Contacts of the helix formed by residues 183 - 190 (chain A) in PDB entry 3IKH
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 GLU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ASN* 1.3 74.2 - - - +
184A SER* 1.3 64.9 + - - +
186A ALA* 3.2 8.1 + - - +
187A GLU* 3.1 22.3 + - - +
199A ILE* 4.5 3.6 - - + -
200A THR 3.1 4.9 + - - +
201A GLN* 2.4 62.9 + - + +
204A ALA* 5.0 3.1 - - - +
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Residues in contact with SER 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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165A VAL* 6.1 0.7 - - - +
182A ASN* 2.9 16.1 + - - -
183A GLU* 1.3 78.1 - - - +
185A GLU* 1.3 73.1 + - - +
187A GLU* 3.2 6.7 + - - +
188A LEU* 2.9 33.7 + - - +
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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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161A ASN* 4.2 8.0 - - - +
162A PRO 3.7 19.6 - - - +
163A SER* 3.2 25.7 + - - -
165A VAL* 4.5 15.6 + - + +
180A VAL 4.4 0.2 - - - +
181A VAL* 3.4 21.1 - - + +
182A ASN* 2.9 45.7 + - - +
184A SER* 1.3 86.8 + - - +
186A ALA* 1.3 56.0 + - - +
188A LEU* 4.6 4.9 - - - -
189A LEU* 3.0 41.3 + - + +
191A PRO* 4.4 0.7 - - - +
900A ATP 5.4 1.6 + - - -
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Residues in contact with ALA 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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181A VAL* 3.6 21.5 - - + +
182A ASN 2.9 18.0 + - - +
183A GLU* 3.2 5.4 + - - +
185A GLU* 1.3 73.7 - - - +
187A GLU* 1.3 57.7 + - - +
190A GLN* 3.1 29.0 + - - -
191A PRO* 3.3 13.8 - - + +
199A ILE* 4.0 26.2 - - + -
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Residues in contact with GLU 187 (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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183A GLU 3.1 12.2 + - - +
184A SER* 3.8 7.1 - - - +
186A ALA* 1.3 79.5 - - - +
188A LEU* 1.3 59.6 + - - +
190A GLN* 2.9 26.0 + - - +
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Residues in contact with LEU 188 (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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165A VAL* 3.6 31.9 - - + -
167A PRO* 4.8 20.4 - - + +
170A CYS* 5.1 2.9 - - - +
184A SER* 2.9 18.7 + - - +
185A GLU* 4.2 2.7 - - - +
187A GLU* 1.3 79.0 - - - +
189A LEU* 1.3 71.7 + - + +
190A GLN* 5.1 1.0 - - - +
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Residues in contact with LEU 189 (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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162A PRO* 3.5 40.8 - - + +
165A VAL* 3.5 32.3 - - + -
166A ASN 3.7 13.9 - - - +
167A PRO* 4.2 10.1 - - + +
169A PHE* 4.3 12.1 - - + -
170A CYS* 3.5 17.9 - - + +
173A TRP* 3.1 28.5 + - + +
181A VAL* 5.2 0.2 - - + -
185A GLU* 3.0 23.5 + - + +
188A LEU* 1.3 84.3 - - + +
190A GLN* 1.3 69.7 + - - +
191A PRO* 4.5 0.2 - - + -
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Residues in contact with GLN 190 (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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186A ALA 3.1 12.9 + - - -
187A GLU* 2.9 30.4 - - - +
188A LEU 3.4 2.5 - - - +
189A LEU* 1.3 78.7 - - - +
191A PRO* 1.3 79.1 + - - +
192A TYR* 3.3 19.9 + - + +
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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