Contacts of the helix formed by residues 169 - 179 (chain F) in PDB entry 4Q9U
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 169 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160F MET* 4.4 20.6 - - - +
161F GLU 2.4 30.9 + - - +
162F THR* 3.6 19.9 - - + +
163F SER 4.2 3.4 + - - +
168F MET* 1.3 84.8 - - - +
170F VAL* 1.3 61.9 + - - +
171F ASN 3.5 1.8 - - - -
172F GLU* 3.8 15.3 - - + +
173F ILE* 3.2 26.5 + - - +
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Residues in contact with VAL 170 (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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36F LEU* 3.7 12.8 - - + +
39F ARG* 3.6 16.8 - - + +
40F PHE* 3.4 44.4 - - + +
162F THR* 5.4 4.5 - - - -
163F SER 3.6 7.2 - - - +
164F ALA* 3.4 35.2 - - + -
167F SER* 3.5 18.8 - - - -
168F MET 3.2 3.2 - - - -
169F ASN* 1.3 79.1 - - - +
171F ASN* 1.3 63.6 + - - +
173F ILE* 4.0 5.8 - - - +
174F PHE* 3.7 11.1 - - + -
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Residues in contact with ASN 171 (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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39F ARG* 5.6 5.0 + - - -
40F PHE* 3.7 21.2 - - - +
167F SER 5.3 1.0 + - - -
168F MET 5.0 1.9 + - - +
170F VAL* 1.3 79.3 - - - +
172F GLU* 1.3 65.4 + - - +
174F PHE* 3.5 5.2 + - - +
175F MET* 3.0 57.4 + - + +
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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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160F MET* 4.2 15.9 - - + -
168F MET 5.4 1.1 + - - +
169F ASN* 3.3 23.5 + - + +
170F VAL 3.3 1.0 - - - -
171F ASN* 1.3 77.0 - - - +
173F ILE* 1.3 71.3 + - - +
175F MET* 2.9 9.5 + - - +
176F ALA* 2.8 32.0 + - + +
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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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36F LEU* 6.4 2.5 - - + -
97F ILE* 5.6 4.9 - - + -
129F ALA* 4.1 21.1 - - + +
130F LEU 4.2 15.0 - - - +
131F SER* 4.9 9.2 - - - -
158F LEU* 4.9 1.1 - - + +
160F MET* 3.6 40.4 - - + -
162F THR* 4.9 7.4 - - + -
169F ASN 3.2 12.6 + - - +
170F VAL* 4.0 9.0 - - - +
172F GLU* 1.3 79.3 - - - +
174F PHE* 1.3 70.5 + - + +
176F ALA* 3.5 4.1 + - - +
177F ILE* 2.9 49.7 + - + +
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Residues in contact with PHE 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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23F LEU* 3.5 21.8 - - + -
25F LEU* 4.9 5.6 - - + -
36F LEU* 5.0 9.4 - - + -
37F VAL* 3.7 28.9 - - + -
40F PHE* 3.3 57.9 - + + -
71F PHE* 3.4 32.4 - + + -
73F ILE* 3.5 22.2 - - + -
97F ILE* 6.2 1.8 - - + -
170F VAL* 3.7 8.5 - - + -
171F ASN 3.5 1.7 + - - +
172F GLU 3.1 0.4 - - - -
173F ILE* 1.3 87.3 - - + +
175F MET* 1.3 57.2 + - - +
176F ALA 3.0 4.7 - - - -
177F ILE* 3.1 7.3 + - + +
178F ALA 2.9 26.0 + - - -
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Residues in contact with MET 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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40F PHE* 4.8 8.1 - - + -
71F PHE* 5.1 3.4 - - + -
171F ASN* 3.0 55.3 + - - +
172F GLU* 2.9 10.9 + - - +
174F PHE* 1.3 77.3 - - + +
176F ALA* 1.3 57.5 + - - +
178F ALA* 4.1 7.9 - - - +
179F LYS* 4.0 17.3 + - - +
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Residues in contact with ALA 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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158F LEU* 3.6 26.1 - - + +
160F MET* 5.5 0.4 - - + -
172F GLU* 2.8 29.3 + - + +
173F ILE* 3.9 2.0 - - - +
175F MET* 1.3 76.9 - - - +
177F ILE* 1.3 63.9 + - - +
178F ALA 3.3 1.3 - - - -
179F LYS* 3.7 11.1 - - + +
180F LYS* 3.7 26.2 + - - +
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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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21F PHE* 4.6 9.6 - - + -
23F LEU* 4.7 12.1 - - + -
71F PHE* 5.0 2.0 - - + -
95F ALA* 4.5 12.3 - - + -
96F ALA 4.9 1.3 - - - +
97F ILE* 3.7 22.2 - - + -
127F VAL* 5.4 4.7 - - + +
128F ILE 5.9 0.2 - - - -
129F ALA* 3.6 32.3 - - + -
158F LEU* 4.6 5.2 - - + -
173F ILE* 2.9 34.3 + - + +
174F PHE* 3.1 9.2 + - + +
176F ALA* 1.3 77.8 - - - +
178F ALA* 1.3 62.9 + - - +
180F LYS* 3.6 15.3 + - + +
181F LEU* 3.2 28.6 - - + +
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Residues in contact with ALA 178 (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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21F PHE* 5.7 4.3 - - + -
71F PHE* 3.9 19.5 - - + -
174F PHE 2.9 15.5 + - - +
175F MET* 4.4 7.6 - - - +
176F ALA 3.3 0.2 - - - -
177F ILE* 1.3 76.3 - - - +
179F LYS* 1.3 60.1 + - - +
180F LYS 3.1 5.5 + - - -
181F LEU* 3.5 19.7 + - - +
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Residues in contact with LYS 179 (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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175F MET 4.0 13.1 + - - +
176F ALA* 3.7 15.3 - - - +
178F ALA* 1.3 78.2 - - - +
180F LYS* 1.3 67.4 + - + +
181F LEU 4.6 2.9 - - - +
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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