Contacts of the helix formed by residues 174 - 185 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A CYS* 3.8 1.8 - - - -
67A HIS* 3.5 8.3 - - + -
68A GLU* 3.3 15.8 - - + +
93A PHE* 3.8 14.1 - - + -
171A LEU 3.1 4.4 + - - -
172A ILE 3.5 0.6 - - - -
173A GLY* 1.3 82.6 - - - +
175A GLY* 1.3 70.7 + - - +
177A SER* 3.2 6.4 + - - -
178A THR* 2.9 21.4 + - - -
319A PHE* 3.9 2.4 - - - -
376A ZN 2.0 38.4 - - - -
501A ACT 3.2 7.6 - - - -
1377A NAD 3.4 16.4 - - - -
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 2.9 10.7 + - - -
171A LEU* 3.6 1.1 + - - -
174A CYS* 1.3 79.8 - - - +
176A PHE* 1.3 62.9 + - - +
178A THR* 3.1 9.6 + - - -
179A GLY 3.1 12.0 + - - -
202A GLY 5.0 1.1 - - - -
203A VAL* 3.9 19.0 - - - +
206A SER* 3.7 8.2 + - - -
369A ARG* 3.6 22.0 - - - -
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 3.1 26.1 + - + +
172A ILE* 4.0 14.4 - - + -
175A GLY* 1.3 71.8 - - - +
177A SER* 1.3 56.0 - - - +
180A TYR* 2.8 71.9 + + + +
202A GLY 5.2 0.2 + - - -
206A SER* 3.4 19.5 + - - +
209A MET* 3.6 25.6 - - + -
331A LEU* 3.9 17.0 - - + -
340A PHE* 3.2 48.2 - + - -
342A LEU* 3.5 22.0 - - + -
345A LEU* 4.1 8.7 - - + +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU 3.9 1.0 + - - -
172A ILE* 3.2 25.0 + - - +
174A CYS 3.2 2.5 + - - -
176A PHE* 1.3 78.2 - - - +
178A THR* 1.3 63.3 + - - +
180A TYR* 4.6 0.7 - - - -
181A GLY* 3.0 21.0 + - - -
319A PHE* 3.4 32.1 - - - +
320A GLY* 3.6 5.4 - - - +
322A LEU* 3.8 14.5 - - - +
328A VAL* 5.1 0.2 - - - +
331A LEU* 3.1 27.1 - - - +
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 4.7 0.2 - - - -
174A CYS* 2.9 16.6 + - - -
175A GLY 3.1 9.4 + - - -
177A SER* 1.3 76.3 - - - +
179A GLY* 1.3 58.8 + - - +
182A ALA* 2.9 27.2 + - - +
203A VAL* 3.6 4.0 - - + -
292A VAL* 3.4 26.9 - - + -
317A CYS* 5.2 0.2 - - - -
319A PHE* 3.8 10.3 - - - -
320A GLY* 3.0 20.3 - - - +
1377A NAD 3.0 48.2 + - + +
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLY 3.1 7.5 + - - -
178A THR* 1.3 77.4 - - - +
180A TYR* 1.3 68.7 + - - +
182A ALA* 3.2 12.2 + - - +
183A ALA* 3.4 2.3 + - - +
203A VAL* 3.6 11.1 - - - +
206A SER* 3.8 1.3 - - - -
207A VAL* 3.1 47.5 - - - -
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A PHE* 2.8 59.6 + + + +
177A SER* 4.3 2.2 - - - +
179A GLY* 1.3 75.0 - - - +
181A GLY* 1.3 65.3 + - - +
183A ALA* 3.1 11.1 + - - +
184A VAL* 3.2 25.0 + - + +
206A SER 3.5 8.0 + - - -
209A MET* 4.0 8.7 - - + -
210A GLY* 3.6 19.2 - - - -
213A SER* 3.7 30.7 + - - -
331A LEU* 4.1 25.8 - - + -
334A GLU* 4.4 12.4 + - - -
339A LYS* 5.4 3.3 + - - +
340A PHE* 4.4 16.1 - + + +
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A SER 3.0 14.2 + - - -
180A TYR* 1.3 80.6 - - - +
182A ALA* 1.3 58.1 + - - +
184A VAL* 4.8 2.5 - - - -
185A LYS* 2.7 35.6 + - - -
186A THR 3.0 8.1 + - - -
320A GLY 3.1 23.1 - - - -
322A LEU* 4.5 7.8 - - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A THR 2.9 19.6 + - - +
179A GLY* 3.3 12.3 - - - +
180A TYR 3.2 0.4 - - - -
181A GLY* 1.3 77.4 - - - +
183A ALA* 1.3 56.9 + - - +
186A THR* 3.8 3.2 - - - -
187A GLY 3.0 21.3 + - - -
207A VAL* 4.0 6.5 - - + -
266A PHE* 3.1 16.5 - - + -
290A VAL* 4.3 2.8 - - + +
292A VAL* 3.9 27.8 - - + -
317A CYS* 4.0 16.2 - - - -
320A GLY* 3.6 0.2 - - - -
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLY 3.4 1.8 + - - +
180A TYR 3.1 5.5 + - - +
181A GLY 3.1 0.2 - - - -
182A ALA* 1.3 80.9 - - - +
184A VAL* 1.3 60.6 + - - +
185A LYS 3.5 0.2 - - - -
188A LYS 2.9 23.4 + - - -
189A VAL* 3.0 17.1 + - + +
207A VAL* 3.7 9.2 - - + +
210A GLY 3.5 29.2 - - - -
211A CYS* 3.5 18.2 - - - +
266A PHE* 3.7 11.2 - - + -
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.2 28.4 + - + +
181A GLY* 4.8 1.3 - - - -
183A ALA* 1.3 79.6 - - - +
185A LYS* 1.3 72.2 + - + +
188A LYS* 3.7 15.9 - - - +
189A VAL 5.0 0.9 - - - +
210A GLY* 3.5 23.8 - - - +
213A SER* 3.6 14.1 - - - +
214A ALA* 4.6 9.2 - - + +
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLY* 2.7 17.7 + - - +
184A VAL* 1.3 87.8 - - + +
186A THR* 1.3 62.4 + - - +
188A LYS* 3.3 28.9 + - - +
320A GLY 3.8 7.4 - - - +
321A GLY* 4.0 13.2 - - - +
322A LEU* 3.3 26.4 - - + +
327A ASP* 3.6 27.0 + - - -
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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