Contacts of the helix formed by residues 167 - 177 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F PHE* 3.0 39.0 - - + -
160F ALA* 2.9 34.0 + - - +
161F ILE* 3.4 24.0 - - + +
164F GLU* 2.8 36.2 + - - +
165F GLN 2.5 9.3 + - - -
166F SER* 1.3 75.9 - - - +
168F GLU* 1.3 62.4 + - - +
169F VAL 3.5 0.2 - - - -
170F TYR* 3.9 7.6 - - - +
171F TYR 4.3 0.3 + - - -
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Residues in contact with GLU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ASP 4.9 0.7 - - - +
85F LEU* 2.8 27.4 - - + +
88F LYS* 2.7 34.3 + - - +
141F PHE* 5.4 0.2 - - - -
161F ILE* 3.0 32.9 - - + +
162F ASN* 4.9 1.9 - - - +
165F GLN 2.5 15.4 + - - +
167F LYS* 1.3 72.7 - - - +
169F VAL* 1.3 52.1 + - - +
170F TYR 2.5 18.8 + - - -
171F TYR* 2.7 20.3 + - + +
172F GLU* 3.0 20.8 + - - +
251F PRO* 3.3 28.1 - - + +
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Residues in contact with VAL 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ARG* 4.4 20.9 - - - +
165F GLN 3.2 7.9 + - - +
166F SER* 3.1 33.0 - - - +
168F GLU* 1.3 74.9 - - - +
170F TYR* 1.3 65.6 + - + +
172F GLU* 3.8 7.0 - - - -
173F ILE* 2.8 27.3 + - + +
246F SER* 3.6 24.3 - - - +
247F TYR* 4.5 7.0 - - + -
250F ALA* 4.4 8.0 - - + +
251F PRO* 5.8 0.2 - - - +
252F ASP* 5.7 0.4 + - - -
253F HIS* 3.5 34.8 - - + +
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Residues in contact with TYR 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F SER* 2.8 25.3 + - - -
131F ARG* 2.5 58.0 + - + +
140F ARG* 3.1 35.2 - - - +
141F PHE* 4.4 6.7 - + + -
142F VAL* 5.0 4.3 - - + -
166F SER 4.4 14.1 - - - -
167F LYS* 3.9 11.9 + - - +
168F GLU 2.5 5.7 + - - -
169F VAL* 1.3 77.4 - - + +
171F TYR* 1.3 52.6 + - - +
172F GLU 2.5 12.3 + - - -
173F ILE* 2.9 16.1 + - + -
174F GLY* 2.5 36.0 + - - -
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Residues in contact with TYR 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LEU* 3.3 38.4 - - + -
86F LEU* 3.0 25.8 - - - +
88F LYS* 3.9 0.7 - - - -
89F ILE* 3.9 10.5 - - + +
104F ILE* 3.5 14.4 - - - +
106F PHE* 3.6 7.8 - + - -
141F PHE* 5.4 2.2 - - + -
142F VAL* 3.7 22.9 - - + +
152F LEU* 3.6 14.1 - - + +
154F ILE* 3.1 45.5 - - + -
161F ILE* 6.5 0.7 - - + -
167F LYS 4.3 2.1 + - - +
168F GLU* 2.7 17.2 + - + +
170F TYR* 1.3 75.3 - - - +
172F GLU* 1.3 63.2 + - - +
174F GLY 4.3 0.9 - - - -
175F LYS* 2.7 44.4 + - - +
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Residues in contact with GLU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F LYS* 2.4 51.7 + - - +
89F ILE* 4.4 3.8 - - + +
168F GLU* 3.0 18.8 + - - +
169F VAL* 3.7 12.8 - - - +
170F TYR 2.5 5.1 + - - -
171F TYR* 1.3 87.3 - - - +
173F ILE* 1.3 59.9 + - - +
175F LYS* 3.0 25.0 + - - +
176F GLY 3.3 3.8 + - - -
245F PHE* 3.4 18.9 - - + -
246F SER* 4.0 17.5 - - - +
249F PHE* 4.2 19.9 - - + +
250F ALA* 4.5 1.3 - - - +
251F PRO* 3.9 9.2 - - - +
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Residues in contact with ILE 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F SER* 4.6 20.2 - - - +
131F ARG* 4.7 2.0 - - + +
169F VAL* 2.8 20.4 + - + +
170F TYR* 3.4 23.3 - - + +
172F GLU* 1.3 72.6 - - - +
174F GLY* 1.3 65.6 + - - +
175F LYS 2.3 19.8 + - - -
176F GLY* 2.6 17.3 + - - +
177F ILE* 3.6 7.1 + - + +
239F HIS* 5.0 5.4 - - - +
242F SER* 3.3 37.7 - - - +
243F LEU* 3.1 31.4 - - + -
246F SER* 3.8 6.5 - - - -
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Residues in contact with GLY 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F VAL* 4.5 17.1 - - - +
144F GLU* 4.3 10.0 - - - +
152F LEU* 5.1 1.3 - - - +
170F TYR* 2.5 25.3 + - - -
173F ILE* 1.3 77.0 - - - +
175F LYS* 1.3 55.5 + - - +
177F ILE* 3.0 30.7 - - - +
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Residues in contact with LYS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ILE* 3.9 23.0 - - + +
93F VAL* 4.3 13.0 - - + -
94F LEU* 5.3 2.7 - - + -
97F TYR* 4.1 9.2 - - + -
104F ILE* 4.6 4.5 - - - -
144F GLU* 4.9 0.4 - - - +
152F LEU* 3.6 28.2 - - + +
171F TYR* 2.7 41.2 + - - -
172F GLU* 3.0 12.5 + - - +
173F ILE 2.3 13.6 + - - -
174F GLY* 1.3 71.0 - - - +
176F GLY* 1.3 54.0 + - - +
177F ILE* 2.3 21.5 + - - +
178F SER* 2.4 37.7 + - - +
179F LEU* 4.5 1.6 - - + -
245F PHE* 4.2 20.8 - - + -
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Residues in contact with GLY 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F GLU 3.3 5.1 + - - -
173F ILE 2.6 10.9 + - - -
175F LYS* 1.3 76.1 - - - +
177F ILE* 1.3 48.3 + - - -
178F SER* 2.7 4.0 - - - -
179F LEU* 2.6 21.2 + - - +
180F ASP* 2.4 31.9 + - - +
241F PHE* 4.9 3.0 - - - -
242F SER* 4.0 15.7 - - - -
245F PHE* 4.6 13.2 - - - -
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Residues in contact with ILE 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLU* 4.4 23.9 - - + +
173F ILE* 3.6 5.2 + - + +
174F GLY* 3.0 32.1 - - - +
175F LYS 2.3 12.1 + - - +
176F GLY* 1.3 62.6 - - - -
178F SER* 1.3 55.4 + - - -
180F ASP* 2.7 29.3 - - - +
181F ILE* 4.5 7.6 - - - +
238F GLN* 4.6 11.2 - - + +
239F HIS* 5.8 8.3 - - + +
242F 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