Contacts of the helix formed by residues 164 - 172 (chain E) in PDB entry 1C9T
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 SER 164 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E ALA* 3.8 16.9 - - - +
163E LEU* 1.3 73.7 - - - +
165E ASP* 1.3 56.6 + - - +
166E SER* 2.7 29.7 + - - -
167E SER* 2.8 36.9 + - - -
168E CYS* 2.9 10.3 + - - +
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Residues in contact with ASP 165 (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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132E ALA* 5.1 1.6 - - - +
163E LEU 3.6 3.6 + - - -
164E SER* 1.3 70.0 - - - +
166E SER* 1.3 55.3 + - - +
168E CYS* 3.4 7.5 - - - +
169E LYS* 2.8 58.9 + - - +
176E ILE* 4.1 12.3 - - - +
177E THR 5.0 2.1 - - - +
178E SER* 6.1 0.7 - - - -
180E MET 5.0 4.5 - - - +
181E PHE* 6.1 1.7 - - - +
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Residues in contact with SER 166 (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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164E SER* 2.7 24.3 + - - -
165E ASP* 1.3 72.4 + - - +
167E SER* 1.3 64.1 + - - -
168E CYS 3.0 1.1 + - - -
169E LYS* 3.2 5.8 + - - +
170E SER* 2.8 32.1 + - - -
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Residues in contact with SER 167 (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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163E LEU* 4.8 7.0 - - - -
164E SER* 2.8 28.1 + - - -
166E SER* 1.3 75.0 + - - +
168E CYS* 1.3 60.8 + - - +
170E SER* 2.7 20.1 + - - -
171E ALA* 3.1 16.3 + - - +
185E LEU* 4.2 32.2 - - - +
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Residues in contact with CYS 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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163E LEU* 5.2 0.4 - - - +
164E SER 2.9 11.3 + - - +
165E ASP* 3.4 14.4 - - - +
167E SER* 1.3 77.6 - - - +
169E LYS* 1.3 63.1 + - - +
171E ALA* 3.0 15.8 + - - +
172E TYR* 3.0 10.9 + - - -
176E ILE* 3.4 35.3 - - + +
181E PHE* 4.1 2.7 - - - -
182E CYS* 2.0 67.5 - - + +
225E PRO* 5.6 0.2 - - - -
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Residues in contact with LYS 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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165E ASP* 2.8 48.0 + - - +
166E SER* 3.8 5.2 - - - +
168E CYS* 1.3 74.7 - - - +
170E SER* 1.3 60.8 + - - +
172E TYR 3.2 1.0 - - - -
173E PRO* 3.1 27.5 - - - +
174E GLY* 4.1 11.5 + - - +
176E ILE* 2.9 48.2 + - + +
177E THR* 4.9 4.3 - - - +
178E SER* 6.4 0.2 - - - +
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Residues in contact with SER 170 (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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166E SER 2.8 13.8 + - - -
167E SER* 2.7 29.1 + - - -
169E LYS* 1.3 79.3 - - - +
171E ALA* 1.3 59.9 + - - +
172E TYR 3.5 0.2 + - - -
173E PRO* 3.6 10.1 - - - +
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Residues in contact with ALA 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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167E SER 3.1 13.6 + - - +
168E CYS 3.0 10.2 + - - +
170E SER* 1.3 78.5 + - - +
172E TYR* 1.3 61.8 + - + +
173E PRO* 3.4 5.2 - - - +
185E LEU* 5.2 2.9 - - + -
223E ASN* 3.5 23.6 - - - +
224E LYS* 2.8 29.0 + - - +
225E PRO* 3.8 21.1 - - + -
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Residues in contact with TYR 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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168E CYS 3.0 10.4 + - - -
169E LYS 3.2 6.0 - - - +
171E ALA* 1.3 82.8 - - + +
173E PRO* 1.3 68.9 - - - +
174E GLY 3.3 1.4 + - - -
175E GLN* 3.2 30.2 + - + +
176E ILE* 3.4 25.1 + - + +
182E CYS* 4.1 3.4 - - - -
215E TRP* 3.8 19.7 - + + -
216E GLY* 4.4 0.4 - - - -
217E SER* 3.2 35.3 + - - -
224E LYS* 3.0 31.3 + - + +
225E PRO* 2.6 44.9 + - + -
227E VAL* 3.7 20.2 - - + -
31K LEU* 4.8 1.1 - - + -
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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