Contacts of the helix formed by residues 175 - 186 (chain A) in PDB entry 1YI1
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 LEU 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLU* 3.7 15.5 - - + +
147A GLY* 5.8 0.2 - - - -
148A VAL* 3.6 33.7 - - + +
164A CYS* 4.0 11.4 - - + -
165A ILE 5.7 0.9 - - - -
166A ALA* 3.7 15.3 - - + +
171A GLY 3.8 7.0 - - - +
172A ALA* 2.9 13.3 + - - +
174A ASN* 1.3 78.4 - - - +
176A VAL* 1.3 67.1 + - - +
177A SER 3.3 2.7 - - - -
178A GLY* 2.8 16.9 + - - -
179A LEU* 3.1 26.0 + - + +
191A ALA* 4.6 15.3 - - + -
192A ILE 5.2 0.4 - - - +
193A THR* 3.5 31.4 - - + -
251A LEU* 5.3 2.0 - - + -
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Residues in contact with VAL 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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172A ALA 4.0 1.8 + - - +
173A THR* 3.2 29.1 + - + +
174A ASN 3.6 0.2 - - - -
175A LEU* 1.3 76.7 - - - +
177A SER* 1.3 64.5 + - - +
179A LEU* 3.2 9.1 + - - +
180A ALA* 2.9 24.5 + - + +
211A ILE* 4.9 1.1 - - + -
214A VAL* 4.3 24.0 - - + -
215A THR* 4.8 6.3 - - + -
218A ILE* 3.4 24.7 - - + +
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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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145A GLN* 3.7 23.4 + - - -
149A PHE* 4.4 10.3 - - - -
174A ASN 5.3 1.5 + - - -
175A LEU 3.1 1.4 + - - -
176A VAL* 1.3 80.1 - - - +
178A GLY* 1.3 57.6 + - - +
180A ALA* 4.6 4.0 - - - -
181A ASP* 2.9 28.9 + - - +
510A LEU* 3.6 11.8 - - - +
512A ALA* 5.6 3.1 - - - -
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Residues in contact with GLY 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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145A GLN* 6.0 0.6 - - - +
148A VAL* 4.1 21.1 - - - +
149A PHE* 3.9 19.6 - - - -
152A GLU* 3.6 5.3 - - - +
175A LEU 2.8 12.3 + - - -
177A SER* 1.3 72.0 - - - +
179A LEU* 1.3 63.8 + - - +
181A ASP* 3.1 2.6 + - - +
182A ALA* 2.8 31.9 + - - +
189A LEU* 4.9 1.1 - - - -
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Residues in contact with LEU 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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148A VAL* 4.4 6.5 - - + -
172A ALA 5.7 0.4 - - - +
175A LEU* 3.1 26.4 + - + +
176A VAL* 3.6 7.2 - - - +
178A GLY* 1.3 73.7 - - - +
180A ALA* 1.3 64.6 + - - +
182A ALA* 3.0 4.8 + - - +
183A LEU* 2.9 20.4 + - - +
189A LEU* 4.4 14.4 - - + -
191A ALA* 4.1 24.2 - - + -
215A THR* 3.8 28.9 - - + -
218A ILE* 3.5 18.4 - - + +
219A THR* 4.1 10.5 - - + -
249A PRO* 3.7 14.4 - - + +
250A VAL 6.0 0.4 - - - +
251A LEU* 3.8 17.9 - - + +
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Residues in contact with ALA 180 (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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176A VAL* 2.9 18.1 + - + +
177A SER* 3.9 5.6 - - - +
179A LEU* 1.3 75.7 - - - +
181A ASP* 1.3 56.4 + - - +
183A LEU* 3.5 2.9 + - - +
184A LEU* 3.1 33.8 + - + +
218A ILE* 3.7 33.2 + - + +
510A LEU* 4.0 18.4 - - + -
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Residues in contact with ASP 181 (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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149A PHE* 4.4 7.2 - - + -
152A GLU* 2.4 37.0 - - - +
156A ARG* 3.4 7.5 + - - -
177A SER 2.9 19.9 + - - +
178A GLY* 3.3 2.2 - - - +
180A ALA* 1.3 74.5 - - - +
182A ALA* 1.3 63.8 + - - +
184A LEU* 3.4 2.8 + - - +
185A ASP* 3.1 26.3 + - - +
507A SER* 2.8 28.1 + - - -
510A LEU* 3.7 22.6 + - + +
511A GLY 4.4 0.2 + - - -
512A ALA* 4.4 2.8 - - + +
515A PHE* 3.6 9.9 - - - -
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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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152A GLU* 4.0 12.1 + - - -
178A GLY 2.8 19.5 + - - +
179A LEU 3.6 3.1 - - - +
181A ASP* 1.3 69.8 - - - +
183A LEU* 1.3 61.1 + - - +
186A SER* 2.9 9.2 + - - -
187A VAL* 2.8 48.3 + - + +
189A LEU* 3.6 25.4 - - + -
249A PRO* 3.7 9.5 - - + +
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Residues in contact with LEU 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 LEU 2.9 7.8 + - - +
180A ALA 3.8 3.8 - - - +
182A ALA* 1.3 77.6 - - - +
184A LEU* 1.3 65.0 + - + +
186A SER* 3.2 15.4 + - - -
217A SER 3.9 7.6 - - - +
218A ILE* 3.4 43.3 - - - +
219A THR 3.5 9.0 - - - +
220A LYS* 4.1 16.2 - - + +
246A ARG* 5.3 3.1 + - - -
247A PRO 5.7 0.7 - - - +
248A GLY* 5.1 2.9 - - - -
249A PRO* 3.5 18.1 - - + +
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Residues in contact with LEU 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 ALA* 3.1 14.4 + - + +
181A ASP 3.8 4.3 - - - +
183A LEU* 1.3 81.6 - - + +
185A ASP* 1.3 62.0 + - - +
186A SER* 3.7 2.9 + - - -
246A ARG* 4.7 3.1 + - - -
373A ARG* 3.5 47.1 + - - +
509A GLY* 3.9 7.4 - - - +
510A LEU* 3.6 52.0 - - + +
701A FAD 4.3 3.8 + - - -
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Residues in contact with ASP 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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156A ARG* 2.8 32.8 + - - +
181A ASP* 3.1 15.6 + - - +
184A LEU* 1.3 76.2 - - - +
186A SER* 1.3 72.3 + - - +
187A VAL* 3.5 7.8 - - + +
333A MET* 3.3 26.6 - - + +
507A SER* 3.6 1.6 - - - -
508A GLY 2.9 20.1 + - - -
509A GLY* 2.7 29.5 + - - -
701A FAD 3.7 17.0 + - - -
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Residues in contact with SER 186 (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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182A ALA 2.9 9.5 + - - -
183A LEU 3.2 8.0 + - - -
184A LEU 4.4 0.7 + - - -
185A ASP* 1.3 82.7 - - - +
187A VAL* 1.3 56.5 + - - +
188A PRO* 4.0 1.6 - - - +
246A ARG* 2.8 41.8 + - - +
247A PRO* 3.2 41.7 + - - +
248A GLY* 4.7 0.2 - - - -
701A FAD 4.8 12.4 + - - -
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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