Contacts of the helix formed by residues 158 - 168 (chain F) in PDB entry 1KD1
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 158 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F ASP 4.4 1.9 + - - -
102F GLY* 4.1 1.3 - - - -
136F ARG* 5.1 0.7 + - - -
153F THR 5.1 4.5 - - - +
154F LYS 5.3 1.6 - - - +
156F ARG* 3.9 9.8 - - - +
157F LEU* 1.3 78.8 - - - +
159F PRO* 1.3 79.1 - - + +
160F ALA* 4.2 7.0 - - + +
161F ASP* 3.2 27.2 + - - +
162F ALA* 3.1 23.4 + - - +
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Residues in contact with PRO 159 (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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98F PHE* 4.5 13.2 - - + +
99F ASP 3.1 28.3 - - - +
100F ASP* 3.9 16.6 - - - +
102F GLY* 4.1 6.5 - - - -
158F ASN* 1.3 92.0 - - + +
160F ALA* 1.3 61.4 + - + +
162F ALA* 3.2 5.0 - - - +
163F VAL* 3.0 28.9 + - + +
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Residues in contact with ALA 160 (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 ASN* 3.1 6.0 - - + -
159F PRO* 1.3 76.8 - - + +
161F ASP* 1.3 58.0 + - - +
162F ALA 2.8 15.1 + - - -
163F VAL* 2.9 20.0 + - - +
164F ALA* 3.1 12.0 + - - +
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Residues in contact with ASP 161 (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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14F ARG* 5.7 3.0 + - - -
16F PRO* 3.8 16.2 - - + +
136F ARG* 4.1 13.6 + - - +
157F LEU* 3.7 19.7 - - + -
158F ASN* 3.2 33.6 + - - +
160F ALA* 1.3 77.0 - - - +
162F ALA* 1.3 59.9 + - - +
164F ALA* 4.1 8.6 - - - +
165F PHE* 3.8 10.4 + - - +
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Residues in contact with ALA 162 (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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98F PHE* 4.6 5.8 - - + -
102F GLY* 3.5 32.1 - - - +
134F LEU* 4.1 9.0 - - + -
157F LEU* 4.2 9.0 - - + -
158F ASN 3.1 12.0 + - - +
159F PRO* 3.2 10.3 - - + +
160F ALA 2.8 1.6 + - - -
161F ASP* 1.3 77.0 - - - +
163F VAL* 1.3 65.4 + - - +
164F ALA 3.1 1.8 - - - -
165F PHE* 3.1 16.0 + - - +
166F ILE* 3.1 18.2 + - - +
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Residues in contact with VAL 163 (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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94F ALA* 6.1 0.9 - - + -
95F THR* 5.3 12.6 - - + +
98F PHE* 4.4 32.7 - - + -
159F PRO 3.0 19.3 + - - +
160F ALA* 2.9 10.4 + - - +
162F ALA* 1.3 75.1 - - - +
164F ALA* 1.3 55.0 + - - +
166F ILE* 4.2 1.7 - - - +
167F GLU* 2.8 46.8 + - + +
173F GLU* 3.6 36.6 - - + +
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Residues in contact with ALA 164 (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 ALA 3.1 11.2 + - - +
161F ASP* 4.1 9.6 - - - +
162F ALA 3.1 0.2 - - - -
163F VAL* 1.3 80.5 - - - +
165F PHE* 1.3 54.8 + - - +
167F GLU* 3.7 7.9 - - - +
168F SER* 2.8 39.5 + - - -
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Residues in contact with PHE 165 (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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15F GLU* 6.2 1.1 - - + -
16F PRO* 3.6 43.3 - - + -
17F ARG* 4.0 20.4 - - - -
18F ILE* 4.3 25.6 - - + -
134F LEU* 4.5 6.5 - - + -
161F ASP 3.8 7.6 + - - +
162F ALA* 3.1 8.6 + - - +
164F ALA* 1.3 81.0 - - - +
166F ILE* 1.3 74.8 + - + +
168F SER* 3.4 10.5 + - - -
169F THR* 2.9 28.7 + - + -
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Residues in contact with ILE 166 (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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18F ILE* 6.0 2.5 - - + -
88F LEU* 4.4 17.9 - - + -
98F PHE* 4.4 10.3 - - + -
104F PHE* 3.1 41.3 - - + -
132F VAL* 5.0 0.9 - - + -
134F LEU* 3.2 22.2 - - + -
162F ALA 3.1 12.4 + - - +
163F VAL* 4.2 2.7 - - - +
165F PHE* 1.3 88.8 - - + +
167F GLU* 1.3 59.1 + - - +
168F SER 2.8 1.6 - - - -
169F THR* 2.5 40.8 + - - -
171F ASP* 3.7 14.9 - - - +
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Residues in contact with GLU 167 (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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163F VAL* 2.8 31.3 + - + +
164F ALA* 3.8 7.2 - - - +
166F ILE* 1.3 73.7 - - - +
168F SER* 1.3 56.5 + - - +
169F THR 2.9 5.7 + - - -
170F TYR 4.1 0.3 + - - -
171F ASP* 3.2 44.2 + - - +
172F VAL* 3.9 5.3 - - + +
173F GLU* 2.8 59.3 + - - +
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Residues in contact with SER 168 (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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164F ALA 2.8 20.5 + - - -
165F PHE* 3.4 7.6 - - - -
166F ILE 2.8 0.2 + - - -
167F GLU* 1.3 74.0 - - - +
169F THR* 1.3 65.0 + - - +
170F TYR 4.1 0.9 - - - -
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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