Contacts of the strand formed by residues 184 - 190 (chain C) in PDB entry 1AX4
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 ILE 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C LYS* 2.8 27.0 + - - -
125C VAL* 3.3 27.8 - - + +
127C ILE* 3.6 29.8 - - + -
175C ASN 4.4 5.4 - - - +
176C ILE* 4.7 5.2 - - + -
179C HIS* 3.9 13.9 - - + -
180C GLY 3.5 18.2 - - - +
181C ALA* 3.1 14.5 + - - +
183C ASN* 1.3 76.7 - - - +
185C VAL* 1.3 63.9 - - - +
186C ALA 3.8 19.3 - - - +
187C ILE* 4.5 3.1 - - + -
218C ILE* 3.9 29.6 - - + +
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Residues in contact with VAL 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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111C LEU* 3.6 14.8 - - + +
112C LEU* 3.6 37.9 - - + +
115C LYS* 4.5 13.7 + - + +
121C ALA* 4.5 7.2 - - + -
124C PRO* 3.6 31.4 - - + -
125C VAL 2.9 11.1 + - - +
126C PHE* 3.5 35.4 - - + -
183C ASN 4.2 1.1 - - - +
184C ILE* 1.3 72.0 - - - +
186C ALA* 1.3 62.8 + - - +
219C PHE* 3.9 15.1 + - - +
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Residues in contact with ALA 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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111C LEU* 4.1 17.3 - - + -
125C VAL 4.0 0.8 + - - -
126C PHE* 3.5 26.5 - - + -
127C ILE 3.2 21.8 + - - -
184C ILE* 3.3 7.0 - - - +
185C VAL* 1.3 84.8 - - - +
187C ILE* 1.3 70.2 + - - +
188C VAL* 5.1 0.2 - - + -
218C ILE* 4.0 3.6 - - - -
219C PHE* 3.2 16.6 - - + +
221C VAL* 4.4 4.9 - - + -
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Residues in contact with ILE 187 (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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127C ILE* 3.1 23.6 - - + +
167C PHE* 3.8 28.3 - - + -
172C LEU* 4.1 22.4 - - + -
176C ILE* 5.2 1.6 - - + -
184C ILE* 4.5 3.1 - - + -
186C ALA* 1.3 78.5 - - - +
188C VAL* 1.3 63.3 + - - +
189C SER* 4.5 3.1 - - - +
209C VAL* 3.9 15.9 - - + -
213C ALA* 3.8 29.2 - - + -
218C ILE* 3.9 17.2 - - + +
219C PHE 2.9 10.0 + - - +
220C VAL* 3.4 8.5 - - + +
221C VAL* 2.9 27.4 + - - +
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Residues in contact with VAL 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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108C PHE* 4.2 17.7 - - + -
126C PHE* 4.1 25.8 - - + -
127C ILE 2.8 9.4 + - - +
128C SER* 2.5 43.9 + - - +
129C ASN* 3.6 1.2 - - - +
131C HIS* 4.3 11.7 - - + +
135C THR* 4.4 13.2 - - + -
167C PHE* 3.7 2.6 - - - -
186C ALA* 5.1 1.1 - - + -
187C ILE* 1.3 73.7 - - - +
189C SER* 1.3 59.1 + - - +
190C THR* 3.9 7.4 - - - +
221C VAL* 3.2 14.8 - - + +
223C ASP* 3.9 26.9 - - + +
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Residues in contact with SER 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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129C ASN* 3.9 0.7 - - - -
167C PHE* 3.6 26.1 - - - -
187C ILE* 3.9 0.9 + - - +
188C VAL* 1.3 71.2 - - - +
190C THR* 1.3 61.4 + - - +
191C VAL* 3.6 1.1 + - - -
206C LEU* 4.0 14.8 + - - +
209C VAL* 4.4 5.7 - - - +
220C VAL* 3.9 17.5 - - - +
221C VAL 2.8 11.0 + - - -
222C MET* 3.4 25.0 - - - +
223C ASP 2.8 25.0 + - - +
256C TYR 5.0 2.1 + - - -
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Residues in contact with THR 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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128C SER* 3.3 9.5 + - - -
129C ASN* 2.8 33.9 + - - -
130C PHE 3.2 24.4 + - - +
131C HIS* 4.7 1.4 - - - -
132C PHE* 4.9 2.9 + - + -
135C THR* 6.0 0.2 - - - +
188C VAL* 3.9 9.5 - - - +
189C SER* 1.3 70.2 - - - +
191C VAL* 1.3 59.2 + - - +
192C THR 3.3 22.5 - - - +
193C CYS* 3.4 2.1 + - - -
194C ASN* 4.2 9.4 - - + +
201C VAL* 3.5 4.2 - - - +
223C ASP* 3.8 9.8 + - - +
266C LLP 3.6 29.2 - - + -
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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