Contacts of the helix formed by residues 172 - 185 (chain A) in PDB entry 3IAY
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 ASP 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ASP* 3.2 19.5 + - + +
171A ASN* 1.3 78.2 - - - +
173A GLN* 1.3 64.1 + - - +
174A GLU* 2.9 24.0 + - - +
175A GLN* 3.0 32.7 + - + +
176A ILE* 3.1 15.2 + - - +
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Residues in contact with GLN 173 (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 ASN 3.2 7.7 + - - +
172A ASP* 1.3 73.7 + - - +
174A GLU* 1.3 64.0 + - - +
176A ILE* 3.1 26.4 + - - +
177A ASN* 2.9 57.3 + - - +
194A ILE 5.4 4.2 + - - -
196A VAL* 6.0 1.4 - - - +
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Residues in contact with GLU 174 (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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172A ASP* 2.9 14.5 + - - +
173A GLN* 1.3 78.0 - - - +
175A GLN* 1.3 62.8 + - - +
177A ASN* 3.4 11.8 + - - +
178A LYS* 3.0 51.6 + - - +
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Residues in contact with GLN 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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169A ASP* 4.0 13.9 - - + +
172A ASP* 3.0 31.4 + - + +
174A GLU* 1.3 79.7 - - - +
176A ILE* 1.3 61.4 + - - +
178A LYS* 3.2 24.9 + - - +
179A PHE* 2.9 28.2 + - - +
238A PHE* 3.6 14.4 - - - -
239A ASN* 3.0 26.0 + - - +
241A TRP* 3.9 17.0 - - + -
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Residues in contact with ILE 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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170A ALA 3.5 23.8 - - - +
171A ASN* 4.8 4.3 - - - +
172A ASP 3.1 13.5 + - - +
173A GLN* 3.1 31.6 + - - +
175A GLN* 1.3 76.0 - - - +
177A ASN* 1.3 57.9 + - - +
179A PHE* 3.2 8.5 + - - +
180A VAL* 2.9 31.1 + - + +
194A ILE* 4.0 35.0 - - + +
196A VAL* 4.4 17.7 - - + -
214A TRP* 3.9 22.4 - - + -
241A TRP* 4.5 3.8 - - + -
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Residues in contact with ASN 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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173A GLN* 2.9 46.2 + - - +
174A GLU* 3.4 12.7 + - - +
176A ILE* 1.3 77.3 - - - +
178A LYS* 1.3 62.6 + - + +
180A VAL* 3.3 10.8 + - - +
181A HIS* 3.1 20.3 + - - +
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Residues in contact with LYS 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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174A GLU* 3.0 43.3 + - - +
175A GLN* 3.2 27.3 + - - +
177A ASN* 1.3 73.7 - - + +
179A PHE* 1.3 60.1 + - - +
181A HIS* 3.2 10.3 + - + +
182A TYR* 2.9 28.1 + - - +
238A PHE* 3.6 19.1 - - + -
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Residues in contact with PHE 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 GLN 2.9 13.4 + - - +
176A ILE 3.2 7.4 + - - +
178A LYS* 1.3 75.8 - - - +
180A VAL* 1.3 58.1 + - - +
182A TYR* 3.2 12.3 + + - +
183A LEU* 2.8 63.1 + - + +
194A ILE* 3.7 22.7 - - + -
214A TRP* 3.8 15.0 - + - -
216A ILE* 4.8 0.4 - - + -
231A PHE* 3.9 14.1 - + - -
236A LEU* 4.9 6.1 - - + -
238A PHE* 3.5 42.8 - + + -
241A TRP* 3.7 8.3 - + + -
242A PHE* 3.8 36.3 - + - -
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Residues in contact with VAL 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 ILE* 2.9 21.2 + - + +
177A ASN* 3.5 11.9 - - - +
179A PHE* 1.3 76.3 - - - +
181A HIS* 1.3 57.3 + - - +
183A LEU* 3.3 8.5 + - - +
184A ASN* 2.9 43.3 + - - +
191A ILE* 4.0 17.0 - - + +
192A ASP 4.5 9.9 - - - +
193A SER* 4.5 2.2 - - - -
194A ILE* 3.7 38.6 - - + +
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Residues in contact with HIS 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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177A ASN 3.1 12.9 + - - +
178A LYS* 3.2 13.2 + - + +
180A VAL* 1.3 75.7 - - - +
182A TYR* 1.3 64.8 + - - +
184A ASN* 3.2 10.0 + - + +
185A GLU* 3.0 46.7 + - - +
988A ACT 4.0 16.7 + - - +
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Residues in contact with TYR 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 LYS 2.9 14.5 + - - +
179A PHE* 3.3 18.8 - + - +
181A HIS* 1.3 78.2 - - - +
183A LEU* 1.3 62.9 + - + +
185A GLU* 3.4 26.1 + - - +
186A THR* 2.8 29.5 + - - -
235A HIS 3.5 6.1 + - - -
236A LEU* 3.5 32.3 - - + +
237A SER* 3.1 29.4 + - - -
238A PHE* 3.9 39.7 - + + -
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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 PHE* 2.8 61.4 + - + +
180A VAL* 3.7 8.3 - - - +
182A TYR* 1.3 76.9 - - + +
184A ASN* 1.3 61.3 + - - +
186A THR* 2.9 2.3 + - - -
187A PHE* 2.8 47.8 + - + -
191A ILE* 3.6 34.0 - - + +
194A ILE* 4.7 2.2 - - + -
216A ILE* 4.5 17.7 - - + -
227A LEU* 4.2 6.1 - - + -
231A PHE* 4.9 0.7 - - + -
236A LEU* 4.0 22.0 - - + -
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Residues in contact with ASN 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 VAL* 2.9 31.1 + - - +
181A HIS* 3.2 9.5 + - + +
183A LEU* 1.3 75.8 - - - +
185A GLU* 1.3 61.8 + - - +
186A THR 3.2 0.7 + - - -
187A PHE 3.7 0.9 + - - -
188A ASP 3.8 0.5 + - - -
189A HIS* 2.9 59.9 + - + +
191A ILE* 2.7 49.9 + - - +
988A ACT 5.7 0.4 - - - +
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Residues in contact with GLU 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 HIS* 3.0 33.5 + - - +
182A TYR* 3.4 27.4 - - - +
183A LEU 3.2 0.2 - - - -
184A ASN* 1.3 75.8 - - - +
186A THR* 1.3 59.3 + - - +
188A ASP 5.0 1.0 + - - -
189A HIS* 5.5 1.2 - - - -
988A ACT 2.9 47.9 + - + +
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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