Contacts of the helix formed by residues 168 - 176 (chain K) in PDB entry 2I2X
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 GLY 168 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166K MET 3.1 0.6 + - - -
167K GLY* 1.3 69.5 - - - -
169K LYS* 1.3 64.9 + - - +
170K GLU* 3.1 14.2 + - - +
172K PHE* 3.1 19.6 + - - +
187K SER* 3.4 17.9 - - - -
191K LEU* 3.9 10.8 - - - -
222K GLN* 3.3 13.5 + - - -
459K TYR* 2.9 17.0 + - - -
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Residues in contact with LYS 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K GLU* 3.2 25.0 + - - -
136K LEU* 4.2 9.9 - - + -
166K MET* 3.1 50.9 + - + +
167K GLY 3.3 1.6 + - - -
168K GLY* 1.3 78.1 - - - +
170K GLU* 1.3 58.6 + - + +
172K PHE* 3.8 3.9 - - - +
173K ASP* 3.0 52.9 + - - +
221K ALA* 4.4 16.2 - - + +
222K GLN* 4.4 8.7 - - + +
135L VAL* 3.6 14.1 + - - +
159L ARG* 5.0 1.0 - - - +
500L B13 3.5 35.9 + - + +
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Residues in contact with GLU 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K LEU* 3.4 23.9 - - + +
168K GLY* 3.1 17.0 - - - -
169K LYS* 1.3 78.0 - - - +
171K VAL* 1.3 71.2 + - + +
173K ASP* 3.7 6.4 + - - +
174K TYR* 3.6 16.5 + - - +
191K LEU* 4.1 0.3 - - - +
451K VAL* 4.0 7.8 - - + +
453K VAL* 4.0 23.9 - - + +
454K PHE* 3.7 37.4 - - + +
455K LYS 4.8 2.3 + - - -
458K ASN* 4.8 1.4 + - - -
459K TYR* 2.5 34.2 + - - -
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Residues in contact with VAL 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K GLY 3.5 0.2 + - - -
170K GLU* 1.3 83.8 + - + +
172K PHE* 1.3 61.6 + - - +
174K TYR* 3.2 7.1 + - - +
175K ALA* 2.9 26.3 + - - +
183K GLY* 4.1 9.4 - - - +
186K TYR* 4.2 4.5 - - + -
187K SER* 3.8 19.1 - - - -
191K LEU* 3.8 20.4 - - + -
447K TYR* 3.9 43.5 - - + -
451K VAL* 4.7 5.2 - - + -
454K PHE* 3.9 26.5 - - + -
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Residues in contact with PHE 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K GLY 3.1 18.5 + - - +
169K LYS 3.8 2.9 - - - +
171K VAL* 1.3 72.2 - - - +
173K ASP* 1.3 86.4 + - - +
174K TYR 3.0 2.2 + - - -
175K ALA* 3.1 3.5 + - - +
176K VAL* 2.9 58.9 + - + +
184K LEU* 3.8 18.8 - - + -
187K SER* 3.4 15.5 - - - +
188K ILE* 4.1 10.8 - - + -
221K ALA 3.8 4.3 - - - -
222K GLN* 2.9 57.4 - - + +
225K THR* 3.8 14.1 - - + -
226K ALA* 3.9 12.6 - - + -
246K ALA* 5.1 1.1 - - + -
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Residues in contact with ASP 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K LYS* 3.0 35.3 + - - +
170K GLU* 4.0 6.9 - - - +
171K VAL 3.4 0.4 - - - -
172K PHE* 1.3 95.7 - - - +
174K TYR* 1.3 60.8 + - - +
176K VAL* 3.6 14.3 - - - +
177K LEU* 3.8 18.0 - - - +
221K ALA 4.6 3.5 - - - +
225K THR* 4.5 0.5 - - - +
137L ASP* 4.9 2.3 - - - +
138L ILE* 4.3 9.2 - - + +
500L B13 3.4 35.9 + - - +
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Residues in contact with TYR 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K GLU 3.6 9.7 + - - +
171K VAL 3.2 8.9 + - - +
172K PHE 3.0 0.6 - - - -
173K ASP* 1.3 80.6 - - - +
175K ALA* 1.3 66.9 + - - +
176K VAL 3.3 0.7 + - - -
177K LEU* 3.5 6.8 + - - -
178K ARG* 3.0 67.8 + - - +
180K ASP* 4.8 4.7 - - - -
447K TYR* 4.3 13.7 - + - -
450K GLU* 2.6 56.9 + - + +
451K VAL* 3.7 24.2 - - + -
103L ASP* 4.8 3.2 + - - -
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Residues in contact with ALA 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K VAL* 2.9 20.3 + - + +
172K PHE* 3.9 0.9 - - - +
174K TYR* 1.3 78.1 - - + +
176K VAL* 1.3 60.5 + - - +
177K LEU 3.3 0.2 - - - -
178K ARG* 3.3 5.1 + - - -
179K ASN* 3.4 1.4 + - - -
180K ASP* 3.1 55.9 + - + +
183K GLY* 3.7 24.0 - - - +
184K LEU* 3.9 9.9 - - + +
447K TYR* 5.5 0.2 - - + -
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Residues in contact with VAL 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K PHE* 2.9 59.7 + - + +
173K ASP* 3.6 12.6 - - - +
175K ALA* 1.3 69.3 - - - +
177K LEU* 1.3 75.3 + - + +
178K ARG 3.1 6.0 + - - -
179K ASN* 4.3 1.6 + - - +
184K LEU* 4.0 10.1 - - + +
225K THR* 5.1 0.4 - - + -
226K ALA* 4.2 8.7 - - + -
229K ILE* 4.1 12.5 - - + +
237K ASN 5.4 0.2 - - - +
238K LEU* 3.5 42.3 - - + +
242K ILE* 6.0 1.3 - - + -
96L PRO* 4.2 2.6 - - - +
138L ILE* 5.4 1.1 - - + -
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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