Contacts of the helix formed by residues 174 - 185 (chain C) in PDB entry 1D1T
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 CYS 174 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C CYS* 3.7 4.9 - - - -
67C HIS* 3.8 12.1 - - + -
68C GLU* 3.5 13.4 - - + +
93C PHE* 4.0 5.2 - - + -
171C LEU 3.3 2.4 + - - -
172C ILE 3.2 2.2 + - - -
173C GLY* 1.3 81.7 - - - +
175C GLY* 1.3 78.7 + - - +
176C PHE 3.1 3.1 + - - -
177C SER* 3.3 4.3 + - - -
178C THR* 3.0 24.9 + - - -
319C PHE* 4.0 7.6 - - - -
376C ZN 2.1 38.8 - - - -
505C ACT 3.5 1.6 - - - -
3377C NAD 3.3 20.0 - - - -
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Residues in contact with GLY 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLU* 3.0 9.3 + - - -
171C LEU* 3.6 1.7 + - - -
174C CYS* 1.3 83.1 - - - +
176C PHE* 1.3 62.8 + - - +
178C THR* 3.6 2.4 + - - -
179C GLY 3.3 13.7 + - - -
202C GLY 4.7 2.2 - - - -
203C VAL* 3.8 17.9 - - - +
206C SER* 3.8 7.1 + - - -
369C ARG* 3.4 24.9 - - - -
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Residues in contact with PHE 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU* 3.1 22.0 + - + +
172C ILE* 4.6 8.3 - - + -
175C GLY* 1.3 65.1 - - - -
177C SER* 1.3 84.6 + - - +
178C THR 2.9 3.0 + - - -
179C GLY 3.0 2.8 + - - -
180C TYR* 2.9 59.8 + + + +
206C SER* 3.3 21.3 + - - +
209C MET* 3.6 27.8 - - + -
331C LEU* 4.0 17.7 - - + -
340C PHE* 3.9 36.1 - + + -
342C LEU* 3.7 29.6 - - + -
345C LEU* 4.1 8.6 - - + +
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Residues in contact with SER 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU 3.9 0.8 + - - -
172C ILE* 2.9 34.7 + - - +
174C CYS 3.3 1.0 + - - -
176C PHE* 1.3 84.2 - - - +
178C THR* 1.3 56.1 + - - +
180C TYR* 4.6 3.3 - - - -
181C GLY* 3.0 25.5 + - - -
319C PHE* 3.5 18.4 - - - +
320C GLY* 3.6 5.7 - - - -
322C LEU* 3.6 17.9 - - - +
331C LEU* 3.4 19.6 - - - +
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Residues in contact with THR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C PHE* 4.8 0.2 - - - -
174C CYS* 3.0 19.7 + - - -
175C GLY 3.7 4.7 - - - -
176C PHE 2.9 0.8 + - - -
177C SER* 1.3 74.9 - - - +
179C GLY* 1.3 60.9 + - - +
182C ALA* 2.9 30.1 + - - +
203C VAL* 3.7 3.8 - - + -
292C VAL* 3.4 24.0 - - + -
317C CYS* 5.1 0.2 - - - -
319C PHE* 3.5 15.6 - - - -
320C GLY* 3.2 18.0 - - - +
3377C NAD 3.1 45.2 - - + +
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Residues in contact with GLY 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C GLY 3.3 4.9 + - - -
176C PHE 3.0 4.9 + - - -
178C THR* 1.3 76.1 - - - +
180C TYR* 1.3 67.5 + - - +
182C ALA* 3.1 18.5 - - - +
203C VAL* 3.5 29.6 - - - +
206C SER* 3.5 7.9 - - - -
207C VAL* 3.0 19.8 - - - +
292C VAL* 5.1 0.4 - - - -
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Residues in contact with TYR 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C PHE* 2.9 53.6 + + + +
177C SER* 4.4 1.6 - - - +
179C GLY* 1.3 74.3 - - - +
181C GLY* 1.3 68.7 + - - +
183C ALA* 3.0 16.3 + - - +
184C VAL* 3.0 35.0 + - + +
206C SER 3.3 10.6 + - - +
209C MET* 4.5 3.4 - - + -
210C GLY* 3.6 27.1 - - - -
213C SER* 4.2 20.9 + - - -
322C LEU* 6.1 2.0 - - + -
331C LEU* 4.2 22.0 - - + -
334C GLU* 4.3 11.7 + - - -
340C PHE* 4.9 11.3 - + + -
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Residues in contact with GLY 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C SER 3.0 14.7 + - - -
180C TYR* 1.3 84.9 - - - +
182C ALA* 1.3 59.0 + - - +
184C VAL* 4.5 2.0 - - - -
185C LYS* 2.8 31.7 + - - -
186C THR 3.0 4.2 + - - -
320C GLY 2.9 25.9 - - - +
322C LEU* 4.7 7.6 - - - -
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C THR 2.9 16.8 + - - +
179C GLY* 3.1 15.0 - - - +
181C GLY* 1.3 77.7 - - - +
183C ALA* 1.3 57.1 + - - +
186C THR* 3.3 4.5 - - - +
187C GLY 2.9 26.5 + - - -
207C VAL* 4.2 1.8 - - + -
266C PHE* 3.6 15.6 - - + -
290C VAL* 4.8 1.1 - - + -
292C VAL* 4.0 27.1 - - + -
317C CYS* 4.0 17.3 - - - -
320C GLY* 3.5 0.2 - - - -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C GLY 3.5 0.4 + - - -
180C TYR 3.0 7.6 + - - +
182C ALA* 1.3 78.2 - - - +
184C VAL* 1.3 59.4 + - - +
188C LYS 2.8 31.9 + - - -
189C VAL* 3.2 14.0 + - + -
207C VAL* 3.9 7.4 - - + +
210C GLY 3.7 2.5 - - - -
211C CYS* 3.6 44.2 - - - +
266C PHE* 3.8 12.3 - - + -
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Residues in contact with VAL 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TYR* 3.0 44.3 + - + +
181C GLY* 4.5 4.7 - - - -
183C ALA* 1.3 81.3 - - - +
185C LYS* 1.3 78.6 + - + +
188C LYS* 3.6 17.4 - - - +
189C VAL 5.0 1.3 - - - +
210C GLY* 4.0 17.5 + - - +
213C SER* 5.5 3.4 - - - -
214C ALA* 5.2 7.6 - - + -
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Residues in contact with LYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C GLY* 2.8 18.7 + - - +
184C VAL* 1.3 92.1 - - + +
186C THR* 1.3 59.3 + - - +
188C LYS* 3.0 30.6 + - - +
320C GLY 3.7 6.7 - - - +
321C GLY* 4.4 12.8 - - - +
322C LEU* 3.5 25.3 - - + +
327C ASP* 3.5 22.9 - - - +
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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