Contacts of the helix formed by residues 183 - 192 (chain C) in PDB entry 3IXK
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 PRO 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C SER* 3.4 27.1 - - - +
86C PHE 6.0 0.2 - - - +
168C GLY 4.5 4.3 - - - +
169C LEU 6.0 0.2 - - - -
170C ALA 4.0 11.4 - - - +
171C TYR 4.1 0.7 - - - -
172C ALA* 3.7 36.6 - - + +
175C ALA* 4.9 0.4 - - + -
181C LEU 3.4 7.6 - - - +
182C GLU* 1.3 89.2 - - + +
184C PHE* 1.3 69.3 + - - +
185C PHE* 4.5 2.5 - - + +
186C ASP* 3.0 35.6 + - - +
187C SER* 3.0 12.1 + - - -
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Residues in contact with PHE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C MET* 4.1 12.1 - - + -
84C SER 4.9 1.0 + - - -
86C PHE* 4.3 20.9 - + + +
133C VAL* 3.6 27.4 - - + -
135C ILE* 4.1 19.3 - - + -
143C VAL* 3.7 23.8 - - + -
145C ALA* 3.7 20.2 - - + -
146C ASN 5.6 1.4 + - - +
167C LEU* 3.6 33.7 - - + -
168C GLY 4.9 3.6 + - - +
169C LEU* 5.3 1.8 - - + -
182C GLU 3.8 0.8 + - - -
183C PRO* 1.3 72.8 - - - +
185C PHE* 1.3 73.4 + + + +
187C SER* 3.0 9.9 + - - -
188C LEU* 2.9 46.8 + - + +
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Residues in contact with PHE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C GLY 5.4 1.6 + - - -
169C LEU* 4.2 25.1 - - + +
183C PRO* 3.3 2.8 - - + +
184C PHE* 1.3 83.7 - + + +
186C ASP* 1.3 64.6 + - - +
188C LEU* 3.7 14.8 - - + +
189C VAL* 3.1 41.5 + - + +
194C VAL* 4.9 0.4 - - + -
195C PRO 3.9 8.3 - - - -
196C ASN* 3.5 11.2 - - - -
197C LEU 3.7 28.9 - - - -
198C PHE* 3.9 20.0 - + + -
222C MET* 5.3 2.0 - - + -
224C ILE* 4.0 25.1 - - + -
395C ARG* 3.5 34.8 - - - +
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Residues in contact with ASP 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ALA 4.6 2.3 - - - +
171C TYR* 5.0 6.1 - - - -
172C ALA* 4.8 6.8 + - - +
182C GLU* 4.0 19.5 - - + +
183C PRO* 3.0 34.3 + - - +
185C PHE* 1.3 78.5 + - - +
187C SER* 1.3 62.8 + - - +
189C VAL* 3.8 4.4 - - - +
190C LYS* 2.9 29.5 + - + +
395C ARG* 3.3 25.1 + - - +
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C VAL* 4.7 3.1 - - - -
144C ARG 3.9 11.2 + - - -
145C ALA* 4.3 11.7 - - - -
146C ASN* 4.9 1.4 + - - -
182C GLU* 2.6 31.1 + - - +
183C PRO 3.0 11.5 + - - -
184C PHE* 3.0 11.2 + - - -
186C ASP* 1.3 76.1 - - - +
188C LEU* 1.3 53.3 + - - +
190C LYS* 3.1 2.7 + - - -
191C GLN* 2.8 57.3 + - - +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ILE* 5.2 4.5 - - + -
139C PRO* 4.8 2.9 - - + -
141C VAL* 3.6 30.7 - - + -
143C VAL* 3.9 18.3 - - + +
184C PHE* 2.9 42.5 + - + +
185C PHE* 3.7 18.6 - - + +
187C SER* 1.3 77.1 - - - +
189C VAL* 1.3 60.5 + - + +
192C THR* 2.8 38.4 + - + +
194C VAL* 4.2 13.0 - - + -
224C ILE* 3.7 29.4 - - + -
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Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C PHE* 3.1 47.4 + - + +
186C ASP* 3.9 4.3 - - - +
188C LEU* 1.3 77.5 - - + +
190C LYS* 1.3 72.4 + - + +
192C THR* 3.1 16.0 - - - +
194C VAL* 4.0 18.4 - - + +
196C ASN* 3.7 34.5 - - + +
395C ARG* 5.5 0.2 - - - +
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Residues in contact with LYS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C GLU* 3.2 26.7 - - - +
186C ASP* 2.9 18.9 + - + +
187C SER* 3.7 3.1 - - - +
189C VAL* 1.3 82.3 - - + +
191C GLN* 1.3 63.9 + - + +
192C THR 3.5 2.1 + - - +
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Residues in contact with GLN 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C THR 4.7 0.2 - - - +
143C VAL* 3.3 17.6 - - + +
144C ARG* 2.7 53.5 + - - +
182C GLU* 5.0 2.4 + - - -
187C SER* 2.8 26.7 + - - +
190C LYS* 1.3 81.1 - - + +
192C THR* 1.3 62.3 + - + +
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Residues in contact with THR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C VAL* 4.1 27.1 - - + -
142C THR 4.7 2.9 - - - +
143C VAL* 3.6 24.2 - - + -
188C LEU* 2.8 23.3 + - + +
189C VAL 3.1 16.3 - - - +
190C LYS 3.4 2.3 - - - +
191C GLN* 1.3 84.0 - - - +
193C HIS* 1.3 71.7 + - - +
194C VAL* 3.1 20.1 + - - +
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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