.2 31.9 - - - +
168E GLU* 1.3 74.6 - - - +
170E TYR* 1.3 64.6 + - + +
172E GLU* 3.8 7.6 - - - -
173E ILE* 2.8 27.4 + - + +
246E SER* 3.6 25.1 - - - +
247E TYR* 4.5 6.3 - - + -
250E ALA* 4.4 8.2 - - + +
251E PRO* 5.8 0.4 - - - +
252E ASP* 5.7 0.4 + - - -
253E HIS* 3.5 34.5 - - + +
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Residues in contact with TYR 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E SER* 2.9 23.6 + - - -
131E ARG* 2.5 56.4 + - + +
140E ARG* 3.1 35.0 - - - +
141E PHE* 4.5 6.3 - + + -
142E VAL* 5.0 4.3 - - + -
166E SER 4.4 14.1 - - - -
167E LYS* 3.9 11.9 + - - +
168E GLU 2.5 5.9 + - - -
169E VAL* 1.3 77.5 - - + +
171E TYR* 1.3 53.7 + - - +
172E GLU 2.5 11.5 + - - -
173E ILE* 2.9 16.6 + - + -
174E GLY* 2.4 36.2 + - - -
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Residues in contact with TYR 171 (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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85E LEU* 3.4 38.8 - - + -
86E LEU* 3.0 25.8 - - - +
88E LYS* 3.8 2.9 - - - -
89E ILE* 3.9 8.2 - - + +
104E ILE* 3.5 14.0 - - - +
106E PHE* 3.6 8.6 - + - -
141E PHE* 5.2 2.7 - - + -
142E VAL* 3.7 21.1 - - + +
152E LEU* 3.6 14.0 - - + +
154E ILE* 3.1 46.7 - - + -
161E ILE* 6.5 0.2 - - + -
167E LYS 4.3 2.5 + - - +
168E GLU* 2.7 17.2 + - + +
170E TYR* 1.3 74.7 - - - +
172E GLU* 1.3 63.4 + - - +
174E GLY 4.3 0.8 - - - -
175E LYS* 2.7 44.9 + - - +
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Residues in contact with GLU 172 (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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88E LYS* 2.4 51.8 + - - +
89E ILE* 4.4 4.7 - - + +
168E GLU* 3.0 20.1 + - - +
169E VAL* 3.7 12.1 - - - +
170E TYR 2.5 5.3 + - - -
171E TYR* 1.3 88.0 - - - +
173E ILE* 1.3 60.0 + - - +
175E LYS* 3.0 24.9 + - - +
176E GLY 3.3 3.5 + - - -
245E PHE* 3.4 20.1 - - + -
246E SER* 4.0 17.9 - - - +
249E PHE* 4.2 19.7 - - + +
250E ALA* 4.4 2.0 - - - +
251E PRO* 3.9 8.3 - - - +
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Residues in contact with ILE 173 (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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130E SER* 4.6 19.7 - - - +
131E ARG* 4.7 2.0 - - + +
169E VAL* 2.8 21.0 + - + +
170E TYR* 3.4 22.7 - - + +
172E GLU* 1.3 71.8 - - - +
174E GLY* 1.3 63.2 + - - +
175E LYS 2.3 19.4 + - - +
176E GLY* 2.6 17.1 + - - +
177E ILE* 3.6 8.0 + - + +
239E HIS* 5.0 5.2 - - - +
242E SER* 3.3 37.9 - - - +
243E LEU* 3.1 31.2 - - + -
246E SER* 3.8 6.2 - - - -
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Residues in contact with GLY 174 (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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142E VAL* 4.6 16.7 - - - +
144E GLU* 4.3 10.7 + - - +
152E LEU* 5.1 1.7 - - - +
170E TYR* 2.4 25.1 + - - -
171E TYR 4.8 0.2 - - - -
173E ILE* 1.3 76.1 - - - +
175E LYS* 1.3 54.7 + - - +
177E ILE* 3.0 30.0 - - - +
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Residues in contact with LYS 175 (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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89E ILE* 3.9 23.3 - - + +
93E VAL* 4.2 17.3 - - + -
94E LEU* 5.3 2.0 - - + -
97E TYR* 4.1 10.8 - - + -
104E ILE* 4.6 4.0 - - - -
144E GLU* 4.9 0.8 - - - +
152E LEU* 3.6 27.6 - - + +
171E TYR* 2.7 40.4 + - - -
172E GLU* 3.0 12.6 + - - +
173E ILE 2.3 13.4 + - - -
174E GLY* 1.3 70.4 - - - +
176E GLY* 1.3 55.6 + - - +
177E ILE* 2.3 21.0 + - - +
178E SER* 2.4 36.4 + - - +
179E LEU* 4.6 1.6 - - + -
245E PHE* 4.2 16.4 - - + -
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Residues in contact with GLY 176 (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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172E GLU 3.3 5.5 + - - -
173E ILE 2.6 11.7 + - - -
175E LYS* 1.3 76.5 - - - +
177E ILE* 1.3 48.5 + - - -
178E SER* 2.7 4.0 - - - -
179E LEU* 2.5 20.6 + - - +
180E ASP* 2.5 31.6 + - - +
241E PHE* 4.9 3.5 - - - -
242E SER* 4.0 15.0 - - - -
245E PHE* 4.6 13.2 - - - -
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Residues in contact with ILE 177 (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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144E GLU* 4.4 24.2 - - + +
173E ILE* 3.6 6.3 + - + +
174E GLY* 3.0 31.0 - - - +
175E LYS 2.3 11.0 + - - +
176E GLY* 1.3 64.1 - - - -
178E SER* 1.3 52.8 + - - -
180E ASP* 2.8 30.3 - - - +
181E ILE* 4.5 8.0 - - - +
238E GLN* 4.6 11.4 - - + +
239E HIS* 5.8 8.3 - - + +
242E SER* 3.8 14.3 + - - +
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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