Contacts of the helix formed by residues 174 - 185 (chain B) in PDB entry 1U3T
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B CYS* 4.0 1.1 - - - -
67B HIS* 3.9 12.1 - - + -
68B GLU* 3.7 11.5 - - + +
171B LEU 3.4 2.0 + - - -
172B ILE 3.2 2.6 - - - -
173B GLY* 1.3 82.7 - - - +
175B GLY* 1.3 60.9 + - - +
176B PHE 3.6 1.1 - - - -
177B SER* 3.4 2.8 + - - -
178B THR* 2.8 37.9 + - - -
319B LEU* 3.8 7.6 - - + -
376B ZN 2.3 37.7 - - - -
2377B NAD 3.4 15.3 - - - -
2378B CCB 3.3 17.5 - - - -
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLU* 2.8 19.6 + - - -
171B LEU* 3.4 2.6 + - - -
174B CYS* 1.3 81.4 - - - +
176B PHE* 1.3 61.5 + - - +
178B THR* 3.9 1.6 - - - -
179B GLY* 3.1 17.0 + - - -
202B GLY 4.7 1.6 - - - -
203B VAL* 3.9 19.2 - - - -
206B SER* 4.1 3.5 + - - -
345B LEU* 5.9 0.2 - - - -
369B ARG* 3.5 17.5 - - - -
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 2.9 23.0 + - + +
172B ILE* 4.4 9.6 - - + -
175B GLY* 1.3 70.0 - - - -
177B SER* 1.3 63.6 + - - +
179B GLY 3.4 0.2 + - - -
180B TYR* 2.8 78.2 + + + +
206B SER* 3.5 22.8 + - - +
209B MET* 3.8 22.0 - - + -
331B LEU* 4.7 6.5 - - + -
340B PHE* 3.4 55.2 - + + -
342B LEU* 3.7 25.6 - - + -
345B LEU* 4.5 3.9 - - + +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU 4.1 1.2 + - - -
172B ILE* 2.6 30.8 + - - +
174B CYS 3.4 4.1 + - - -
176B PHE* 1.3 82.5 - - - +
178B THR* 1.3 58.0 + - - +
180B TYR* 4.6 1.1 - - - -
181B GLY* 2.9 25.8 + - - -
319B LEU* 4.3 13.0 - - - -
320B GLY* 3.7 0.5 - - - -
322B PHE* 3.3 22.3 - - - -
328B VAL* 5.1 1.9 - - - +
331B LEU* 3.1 28.6 - - - +
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Residues in contact with THR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B CYS* 2.8 29.4 + - - -
175B GLY 3.9 2.5 - - - -
177B SER* 1.3 72.8 - - - +
179B GLY* 1.3 58.5 + - - +
182B SER* 2.6 35.0 + - - +
203B VAL* 3.8 4.7 - - + -
292B VAL* 3.6 17.9 - - + -
317B ALA 5.4 0.4 - - - +
319B LEU* 3.3 17.3 - - - +
320B GLY* 3.5 14.1 - - - +
2377B NAD 3.2 49.4 - - + +
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLY 3.1 7.9 + - - -
176B PHE 3.8 1.1 - - - -
178B THR* 1.3 82.6 - - - +
180B TYR* 1.3 63.2 + - - +
182B SER* 3.4 14.7 + - - -
183B ALA 3.6 2.4 + - - -
203B VAL* 3.3 30.5 - - - +
206B SER* 3.6 9.4 - - - -
207B ALA* 3.3 16.1 - - - -
292B VAL* 5.4 0.4 - - - -
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B PHE* 2.8 59.2 + + + +
177B SER* 4.2 2.0 - - - +
179B GLY* 1.3 70.7 - - - +
181B GLY* 1.3 59.6 + - - +
183B ALA* 3.3 5.2 + - - +
184B VAL* 3.0 53.4 + - + +
206B SER 3.4 9.3 + - - -
209B MET* 4.2 4.5 - - + -
210B GLY* 3.6 27.1 - - - -
213B ALA* 3.6 22.6 - - + +
322B PHE* 4.5 15.5 - + - -
331B LEU* 5.1 7.0 - - + -
340B PHE* 5.1 13.2 - + + -
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B SER 2.9 15.6 + - - -
180B TYR* 1.3 73.6 - - - +
182B SER* 1.3 61.1 + - - +
184B VAL* 4.3 0.9 - - - -
185B ASN* 2.7 30.8 + - - +
186B VAL 3.1 7.6 + - - -
320B GLY 3.4 11.2 - - - -
322B PHE* 3.4 28.0 - - - -
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B THR* 2.6 25.6 + - - +
179B GLY* 3.6 6.5 - - - -
180B TYR 3.3 0.4 - - - -
181B GLY* 1.3 75.6 - - - +
183B ALA* 1.3 58.0 + - - +
186B VAL* 3.3 14.3 - - - +
187B ALA* 2.8 32.6 + - - +
207B ALA* 5.5 1.3 - - - -
266B PHE* 3.5 11.9 - - - -
290B VAL* 4.4 5.0 - - - +
292B VAL* 3.6 32.4 - - - +
317B ALA* 5.4 4.0 + - - +
320B GLY* 3.8 5.6 - - - -
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B GLY 3.6 3.5 + - - +
180B TYR 3.3 7.7 + - - +
181B GLY 3.2 0.2 - - - -
182B SER* 1.3 79.8 - - - +
184B VAL* 1.3 58.2 + - - +
188B LYS 3.0 22.9 + - - -
189B VAL* 3.1 18.3 + - + +
207B ALA* 3.7 14.4 - - - +
210B GLY* 3.7 25.8 - - - -
211B CYS* 3.7 4.7 - - - +
266B PHE* 3.5 21.5 - - + -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B TYR* 3.0 47.8 + - + +
181B GLY* 4.4 1.8 - - - +
183B ALA* 1.3 75.3 - - - +
185B ASN* 1.3 71.0 + - - +
188B LYS* 3.3 26.9 - - - +
189B VAL 5.0 0.7 - - - +
210B GLY* 4.0 17.7 - - - +
213B ALA* 5.3 2.2 - - + -
214B ALA* 5.1 7.9 - - + +
322B PHE* 5.6 1.8 - - + -
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Residues in contact with ASN 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLY* 2.7 14.1 + - - +
184B VAL* 1.3 84.1 - - - +
186B VAL* 1.3 63.8 + - + +
188B LYS* 2.6 35.9 + - - +
320B GLY 3.1 20.1 + - - +
321B GLY* 4.2 5.8 + - - +
322B PHE* 3.1 45.5 - - - +
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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