Contacts of the helix formed by residues 170 - 181 (chain F) in PDB entry 4KYI
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 170 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161F MET* 4.3 19.2 - - - +
162F GLU* 3.4 27.3 + - - +
163F THR* 3.7 5.2 - - + +
168F ALA 3.3 3.2 + - - -
169F MET* 1.3 82.6 - - - +
171F VAL* 1.3 57.1 + - - +
172F ASN 3.5 2.2 - - - -
173F GLU* 3.3 29.3 + - - +
174F ILE* 2.9 30.3 + - - +
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Residues in contact with VAL 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 3.7 35.9 - - + +
40F ARG* 3.6 23.8 - - + -
41F PHE* 4.5 6.7 - - + +
163F THR* 4.3 2.5 - - - -
164F SER 3.2 35.7 - - - +
165F ALA* 4.2 1.6 - - - +
168F ALA* 3.4 16.7 + - + +
169F MET 2.9 9.8 + - - +
170F ASN* 1.3 75.2 - - - +
172F ASN* 1.3 65.1 + - + +
174F ILE* 3.2 20.0 - - - +
175F PHE* 3.2 13.6 - - + -
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Residues in contact with ASN 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 3.4 31.3 - - + -
63F VAL* 4.7 2.5 - - - +
168F ALA* 4.5 2.3 + - - +
171F VAL* 1.3 79.1 - - - +
173F GLU* 1.3 73.3 + - - +
175F PHE* 3.5 3.1 + - - +
176F MET* 3.2 32.4 + - - +
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Residues in contact with GLU 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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161F MET* 4.2 8.3 - - + +
168F ALA 4.4 3.3 - - - +
170F ASN* 3.3 41.6 + - + +
171F VAL 3.3 0.4 + - - -
172F ASN* 1.3 87.1 + - - +
174F ILE* 1.3 56.9 + - - +
176F MET* 3.5 7.4 + - - +
177F ALA* 2.9 30.1 + - - +
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Residues in contact with ILE 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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37F LEU* 6.0 3.8 - - + -
98F ILE* 4.7 13.0 - - + -
130F ALA* 4.5 17.9 - - + -
131F LEU 3.9 23.6 - - - +
132F ALA* 4.1 10.8 - - + -
159F LEU* 4.8 3.8 - - + -
161F MET* 3.6 25.1 - - + +
163F THR* 4.1 21.5 - - + -
170F ASN 2.9 17.2 + - - +
171F VAL* 3.2 20.6 - - - +
173F GLU* 1.3 74.3 - - - +
175F PHE* 1.3 71.8 + - + +
177F ALA* 3.7 3.1 + - - +
178F ILE* 3.2 25.2 + - - +
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Residues in contact with PHE 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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24F LEU* 3.7 22.4 - - + -
26F LEU* 5.2 3.4 - - + -
37F LEU* 4.6 10.8 - - + -
38F VAL* 5.0 13.0 - - + -
41F PHE* 3.4 63.7 - + + -
72F PHE* 3.9 20.7 - + + -
74F ILE* 4.5 8.1 - - + -
98F ILE* 3.6 29.6 - - + -
171F VAL* 3.2 24.9 - - + -
172F ASN 3.5 6.4 + - - +
173F GLU 3.3 0.6 - - - -
174F ILE* 1.3 82.8 - - + +
176F MET* 1.3 64.8 + - - +
178F ILE* 3.1 16.3 + - - +
179F ALA* 3.1 12.1 + - - +
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Residues in contact with MET 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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63F VAL* 3.6 41.5 - - + -
64F CYS 3.5 24.7 - - - +
65F LEU* 3.7 23.7 - - + +
172F ASN* 3.2 29.5 + - - +
173F GLU* 3.9 6.5 - - - +
175F PHE* 1.3 77.9 - - - +
177F ALA* 1.3 61.8 + - - +
179F ALA* 3.1 15.1 + - + +
180F LYS* 3.2 31.8 + - - +
67H ASP* 5.7 2.0 - - + +
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Residues in contact with ALA 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU* 3.4 39.2 - - + +
161F MET* 3.7 15.7 - - + -
173F GLU 2.9 19.5 + - - +
174F ILE 3.7 4.0 - - - +
175F PHE 3.2 0.2 - - - -
176F MET* 1.3 77.5 - - - +
178F ILE* 1.3 61.2 + - - +
180F LYS* 3.9 13.1 + - - +
181F LYS* 3.7 11.8 + - - +
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Residues in contact with ILE 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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24F LEU* 3.8 13.0 - - + -
72F PHE* 4.8 2.7 - - + -
96F ALA* 3.6 26.9 - - + -
97F ALA 4.6 2.9 - - - +
98F ILE* 3.7 35.0 - - + -
128F VAL* 4.0 16.4 - - + +
130F ALA* 3.9 20.2 - - + -
159F LEU* 4.5 4.7 - - + -
174F ILE 3.2 17.9 - - - +
175F PHE* 3.1 9.1 + - - +
177F ALA* 1.3 77.4 - - - +
179F ALA* 1.3 60.3 + - - +
180F LYS 3.2 0.2 - - - -
181F LYS* 2.9 22.6 + - - +
182F LEU* 3.3 18.0 + - + +
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Residues in contact with ALA 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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22F PHE* 5.5 0.2 - - - -
65F LEU* 3.7 22.8 - - + +
70F VAL* 4.2 25.8 - - + +
72F PHE* 4.3 8.5 - - + -
175F PHE 3.1 11.7 + - - +
176F MET* 3.1 16.6 + - + +
178F ILE* 1.3 77.4 - - - +
180F LYS* 1.3 59.9 + - - +
182F LEU* 3.4 27.6 + - + +
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Residues in contact with LYS 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 3.4 36.7 - - + +
176F MET* 3.2 29.3 + - - +
177F ALA* 4.1 11.6 - - - +
178F ILE 3.2 0.2 - - - -
179F ALA* 1.3 71.7 - - - +
181F LYS* 1.3 59.2 + - + +
182F LEU 3.1 12.0 + - - -
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Residues in contact with LYS 181 (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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128F VAL* 3.5 32.3 - - + +
159F LEU* 3.7 24.9 - - + -
177F ALA 3.7 4.7 + - - +
178F ILE 2.9 11.4 + - - +
180F LYS* 1.3 78.1 - - + +
182F LEU* 1.3 58.6 + - - +
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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